Starting phenix.real_space_refine on Tue Sep 24 03:36:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t53_41042/09_2024/8t53_41042.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t53_41042/09_2024/8t53_41042.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t53_41042/09_2024/8t53_41042.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t53_41042/09_2024/8t53_41042.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t53_41042/09_2024/8t53_41042.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t53_41042/09_2024/8t53_41042.cif" } resolution = 4.1 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= 0.023 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 38 5.16 5 C 4418 2.51 5 N 1094 2.21 5 O 1110 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6660 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3330 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 13, 'TRANS': 384} Chain breaks: 5 Chain: "B" Number of atoms: 3330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3330 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 13, 'TRANS': 384} Chain breaks: 5 Time building chain proxies: 4.17, per 1000 atoms: 0.63 Number of scatterers: 6660 At special positions: 0 Unit cell: (98.8, 113.1, 91, 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 38 16.00 O 1110 8.00 N 1094 7.00 C 4418 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.44 Conformation dependent library (CDL) restraints added in 796.3 milliseconds 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1528 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 7 sheets defined 68.8% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 9 through 41 removed outlier: 3.812A pdb=" N LEU A 29 " --> pdb=" O PHE A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 72 removed outlier: 3.772A pdb=" N LEU A 52 " --> pdb=" O PRO A 48 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASP A 53 " --> pdb=" O GLN A 49 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N THR A 54 " --> pdb=" O ASP A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 107 Processing helix chain 'A' and resid 114 through 142 Proline residue: A 129 - end of helix Processing helix chain 'A' and resid 155 through 167 Processing helix chain 'A' and resid 168 through 171 Processing helix chain 'A' and resid 197 through 204 removed outlier: 3.593A pdb=" N ASN A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 218 No H-bonds generated for 'chain 'A' and resid 216 through 218' Processing helix chain 'A' and resid 219 through 233 removed outlier: 3.582A pdb=" N THR A 223 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 272 Processing helix chain 'A' and resid 273 through 307 Proline residue: A 297 - end of helix Processing helix chain 'A' and resid 308 through 310 No H-bonds generated for 'chain 'A' and resid 308 through 310' Processing helix chain 'A' and resid 322 through 324 No H-bonds generated for 'chain 'A' and resid 322 through 324' Processing helix chain 'A' and resid 376 through 380 Processing helix chain 'A' and resid 381 through 384 Processing helix chain 'A' and resid 385 through 393 removed outlier: 3.625A pdb=" N ASN A 389 " --> pdb=" O PRO A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 413 removed outlier: 3.844A pdb=" N GLU A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ASP A 413 " --> pdb=" O ARG A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 removed outlier: 4.312A pdb=" N ALA A 421 " --> pdb=" O TYR A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 432 removed outlier: 3.819A pdb=" N VAL A 431 " --> pdb=" O GLY A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 452 Processing helix chain 'A' and resid 454 through 471 Processing helix chain 'B' and resid 9 through 41 removed outlier: 3.821A pdb=" N LEU B 29 " --> pdb=" O PHE B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 72 removed outlier: 4.270A pdb=" N THR B 54 " --> pdb=" O ASP B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 107 Processing helix chain 'B' and resid 114 through 142 Proline residue: B 129 - end of helix Processing helix chain 'B' and resid 155 through 167 Processing helix chain 'B' and resid 168 through 171 removed outlier: 4.070A pdb=" N MET B 171 " --> pdb=" O GLU B 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 168 through 171' Processing helix chain 'B' and resid 196 through 203 removed outlier: 4.308A pdb=" N ILE B 200 " --> pdb=" O ASP B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 218 No H-bonds generated for 'chain 'B' and resid 216 through 218' Processing helix chain 'B' and resid 219 through 233 removed outlier: 3.569A pdb=" N THR B 223 " --> pdb=" O GLU B 219 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER B 231 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS B 233 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 272 Processing helix chain 'B' and resid 273 through 307 Proline residue: B 297 - end of helix Processing helix chain 'B' and resid 308 through 310 No H-bonds generated for 'chain 'B' and resid 308 through 310' Processing helix chain 'B' and resid 322 through 324 No H-bonds generated for 'chain 'B' and resid 322 through 324' Processing helix chain 'B' and resid 376 through 380 Processing helix chain 'B' and resid 381 through 384 Processing helix chain 'B' and resid 385 through 393 removed outlier: 3.632A pdb=" N ASN B 389 " --> pdb=" O PRO B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 413 removed outlier: 3.789A pdb=" N GLU B 409 " --> pdb=" O ASP B 406 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ASP B 413 " --> pdb=" O ARG B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 421 removed outlier: 4.321A pdb=" N ALA B 421 " --> pdb=" O TYR B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 432 removed outlier: 3.794A pdb=" N VAL B 431 " --> pdb=" O GLY B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 452 Processing helix chain 'B' and resid 454 through 471 Processing sheet with id=AA1, first strand: chain 'A' and resid 187 through 188 removed outlier: 5.839A pdb=" N LYS A 147 " --> pdb=" O ASP A 174 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE A 176 " --> pdb=" O LYS A 147 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N THR A 149 " --> pdb=" O ILE A 176 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N PHE A 178 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ILE A 151 " --> pdb=" O PHE A 178 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LYS A 148 " --> pdb=" O HIS A 210 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ILE A 212 " --> pdb=" O LYS A 148 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE A 150 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 314 through 320 Processing sheet with id=AA3, first strand: chain 'A' and resid 396 through 398 removed outlier: 6.285A pdb=" N LEU A 397 " --> pdb=" O THR A 426 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 173 through 179 removed outlier: 7.821A pdb=" N ILE B 151 " --> pdb=" O ILE B 176 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N PHE B 178 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LYS B 148 " --> pdb=" O HIS B 210 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ILE B 212 " --> pdb=" O LYS B 148 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE B 150 " --> pdb=" O ILE B 212 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 188 Processing sheet with id=AA6, first strand: chain 'B' and resid 314 through 320 Processing sheet with id=AA7, first strand: chain 'B' and resid 396 through 398 removed outlier: 6.480A pdb=" N LEU B 397 " --> pdb=" O THR B 426 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 382 hydrogen bonds defined for protein. 1095 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: 1.87 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1993 1.34 - 1.46: 1641 1.46 - 1.58: 3154 1.58 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 6848 Sorted by residual: bond pdb=" CG GLN B 166 " pdb=" CD GLN B 166 " ideal model delta sigma weight residual 1.516 1.491 0.025 2.50e-02 1.60e+03 9.64e-01 bond pdb=" CG PRO A 328 " pdb=" CD PRO A 328 " ideal model delta sigma weight residual 1.503 1.473 0.030 3.40e-02 8.65e+02 7.94e-01 bond pdb=" CB PRO A 328 " pdb=" CG PRO A 328 " ideal model delta sigma weight residual 1.492 1.534 -0.042 5.00e-02 4.00e+02 7.11e-01 bond pdb=" C SER A 296 " pdb=" N PRO A 297 " ideal model delta sigma weight residual 1.335 1.346 -0.010 1.36e-02 5.41e+03 5.83e-01 bond pdb=" C MET B 190 " pdb=" N LEU B 191 " ideal model delta sigma weight residual 1.331 1.343 -0.011 1.59e-02 3.96e+03 5.13e-01 ... (remaining 6843 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 9105 1.78 - 3.57: 141 3.57 - 5.35: 24 5.35 - 7.13: 6 7.13 - 8.91: 2 Bond angle restraints: 9278 Sorted by residual: angle pdb=" N VAL B 43 " pdb=" CA VAL B 43 " pdb=" C VAL B 43 " ideal model delta sigma weight residual 113.42 108.43 4.99 1.17e+00 7.31e-01 1.82e+01 angle pdb=" CA PRO A 328 " pdb=" N PRO A 328 " pdb=" CD PRO A 328 " ideal model delta sigma weight residual 112.00 107.21 4.79 1.40e+00 5.10e-01 1.17e+01 angle pdb=" N VAL A 43 " pdb=" CA VAL A 43 " pdb=" C VAL A 43 " ideal model delta sigma weight residual 113.39 108.57 4.82 1.47e+00 4.63e-01 1.07e+01 angle pdb=" N PRO A 328 " pdb=" CD PRO A 328 " pdb=" CG PRO A 328 " ideal model delta sigma weight residual 103.20 98.55 4.65 1.50e+00 4.44e-01 9.60e+00 angle pdb=" CA TRP A 121 " pdb=" CB TRP A 121 " pdb=" CG TRP A 121 " ideal model delta sigma weight residual 113.60 107.89 5.71 1.90e+00 2.77e-01 9.02e+00 ... (remaining 9273 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.00: 3578 16.00 - 32.01: 338 32.01 - 48.01: 47 48.01 - 64.01: 5 64.01 - 80.01: 6 Dihedral angle restraints: 3974 sinusoidal: 1622 harmonic: 2352 Sorted by residual: dihedral pdb=" CA TRP A 121 " pdb=" C TRP A 121 " pdb=" N THR A 122 " pdb=" CA THR A 122 " ideal model delta harmonic sigma weight residual 180.00 158.66 21.34 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA GLN B 44 " pdb=" C GLN B 44 " pdb=" N ARG B 45 " pdb=" CA ARG B 45 " ideal model delta harmonic sigma weight residual 180.00 161.20 18.80 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA GLN A 44 " pdb=" C GLN A 44 " pdb=" N ARG A 45 " pdb=" CA ARG A 45 " ideal model delta harmonic sigma weight residual 180.00 162.02 17.98 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 3971 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 769 0.042 - 0.084: 186 0.084 - 0.126: 64 0.126 - 0.168: 3 0.168 - 0.210: 2 Chirality restraints: 1024 Sorted by residual: chirality pdb=" CA TRP A 121 " pdb=" N TRP A 121 " pdb=" C TRP A 121 " pdb=" CB TRP A 121 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA TRP B 121 " pdb=" N TRP B 121 " pdb=" C TRP B 121 " pdb=" CB TRP B 121 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.09e-01 chirality pdb=" CG LEU B 125 " pdb=" CB LEU B 125 " pdb=" CD1 LEU B 125 " pdb=" CD2 LEU B 125 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.14e-01 ... (remaining 1021 not shown) Planarity restraints: 1122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 327 " -0.058 5.00e-02 4.00e+02 8.55e-02 1.17e+01 pdb=" N PRO A 328 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO A 328 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 328 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 121 " 0.026 2.00e-02 2.50e+03 2.09e-02 1.09e+01 pdb=" CG TRP B 121 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP B 121 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP B 121 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 121 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 121 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 121 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 121 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 121 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 121 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 201 " 0.021 2.00e-02 2.50e+03 1.60e-02 6.36e+00 pdb=" CG TRP B 201 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP B 201 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP B 201 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 201 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 201 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 201 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 201 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 201 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP B 201 " -0.001 2.00e-02 2.50e+03 ... (remaining 1119 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 513 2.74 - 3.28: 7038 3.28 - 3.82: 11549 3.82 - 4.36: 12982 4.36 - 4.90: 21407 Nonbonded interactions: 53489 Sorted by model distance: nonbonded pdb=" O PHE A 60 " pdb=" OG SER A 63 " model vdw 2.201 3.040 nonbonded pdb=" O GLN A 51 " pdb=" OG1 THR A 54 " model vdw 2.210 3.040 nonbonded pdb=" O ALA A 164 " pdb=" OG SER A 167 " model vdw 2.210 3.040 nonbonded pdb=" O GLN B 51 " pdb=" OG1 THR B 54 " model vdw 2.220 3.040 nonbonded pdb=" O PHE B 60 " pdb=" OG SER B 63 " model vdw 2.221 3.040 ... (remaining 53484 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 group one per residue 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: 1.050 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 17.580 Find NCS groups from input model: 0.160 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: 0.010 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4588 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 : 0.002 0.042 6848 Z= 0.155 Angle : 0.590 8.914 9278 Z= 0.330 Chirality : 0.041 0.210 1024 Planarity : 0.005 0.085 1122 Dihedral : 12.603 80.013 2446 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.81 (0.31), residues: 772 helix: 0.93 (0.24), residues: 464 sheet: -0.83 (0.59), residues: 86 loop : 0.61 (0.45), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP B 121 HIS 0.003 0.001 HIS B 137 PHE 0.023 0.002 PHE A 91 TYR 0.011 0.001 TYR B 77 ARG 0.004 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 GLU cc_start: 0.7600 (pp20) cc_final: 0.7191 (pp20) REVERT: B 171 MET cc_start: 0.5928 (ptp) cc_final: 0.5650 (ptp) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.1778 time to fit residues: 24.3230 Evaluate side-chains 81 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4965 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.149 6848 Z= 0.408 Angle : 0.794 6.910 9278 Z= 0.431 Chirality : 0.048 0.208 1024 Planarity : 0.006 0.058 1122 Dihedral : 5.774 26.126 872 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 24.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.41 % Allowed : 7.87 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.36 (0.30), residues: 772 helix: 0.51 (0.23), residues: 456 sheet: -0.65 (0.62), residues: 66 loop : 0.30 (0.42), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A 121 HIS 0.008 0.002 HIS B 137 PHE 0.030 0.003 PHE A 332 TYR 0.021 0.002 TYR B 115 ARG 0.005 0.001 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 99 time to evaluate : 0.670 Fit side-chains REVERT: A 87 LEU cc_start: 0.6949 (tp) cc_final: 0.6738 (tp) REVERT: A 92 ARG cc_start: 0.5018 (tpt170) cc_final: 0.4649 (mmt-90) REVERT: A 142 LEU cc_start: 0.8110 (mt) cc_final: 0.7904 (mt) REVERT: A 425 MET cc_start: -0.0630 (mtp) cc_final: -0.0891 (mtp) REVERT: B 73 ARG cc_start: 0.2614 (tpt170) cc_final: 0.2251 (tpt170) REVERT: B 263 MET cc_start: -0.0396 (mmp) cc_final: -0.0894 (mmp) outliers start: 3 outliers final: 2 residues processed: 102 average time/residue: 0.1709 time to fit residues: 23.7708 Evaluate side-chains 83 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 81 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 76 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4748 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 6848 Z= 0.192 Angle : 0.583 7.108 9278 Z= 0.316 Chirality : 0.043 0.168 1024 Planarity : 0.005 0.056 1122 Dihedral : 4.960 23.129 872 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.82 (0.30), residues: 772 helix: 0.91 (0.23), residues: 472 sheet: -0.54 (0.62), residues: 66 loop : 0.42 (0.46), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 121 HIS 0.012 0.001 HIS A 76 PHE 0.032 0.002 PHE A 60 TYR 0.020 0.002 TYR B 115 ARG 0.008 0.000 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.666 Fit side-chains REVERT: A 79 TYR cc_start: 0.8025 (t80) cc_final: 0.7646 (t80) REVERT: A 92 ARG cc_start: 0.4748 (tpt170) cc_final: 0.4391 (mmt-90) REVERT: A 180 ASP cc_start: 0.4941 (t70) cc_final: 0.4628 (t0) REVERT: A 201 TRP cc_start: 0.6228 (m100) cc_final: 0.4983 (m100) REVERT: B 40 PHE cc_start: 0.4531 (m-80) cc_final: 0.4218 (m-80) REVERT: B 73 ARG cc_start: 0.2730 (tpt170) cc_final: 0.2285 (tpt170) REVERT: B 121 TRP cc_start: 0.6824 (m-90) cc_final: 0.6407 (m-90) REVERT: B 190 MET cc_start: 0.7045 (ttt) cc_final: 0.6811 (ttt) REVERT: B 263 MET cc_start: 0.0129 (mmp) cc_final: -0.1029 (mmm) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.1828 time to fit residues: 25.4433 Evaluate side-chains 85 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 62 optimal weight: 8.9990 chunk 42 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4917 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 6848 Z= 0.274 Angle : 0.650 6.503 9278 Z= 0.353 Chirality : 0.045 0.198 1024 Planarity : 0.005 0.061 1122 Dihedral : 5.265 24.844 872 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.65 (0.30), residues: 772 helix: 0.78 (0.23), residues: 470 sheet: -0.75 (0.60), residues: 66 loop : 0.38 (0.46), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 121 HIS 0.006 0.001 HIS A 76 PHE 0.022 0.002 PHE B 332 TYR 0.018 0.002 TYR B 115 ARG 0.013 0.001 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.764 Fit side-chains revert: symmetry clash REVERT: A 79 TYR cc_start: 0.8015 (t80) cc_final: 0.7636 (t80) REVERT: A 92 ARG cc_start: 0.4890 (tpt170) cc_final: 0.4460 (mmt-90) REVERT: A 180 ASP cc_start: 0.5749 (t70) cc_final: 0.5309 (t0) REVERT: A 201 TRP cc_start: 0.6374 (m100) cc_final: 0.5367 (m100) REVERT: B 40 PHE cc_start: 0.4606 (m-80) cc_final: 0.4140 (m-80) REVERT: B 73 ARG cc_start: 0.2649 (tpt170) cc_final: 0.2244 (tpt170) REVERT: B 121 TRP cc_start: 0.6754 (m-90) cc_final: 0.6358 (m-90) REVERT: B 201 TRP cc_start: 0.6473 (m100) cc_final: 0.5322 (m100) REVERT: B 263 MET cc_start: 0.0412 (mmp) cc_final: 0.0165 (mmp) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1649 time to fit residues: 24.6001 Evaluate side-chains 90 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 0.0970 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4771 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6848 Z= 0.167 Angle : 0.553 6.105 9278 Z= 0.299 Chirality : 0.043 0.277 1024 Planarity : 0.004 0.052 1122 Dihedral : 4.738 21.205 872 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.98 (0.31), residues: 772 helix: 1.03 (0.23), residues: 470 sheet: -0.58 (0.65), residues: 62 loop : 0.52 (0.45), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 121 HIS 0.006 0.001 HIS A 76 PHE 0.026 0.001 PHE A 107 TYR 0.017 0.002 TYR B 77 ARG 0.004 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.687 Fit side-chains revert: symmetry clash REVERT: A 79 TYR cc_start: 0.7974 (t80) cc_final: 0.7715 (t80) REVERT: A 92 ARG cc_start: 0.4863 (tpt170) cc_final: 0.4439 (mmt-90) REVERT: A 180 ASP cc_start: 0.5337 (t70) cc_final: 0.5017 (t0) REVERT: B 73 ARG cc_start: 0.2698 (tpt170) cc_final: 0.2268 (tpt170) REVERT: B 121 TRP cc_start: 0.6948 (m-90) cc_final: 0.6326 (m-90) REVERT: B 180 ASP cc_start: 0.5278 (t70) cc_final: 0.5059 (t0) REVERT: B 263 MET cc_start: 0.0268 (mmp) cc_final: -0.0957 (mmm) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1786 time to fit residues: 27.4842 Evaluate side-chains 93 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 62 optimal weight: 0.0980 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- 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: 0.4886 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 6848 Z= 0.246 Angle : 0.630 7.238 9278 Z= 0.340 Chirality : 0.044 0.173 1024 Planarity : 0.005 0.053 1122 Dihedral : 5.115 21.765 872 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.66 (0.31), residues: 772 helix: 0.86 (0.23), residues: 472 sheet: -1.24 (0.57), residues: 82 loop : 0.52 (0.48), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 121 HIS 0.004 0.001 HIS B 137 PHE 0.018 0.002 PHE A 40 TYR 0.024 0.002 TYR A 77 ARG 0.005 0.000 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.763 Fit side-chains REVERT: A 79 TYR cc_start: 0.7964 (t80) cc_final: 0.7587 (t80) REVERT: A 92 ARG cc_start: 0.4751 (tpt170) cc_final: 0.4460 (mmt-90) REVERT: A 180 ASP cc_start: 0.5530 (t70) cc_final: 0.5146 (t0) REVERT: A 201 TRP cc_start: 0.6502 (m100) cc_final: 0.5373 (m100) REVERT: B 73 ARG cc_start: 0.2573 (tpt170) cc_final: 0.2185 (tpt170) REVERT: B 121 TRP cc_start: 0.6844 (m-90) cc_final: 0.6258 (m-90) REVERT: B 180 ASP cc_start: 0.5798 (t70) cc_final: 0.5462 (t0) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1729 time to fit residues: 26.3062 Evaluate side-chains 97 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 5.9990 chunk 42 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 0.1980 chunk 22 optimal weight: 7.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 317 HIS B 386 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4882 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 6848 Z= 0.231 Angle : 0.631 8.203 9278 Z= 0.337 Chirality : 0.045 0.202 1024 Planarity : 0.004 0.043 1122 Dihedral : 5.137 20.987 872 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.56 (0.31), residues: 772 helix: 0.77 (0.23), residues: 472 sheet: -1.34 (0.56), residues: 82 loop : 0.56 (0.48), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 121 HIS 0.004 0.001 HIS A 76 PHE 0.020 0.002 PHE A 107 TYR 0.022 0.002 TYR B 77 ARG 0.004 0.000 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.729 Fit side-chains REVERT: A 79 TYR cc_start: 0.7985 (t80) cc_final: 0.7725 (t80) REVERT: A 92 ARG cc_start: 0.4888 (tpt170) cc_final: 0.4499 (mmt-90) REVERT: A 201 TRP cc_start: 0.6437 (m100) cc_final: 0.5296 (m100) REVERT: B 73 ARG cc_start: 0.2636 (tpt170) cc_final: 0.2266 (tpt170) REVERT: B 121 TRP cc_start: 0.6990 (m-90) cc_final: 0.6411 (m-90) REVERT: B 180 ASP cc_start: 0.5734 (t70) cc_final: 0.5450 (t0) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.1730 time to fit residues: 26.6061 Evaluate side-chains 94 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 7 optimal weight: 0.4980 chunk 59 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN B 317 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4794 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6848 Z= 0.172 Angle : 0.576 6.879 9278 Z= 0.306 Chirality : 0.042 0.178 1024 Planarity : 0.004 0.042 1122 Dihedral : 4.842 19.637 872 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.81 (0.31), residues: 772 helix: 0.98 (0.23), residues: 472 sheet: -1.17 (0.57), residues: 82 loop : 0.61 (0.48), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 121 HIS 0.004 0.001 HIS A 76 PHE 0.011 0.001 PHE B 332 TYR 0.013 0.001 TYR B 8 ARG 0.008 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 PHE cc_start: 0.4677 (m-80) cc_final: 0.4137 (m-80) REVERT: A 79 TYR cc_start: 0.7972 (t80) cc_final: 0.7701 (t80) REVERT: A 92 ARG cc_start: 0.5056 (tpt170) cc_final: 0.4672 (mmt-90) REVERT: B 73 ARG cc_start: 0.2699 (tpt170) cc_final: 0.2352 (tpt170) REVERT: B 121 TRP cc_start: 0.7124 (m-90) cc_final: 0.6496 (m-90) REVERT: B 216 GLU cc_start: 0.5274 (mp0) cc_final: 0.5013 (mp0) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1684 time to fit residues: 26.3740 Evaluate side-chains 99 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.0870 chunk 55 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 66 optimal weight: 0.0010 chunk 69 optimal weight: 1.9990 chunk 46 optimal weight: 0.0870 chunk 74 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 overall best weight: 0.6144 ------------------------------------------------------------------------------- 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: 0.4767 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6848 Z= 0.153 Angle : 0.556 7.005 9278 Z= 0.296 Chirality : 0.042 0.171 1024 Planarity : 0.004 0.040 1122 Dihedral : 4.610 18.916 872 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.14 (0.31), residues: 772 helix: 1.16 (0.23), residues: 472 sheet: -0.22 (0.65), residues: 66 loop : 0.48 (0.46), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 121 HIS 0.004 0.001 HIS A 76 PHE 0.017 0.001 PHE A 107 TYR 0.013 0.001 TYR A 115 ARG 0.005 0.000 ARG B 80 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 PHE cc_start: 0.4553 (m-80) cc_final: 0.3897 (m-80) REVERT: A 79 TYR cc_start: 0.7996 (t80) cc_final: 0.7736 (t80) REVERT: A 92 ARG cc_start: 0.4976 (tpt170) cc_final: 0.4610 (mmt-90) REVERT: B 73 ARG cc_start: 0.2620 (tpt170) cc_final: 0.2224 (tpt170) REVERT: B 121 TRP cc_start: 0.6891 (m-90) cc_final: 0.6160 (m-90) REVERT: B 216 GLU cc_start: 0.5402 (mp0) cc_final: 0.5188 (mp0) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1664 time to fit residues: 26.9484 Evaluate side-chains 104 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.0270 chunk 71 optimal weight: 0.6980 chunk 61 optimal weight: 0.4980 chunk 6 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 overall best weight: 0.7640 ------------------------------------------------------------------------------- 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: 0.4797 moved from start: 0.4434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6848 Z= 0.166 Angle : 0.569 6.807 9278 Z= 0.303 Chirality : 0.043 0.197 1024 Planarity : 0.004 0.040 1122 Dihedral : 4.677 19.170 872 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.20 (0.31), residues: 772 helix: 1.16 (0.23), residues: 472 sheet: -0.18 (0.65), residues: 66 loop : 0.60 (0.47), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 201 HIS 0.003 0.001 HIS A 76 PHE 0.012 0.001 PHE A 40 TYR 0.013 0.001 TYR A 418 ARG 0.004 0.000 ARG A 236 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 GLN cc_start: 0.8481 (mp10) cc_final: 0.7943 (mt0) REVERT: A 40 PHE cc_start: 0.4500 (m-80) cc_final: 0.3923 (m-80) REVERT: A 79 TYR cc_start: 0.8041 (t80) cc_final: 0.7716 (t80) REVERT: A 92 ARG cc_start: 0.4858 (tpt170) cc_final: 0.4518 (mmt-90) REVERT: A 147 LYS cc_start: 0.7002 (pttt) cc_final: 0.6743 (pttt) REVERT: A 263 MET cc_start: 0.0790 (mmp) cc_final: 0.0580 (mmp) REVERT: B 73 ARG cc_start: 0.2640 (tpt170) cc_final: 0.2241 (tpt170) REVERT: B 121 TRP cc_start: 0.6941 (m-90) cc_final: 0.6142 (m-90) REVERT: B 150 ILE cc_start: 0.6202 (mm) cc_final: 0.5992 (mm) REVERT: B 216 GLU cc_start: 0.5244 (mp0) cc_final: 0.5024 (mp0) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1660 time to fit residues: 27.1291 Evaluate side-chains 101 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 0.0470 chunk 63 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 54 optimal weight: 0.0060 chunk 3 optimal weight: 0.3980 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 0.0270 chunk 41 optimal weight: 1.9990 overall best weight: 0.2152 ------------------------------------------------------------------------------- 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 = 0.5355 r_free = 0.5355 target = 0.316985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.5367 r_free = 0.5367 target = 0.307703 restraints weight = 30651.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.5351 r_free = 0.5351 target = 0.308002 restraints weight = 22297.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.5356 r_free = 0.5356 target = 0.308643 restraints weight = 17486.422| |-----------------------------------------------------------------------------| r_work (final): 0.5037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4104 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6848 Z= 0.142 Angle : 0.566 9.082 9278 Z= 0.297 Chirality : 0.042 0.174 1024 Planarity : 0.003 0.041 1122 Dihedral : 4.345 18.435 872 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.58 (0.31), residues: 772 helix: 1.63 (0.24), residues: 458 sheet: 0.06 (0.65), residues: 66 loop : 0.39 (0.46), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 201 HIS 0.004 0.001 HIS A 76 PHE 0.019 0.001 PHE A 107 TYR 0.012 0.001 TYR A 162 ARG 0.004 0.000 ARG B 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1467.46 seconds wall clock time: 27 minutes 4.75 seconds (1624.75 seconds total)