Starting phenix.real_space_refine on Mon Sep 23 17:13:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rnn_24580/09_2024/7rnn_24580.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rnn_24580/09_2024/7rnn_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rnn_24580/09_2024/7rnn_24580.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rnn_24580/09_2024/7rnn_24580.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rnn_24580/09_2024/7rnn_24580.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rnn_24580/09_2024/7rnn_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-5461/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: 3.22, per 1000 atoms: 0.81 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: 1.03 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 0.50 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: 1.09 Time building geometry restraints manager: 1.21 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: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.530 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:13.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 4093 Z= 0.516 Angle : 0.804 8.621 5571 Z= 0.458 Chirality : 0.143 3.137 621 Planarity : 0.004 0.050 730 Dihedral : 14.961 122.906 1424 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.55 % Allowed : 0.00 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.37), residues: 536 helix: -0.34 (0.44), residues: 136 sheet: -0.74 (0.43), residues: 140 loop : -0.82 (0.41), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 40 HIS 0.002 0.001 HIS D 163 PHE 0.023 0.002 PHE D 257 TYR 0.034 0.002 TYR D 426 ARG 0.010 0.001 ARG C 105 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 65 time to evaluate : 0.459 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: 0.9844 time to fit residues: 67.6053 Evaluate side-chains 40 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4093 Z= 0.163 Angle : 0.631 11.407 5571 Z= 0.315 Chirality : 0.041 0.145 621 Planarity : 0.004 0.044 730 Dihedral : 7.588 58.076 631 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.37 % Allowed : 9.56 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.38), residues: 536 helix: 0.50 (0.44), residues: 144 sheet: -0.55 (0.44), residues: 139 loop : -0.20 (0.43), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 233 HIS 0.004 0.001 HIS D 250 PHE 0.012 0.001 PHE D 352 TYR 0.017 0.001 TYR D 360 ARG 0.007 0.001 ARG D 204 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 50 time to evaluate : 0.516 Fit side-chains REVERT: D 129 MET cc_start: 0.1786 (mmm) cc_final: 0.1179 (ptm) outliers start: 5 outliers final: 2 residues processed: 53 average time/residue: 0.9408 time to fit residues: 52.3936 Evaluate side-chains 40 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.490 ------------------------------------------------------------------------------- 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 26 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 32 optimal weight: 0.1980 chunk 13 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4093 Z= 0.152 Angle : 0.542 7.177 5571 Z= 0.274 Chirality : 0.040 0.148 621 Planarity : 0.004 0.041 730 Dihedral : 5.270 32.982 630 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.91 % Allowed : 12.30 % Favored : 85.79 % 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: 0.00 (0.39), residues: 536 helix: 0.61 (0.44), residues: 151 sheet: -0.32 (0.46), residues: 140 loop : -0.01 (0.45), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 233 HIS 0.004 0.001 HIS D 250 PHE 0.005 0.001 PHE D 263 TYR 0.014 0.001 TYR D 360 ARG 0.007 0.001 ARG D 201 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.468 Fit side-chains revert: symmetry clash REVERT: D 98 PHE cc_start: 0.7928 (OUTLIER) cc_final: 0.7593 (p90) REVERT: D 129 MET cc_start: 0.1997 (mmm) cc_final: 0.1242 (ptm) outliers start: 7 outliers final: 4 residues processed: 45 average time/residue: 1.0052 time to fit residues: 47.4414 Evaluate side-chains 43 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 38 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 345 CYS Chi-restraints excluded: chain D residue 379 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 47 optimal weight: 0.0670 chunk 36 optimal weight: 9.9990 chunk 25 optimal weight: 0.1980 chunk 5 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 32 optimal weight: 0.0870 chunk 48 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 42 optimal weight: 8.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4093 Z= 0.137 Angle : 0.512 7.491 5571 Z= 0.262 Chirality : 0.039 0.143 621 Planarity : 0.004 0.039 730 Dihedral : 4.744 32.412 630 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.64 % Allowed : 14.75 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.39), residues: 536 helix: 0.87 (0.45), residues: 151 sheet: -0.20 (0.46), residues: 140 loop : 0.03 (0.45), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 233 HIS 0.003 0.001 HIS D 250 PHE 0.006 0.001 PHE D 100 TYR 0.009 0.001 TYR D 360 ARG 0.008 0.001 ARG D 201 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: C 33 PHE cc_start: 0.5458 (p90) cc_final: 0.5169 (p90) REVERT: D 98 PHE cc_start: 0.7958 (OUTLIER) cc_final: 0.7648 (p90) REVERT: D 129 MET cc_start: 0.2088 (mmm) cc_final: 0.1876 (mmt) outliers start: 6 outliers final: 4 residues processed: 45 average time/residue: 0.9764 time to fit residues: 46.0924 Evaluate side-chains 41 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 29 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 4093 Z= 0.297 Angle : 0.580 9.426 5571 Z= 0.294 Chirality : 0.042 0.146 621 Planarity : 0.004 0.036 730 Dihedral : 5.074 35.788 630 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.91 % Allowed : 15.85 % 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 (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 (0.39), residues: 536 helix: 0.92 (0.45), residues: 151 sheet: -0.33 (0.45), residues: 139 loop : 0.12 (0.45), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 233 HIS 0.003 0.001 HIS D 250 PHE 0.010 0.001 PHE C 72 TYR 0.013 0.001 TYR C 99 ARG 0.007 0.001 ARG D 201 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 36 time to evaluate : 0.469 Fit side-chains revert: symmetry clash REVERT: D 98 PHE cc_start: 0.8002 (OUTLIER) cc_final: 0.7738 (p90) REVERT: D 129 MET cc_start: 0.2428 (mmm) cc_final: 0.2063 (mmt) outliers start: 7 outliers final: 4 residues processed: 41 average time/residue: 0.9627 time to fit residues: 41.5468 Evaluate side-chains 39 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 34 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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 10 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 4 optimal weight: 0.0010 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 5 optimal weight: 8.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4093 Z= 0.149 Angle : 0.523 10.501 5571 Z= 0.264 Chirality : 0.040 0.139 621 Planarity : 0.004 0.044 730 Dihedral : 4.696 34.179 630 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.19 % Allowed : 16.67 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.32 (0.39), residues: 536 helix: 1.10 (0.45), residues: 151 sheet: -0.31 (0.46), residues: 138 loop : 0.13 (0.45), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 233 HIS 0.002 0.001 HIS D 250 PHE 0.005 0.001 PHE D 50 TYR 0.007 0.001 TYR D 360 ARG 0.007 0.001 ARG D 201 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 36 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: D 98 PHE cc_start: 0.7971 (OUTLIER) cc_final: 0.7770 (p90) REVERT: D 129 MET cc_start: 0.2434 (mmm) cc_final: 0.2108 (mmt) outliers start: 8 outliers final: 4 residues processed: 42 average time/residue: 0.9365 time to fit residues: 41.4317 Evaluate side-chains 38 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 33 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 345 CYS Chi-restraints excluded: chain D residue 379 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4093 Z= 0.259 Angle : 0.560 11.861 5571 Z= 0.281 Chirality : 0.041 0.142 621 Planarity : 0.004 0.043 730 Dihedral : 4.914 35.637 630 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.46 % Allowed : 16.94 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.39), residues: 536 helix: 1.13 (0.45), residues: 151 sheet: -0.40 (0.46), residues: 138 loop : 0.13 (0.44), 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 0.006 0.001 PHE D 69 TYR 0.011 0.001 TYR C 99 ARG 0.009 0.001 ARG D 201 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 34 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: D 98 PHE cc_start: 0.7998 (OUTLIER) cc_final: 0.7791 (p90) REVERT: D 129 MET cc_start: 0.2171 (mmm) cc_final: 0.1909 (mmt) outliers start: 9 outliers final: 5 residues processed: 41 average time/residue: 0.8393 time to fit residues: 36.3636 Evaluate side-chains 38 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 32 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 345 CYS Chi-restraints excluded: chain D residue 379 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 40 optimal weight: 0.4980 chunk 46 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 438 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4093 Z= 0.166 Angle : 0.532 12.497 5571 Z= 0.265 Chirality : 0.040 0.138 621 Planarity : 0.004 0.045 730 Dihedral : 4.680 34.910 630 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 3.70 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: 0.39 (0.39), residues: 536 helix: 1.26 (0.45), residues: 151 sheet: -0.40 (0.46), residues: 138 loop : 0.18 (0.44), 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 0.005 0.001 PHE D 272 TYR 0.012 0.001 TYR C 99 ARG 0.009 0.001 ARG D 201 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 37 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: C 35 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7397 (ptp-170) REVERT: D 129 MET cc_start: 0.2209 (mmm) cc_final: 0.1920 (mmt) outliers start: 7 outliers final: 4 residues processed: 43 average time/residue: 0.9439 time to fit residues: 42.6196 Evaluate side-chains 39 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 34 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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 35 ARG 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 20 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 43 optimal weight: 0.0670 chunk 45 optimal weight: 1.9990 chunk 47 optimal weight: 0.2980 chunk 31 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 overall best weight: 0.5922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4093 Z= 0.143 Angle : 0.520 12.866 5571 Z= 0.261 Chirality : 0.040 0.138 621 Planarity : 0.003 0.043 730 Dihedral : 4.520 34.495 630 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.91 % Allowed : 18.03 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.40 (0.45), residues: 151 sheet: -0.37 (0.47), residues: 132 loop : 0.14 (0.44), residues: 253 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 0.010 0.001 PHE C 72 TYR 0.005 0.001 TYR D 389 ARG 0.009 0.001 ARG D 201 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 37 time to evaluate : 0.486 Fit side-chains revert: symmetry clash REVERT: C 33 PHE cc_start: 0.5942 (p90) cc_final: 0.5538 (p90) REVERT: D 129 MET cc_start: 0.2252 (mmm) cc_final: 0.1976 (mmt) outliers start: 7 outliers final: 4 residues processed: 43 average time/residue: 1.0114 time to fit residues: 45.5832 Evaluate side-chains 36 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 32 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain D residue 345 CYS Chi-restraints excluded: chain D residue 379 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 0.3980 chunk 33 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4093 Z= 0.183 Angle : 0.548 14.588 5571 Z= 0.272 Chirality : 0.040 0.142 621 Planarity : 0.004 0.042 730 Dihedral : 4.525 34.397 630 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % 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: 0.46 (0.39), residues: 536 helix: 1.42 (0.46), residues: 151 sheet: -0.33 (0.47), residues: 130 loop : 0.12 (0.43), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 233 HIS 0.002 0.001 HIS D 250 PHE 0.012 0.001 PHE C 72 TYR 0.012 0.001 TYR C 99 ARG 0.009 0.001 ARG D 201 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 33 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: D 129 MET cc_start: 0.2339 (mmm) cc_final: 0.2070 (mmt) outliers start: 5 outliers final: 4 residues processed: 37 average time/residue: 0.9687 time to fit residues: 37.8705 Evaluate side-chains 37 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 33 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain D residue 345 CYS Chi-restraints excluded: chain D residue 379 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 11 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 30 optimal weight: 0.4980 chunk 48 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3512 r_free = 0.3512 target = 0.093873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.066927 restraints weight = 8320.842| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 3.09 r_work: 0.2857 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4093 Z= 0.216 Angle : 0.560 14.657 5571 Z= 0.278 Chirality : 0.041 0.142 621 Planarity : 0.004 0.042 730 Dihedral : 4.672 34.379 630 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 4.10 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: 0.49 (0.39), residues: 536 helix: 1.42 (0.46), residues: 151 sheet: -0.32 (0.47), residues: 129 loop : 0.15 (0.43), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 233 HIS 0.002 0.001 HIS D 250 PHE 0.014 0.001 PHE C 72 TYR 0.012 0.001 TYR C 99 ARG 0.009 0.001 ARG D 201 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1618.54 seconds wall clock time: 29 minutes 10.87 seconds (1750.87 seconds total)