Starting phenix.real_space_refine on Mon Mar 11 02:36:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t53_41042/03_2024/8t53_41042.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t53_41042/03_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_41042/03_2024/8t53_41042.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t53_41042/03_2024/8t53_41042.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t53_41042/03_2024/8t53_41042.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t53_41042/03_2024/8t53_41042.pdb" } 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 Residue "A PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 3.95, per 1000 atoms: 0.59 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 - 3.50 Amino acid : False - 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: 2.41 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.70 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: 1.83 Time building geometry restraints manager: 2.65 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: 97.19 - 104.57: 80 104.57 - 111.95: 3338 111.95 - 119.33: 2283 119.33 - 126.71: 3437 126.71 - 134.09: 140 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 2.440 nonbonded pdb=" O GLN A 51 " pdb=" OG1 THR A 54 " model vdw 2.210 2.440 nonbonded pdb=" O ALA A 164 " pdb=" OG SER A 167 " model vdw 2.210 2.440 nonbonded pdb=" O GLN B 51 " pdb=" OG1 THR B 54 " model vdw 2.220 2.440 nonbonded pdb=" O PHE B 60 " pdb=" OG SER B 63 " model vdw 2.221 2.440 ... (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 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: 0.820 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: 3.930 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 21.060 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 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:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.800 ------------------------------------------------------------------------------- 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 : 0.695 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: 0.1718 time to fit residues: 23.3264 Evaluate side-chains 81 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.701 ------------------------------------------------------------------------------- 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: 1.9990 chunk 59 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 70 optimal weight: 0.0070 overall best weight: 2.2006 ------------------------------------------------------------------------------- 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** ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4938 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.144 6848 Z= 0.373 Angle : 0.728 6.390 9278 Z= 0.397 Chirality : 0.046 0.190 1024 Planarity : 0.006 0.056 1122 Dihedral : 5.572 25.214 872 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 24.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.83 % Allowed : 6.77 % Favored : 92.40 % 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: 0.70 (0.30), residues: 772 helix: 0.75 (0.23), residues: 462 sheet: -0.38 (0.64), residues: 66 loop : 0.47 (0.43), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP B 121 HIS 0.008 0.002 HIS B 137 PHE 0.030 0.003 PHE A 332 TYR 0.018 0.002 TYR A 162 ARG 0.005 0.001 ARG B 114 *********************** 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 103 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 97 time to evaluate : 0.779 Fit side-chains REVERT: A 87 LEU cc_start: 0.6914 (tp) cc_final: 0.6695 (tp) REVERT: A 92 ARG cc_start: 0.4921 (tpt170) cc_final: 0.4527 (mmt-90) REVERT: A 201 TRP cc_start: 0.6188 (m100) cc_final: 0.5542 (m100) REVERT: A 413 ASP cc_start: 0.0932 (OUTLIER) cc_final: 0.0476 (t0) REVERT: B 73 ARG cc_start: 0.2494 (tpt170) cc_final: 0.2169 (tpt170) REVERT: B 150 ILE cc_start: 0.6290 (mm) cc_final: 0.6064 (mm) REVERT: B 263 MET cc_start: -0.0307 (mmp) cc_final: -0.0792 (mmp) outliers start: 6 outliers final: 4 residues processed: 103 average time/residue: 0.1752 time to fit residues: 24.6595 Evaluate side-chains 84 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 79 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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: 2.9990 chunk 21 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 76 optimal weight: 8.9990 chunk 63 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 chunk 53 optimal weight: 0.0070 overall best weight: 0.6798 ------------------------------------------------------------------------------- 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** B 318 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4711 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 6848 Z= 0.174 Angle : 0.538 6.304 9278 Z= 0.289 Chirality : 0.041 0.155 1024 Planarity : 0.004 0.060 1122 Dihedral : 4.814 21.874 872 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % 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: 1.23 (0.31), residues: 772 helix: 1.17 (0.23), residues: 472 sheet: -0.72 (0.58), residues: 86 loop : 1.04 (0.49), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 121 HIS 0.003 0.001 HIS A 224 PHE 0.029 0.002 PHE A 60 TYR 0.021 0.001 TYR A 162 ARG 0.002 0.000 ARG B 80 *********************** 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 106 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.715 Fit side-chains REVERT: A 79 TYR cc_start: 0.7989 (t80) cc_final: 0.7535 (t80) REVERT: A 92 ARG cc_start: 0.5020 (tpt170) cc_final: 0.4663 (mmt-90) REVERT: A 201 TRP cc_start: 0.6439 (m100) cc_final: 0.5226 (m100) REVERT: B 73 ARG cc_start: 0.2757 (tpt170) cc_final: 0.2404 (tpt170) REVERT: B 263 MET cc_start: 0.0085 (mmp) cc_final: -0.1016 (mmm) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1795 time to fit residues: 25.6967 Evaluate side-chains 87 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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: 5.9990 chunk 7 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 386 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4772 moved from start: 0.2535 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 : 0.535 6.125 9278 Z= 0.289 Chirality : 0.041 0.157 1024 Planarity : 0.004 0.062 1122 Dihedral : 4.727 21.963 872 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % 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: 1.34 (0.31), residues: 772 helix: 1.28 (0.23), residues: 474 sheet: -0.71 (0.61), residues: 82 loop : 0.99 (0.49), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 121 HIS 0.003 0.001 HIS B 137 PHE 0.018 0.002 PHE B 332 TYR 0.019 0.002 TYR A 115 ARG 0.008 0.000 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 106 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.736 Fit side-chains REVERT: A 45 ARG cc_start: 0.6812 (ttp-170) cc_final: 0.6215 (ttp-170) REVERT: A 79 TYR cc_start: 0.7953 (t80) cc_final: 0.7547 (t80) REVERT: A 92 ARG cc_start: 0.4863 (tpt170) cc_final: 0.4340 (mmt-90) REVERT: A 201 TRP cc_start: 0.6416 (m100) cc_final: 0.5303 (m100) REVERT: A 425 MET cc_start: -0.1297 (mtp) cc_final: -0.1575 (mtp) REVERT: B 73 ARG cc_start: 0.2752 (tpt170) cc_final: 0.2335 (tpt170) REVERT: B 79 TYR cc_start: 0.8263 (t80) cc_final: 0.8048 (t80) REVERT: B 150 ILE cc_start: 0.5997 (mm) cc_final: 0.5780 (mm) REVERT: B 263 MET cc_start: 0.0154 (mmp) cc_final: -0.0950 (mmm) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1825 time to fit residues: 25.9523 Evaluate side-chains 87 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.731 ------------------------------------------------------------------------------- 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: 0.9980 chunk 56 optimal weight: 0.0270 chunk 31 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 overall best weight: 0.7238 ------------------------------------------------------------------------------- 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: 0.4743 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 6848 Z= 0.162 Angle : 0.515 5.605 9278 Z= 0.279 Chirality : 0.040 0.170 1024 Planarity : 0.004 0.064 1122 Dihedral : 4.565 20.660 872 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % 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: 1.56 (0.31), residues: 772 helix: 1.49 (0.23), residues: 470 sheet: -0.62 (0.61), residues: 82 loop : 1.00 (0.49), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 121 HIS 0.003 0.001 HIS B 137 PHE 0.031 0.001 PHE B 60 TYR 0.013 0.001 TYR A 115 ARG 0.003 0.000 ARG B 114 *********************** 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 113 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.668 Fit side-chains REVERT: A 45 ARG cc_start: 0.6695 (ttp-170) cc_final: 0.6002 (ttp-170) REVERT: A 79 TYR cc_start: 0.7947 (t80) cc_final: 0.7542 (t80) REVERT: A 92 ARG cc_start: 0.4961 (tpt170) cc_final: 0.4577 (mmt-90) REVERT: A 198 GLU cc_start: 0.7664 (pp20) cc_final: 0.7305 (pp20) REVERT: A 201 TRP cc_start: 0.6265 (m100) cc_final: 0.4990 (m100) REVERT: B 73 ARG cc_start: 0.2750 (tpt170) cc_final: 0.2332 (tpt170) REVERT: B 79 TYR cc_start: 0.8248 (t80) cc_final: 0.7731 (t80) REVERT: B 121 TRP cc_start: 0.6875 (m-90) cc_final: 0.6663 (m-90) REVERT: B 263 MET cc_start: 0.0092 (mmp) cc_final: -0.1016 (mmm) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.1854 time to fit residues: 27.9867 Evaluate side-chains 93 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.780 ------------------------------------------------------------------------------- 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: 0.6980 chunk 18 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 317 HIS B 318 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4964 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 6848 Z= 0.302 Angle : 0.690 7.377 9278 Z= 0.374 Chirality : 0.046 0.163 1024 Planarity : 0.005 0.061 1122 Dihedral : 5.468 25.408 872 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 21.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % 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: 0.73 (0.30), residues: 772 helix: 0.82 (0.23), residues: 464 sheet: -0.49 (0.65), residues: 62 loop : 0.39 (0.45), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 121 HIS 0.006 0.002 HIS B 137 PHE 0.024 0.002 PHE B 46 TYR 0.022 0.002 TYR B 115 ARG 0.008 0.001 ARG B 114 *********************** 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 : 0.743 Fit side-chains revert: symmetry clash REVERT: A 92 ARG cc_start: 0.4864 (tpt170) cc_final: 0.4498 (mmt-90) REVERT: A 201 TRP cc_start: 0.6609 (m100) cc_final: 0.5558 (m100) REVERT: A 263 MET cc_start: 0.0420 (mmp) cc_final: 0.0190 (mmp) REVERT: B 73 ARG cc_start: 0.2695 (tpt170) cc_final: 0.2277 (tpt170) REVERT: B 121 TRP cc_start: 0.6798 (m-90) cc_final: 0.6345 (m-90) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1828 time to fit residues: 27.5954 Evaluate side-chains 90 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.768 ------------------------------------------------------------------------------- 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: 0.0980 chunk 63 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 0.0000 chunk 34 optimal weight: 0.9980 chunk 46 optimal weight: 0.0570 chunk 30 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 overall best weight: 0.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 317 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4724 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 6848 Z= 0.155 Angle : 0.538 7.520 9278 Z= 0.289 Chirality : 0.042 0.154 1024 Planarity : 0.004 0.059 1122 Dihedral : 4.670 19.878 872 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % 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: 1.34 (0.31), residues: 772 helix: 1.37 (0.23), residues: 470 sheet: -0.72 (0.60), residues: 82 loop : 0.79 (0.47), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 121 HIS 0.002 0.001 HIS B 137 PHE 0.016 0.001 PHE A 24 TYR 0.025 0.001 TYR B 77 ARG 0.003 0.000 ARG B 442 *********************** 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 118 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.7810 (t80) cc_final: 0.7367 (t80) REVERT: A 92 ARG cc_start: 0.4908 (tpt170) cc_final: 0.4446 (mmt-90) REVERT: B 73 ARG cc_start: 0.2714 (tpt170) cc_final: 0.2318 (tpt170) REVERT: B 121 TRP cc_start: 0.6641 (m-90) cc_final: 0.6132 (m-90) REVERT: B 136 LYS cc_start: 0.6966 (pttp) cc_final: 0.6544 (pttm) REVERT: B 201 TRP cc_start: 0.6501 (m100) cc_final: 0.6056 (m100) REVERT: B 263 MET cc_start: 0.0397 (mmp) cc_final: -0.0850 (mmm) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1886 time to fit residues: 29.7555 Evaluate side-chains 96 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.791 ------------------------------------------------------------------------------- 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: 0.9980 chunk 47 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 65 optimal weight: 0.0980 chunk 70 optimal weight: 0.6980 chunk 42 optimal weight: 0.0970 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.4775 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6848 Z= 0.152 Angle : 0.543 7.398 9278 Z= 0.288 Chirality : 0.042 0.163 1024 Planarity : 0.004 0.065 1122 Dihedral : 4.598 20.075 872 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % 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: 1.62 (0.31), residues: 772 helix: 1.58 (0.23), residues: 466 sheet: -0.49 (0.62), residues: 82 loop : 0.87 (0.48), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 121 HIS 0.002 0.001 HIS A 233 PHE 0.013 0.001 PHE A 46 TYR 0.013 0.001 TYR A 79 ARG 0.007 0.000 ARG A 45 *********************** 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 113 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 PHE cc_start: 0.4353 (m-80) cc_final: 0.3785 (m-80) REVERT: A 92 ARG cc_start: 0.4890 (tpt170) cc_final: 0.4472 (mmt-90) REVERT: A 147 LYS cc_start: 0.6456 (pttt) cc_final: 0.6232 (pttt) REVERT: A 190 MET cc_start: 0.7178 (ttt) cc_final: 0.6907 (ttt) REVERT: A 216 GLU cc_start: 0.5152 (mp0) cc_final: 0.4902 (mp0) REVERT: B 73 ARG cc_start: 0.2683 (tpt170) cc_final: 0.2294 (tpt170) REVERT: B 121 TRP cc_start: 0.6637 (m-90) cc_final: 0.6067 (m-90) REVERT: B 136 LYS cc_start: 0.6933 (pttp) cc_final: 0.6648 (pttm) REVERT: B 147 LYS cc_start: 0.5985 (pttt) cc_final: 0.5740 (pttt) REVERT: B 216 GLU cc_start: 0.5216 (mp0) cc_final: 0.4922 (mp0) REVERT: B 263 MET cc_start: 0.0395 (mmp) cc_final: -0.0849 (mmm) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.1831 time to fit residues: 27.7526 Evaluate side-chains 98 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.656 ------------------------------------------------------------------------------- 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: 4.9990 chunk 55 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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: 0.4817 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6848 Z= 0.172 Angle : 0.567 7.243 9278 Z= 0.304 Chirality : 0.042 0.155 1024 Planarity : 0.004 0.068 1122 Dihedral : 4.770 21.978 872 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % 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: 1.47 (0.31), residues: 772 helix: 1.48 (0.23), residues: 468 sheet: -0.52 (0.62), residues: 82 loop : 0.75 (0.47), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 121 HIS 0.003 0.001 HIS B 137 PHE 0.022 0.001 PHE A 46 TYR 0.021 0.002 TYR B 77 ARG 0.009 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 114 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.684 Fit side-chains revert: symmetry clash REVERT: A 40 PHE cc_start: 0.4578 (m-80) cc_final: 0.4184 (m-80) REVERT: A 92 ARG cc_start: 0.4895 (tpt170) cc_final: 0.4430 (mmt-90) REVERT: A 190 MET cc_start: 0.7418 (ttt) cc_final: 0.7145 (ttt) REVERT: A 216 GLU cc_start: 0.5187 (mp0) cc_final: 0.4930 (mp0) REVERT: B 73 ARG cc_start: 0.2728 (tpt170) cc_final: 0.2391 (tpt170) REVERT: B 121 TRP cc_start: 0.6767 (m-90) cc_final: 0.6178 (m-90) REVERT: B 136 LYS cc_start: 0.6932 (pttp) cc_final: 0.6678 (pttm) REVERT: B 216 GLU cc_start: 0.5256 (mp0) cc_final: 0.5008 (mp0) REVERT: B 263 MET cc_start: 0.0504 (mmp) cc_final: -0.0800 (mmm) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1818 time to fit residues: 27.8065 Evaluate side-chains 97 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.744 ------------------------------------------------------------------------------- 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: 9.9990 chunk 71 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 49 optimal weight: 0.0010 chunk 65 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4781 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6848 Z= 0.154 Angle : 0.548 7.309 9278 Z= 0.290 Chirality : 0.042 0.159 1024 Planarity : 0.004 0.069 1122 Dihedral : 4.633 20.735 872 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % 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: 1.57 (0.31), residues: 772 helix: 1.56 (0.23), residues: 468 sheet: -0.50 (0.62), residues: 82 loop : 0.79 (0.48), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 121 HIS 0.012 0.001 HIS B 76 PHE 0.019 0.001 PHE A 46 TYR 0.020 0.001 TYR B 77 ARG 0.009 0.000 ARG A 80 ********************** 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 110 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 0.738 Fit side-chains revert: symmetry clash REVERT: A 40 PHE cc_start: 0.4426 (m-80) cc_final: 0.4107 (m-80) REVERT: A 92 ARG cc_start: 0.4974 (tpt170) cc_final: 0.4562 (mmt-90) REVERT: A 136 LYS cc_start: 0.6947 (pttp) cc_final: 0.6677 (pttt) REVERT: A 147 LYS cc_start: 0.6388 (pttt) cc_final: 0.6179 (pttt) REVERT: A 190 MET cc_start: 0.7245 (ttt) cc_final: 0.6974 (ttt) REVERT: A 216 GLU cc_start: 0.5186 (mp0) cc_final: 0.4915 (mp0) REVERT: B 73 ARG cc_start: 0.2900 (tpt170) cc_final: 0.2513 (tpt170) REVERT: B 121 TRP cc_start: 0.6852 (m-90) cc_final: 0.6222 (m-90) REVERT: B 150 ILE cc_start: 0.6134 (mm) cc_final: 0.5891 (mm) REVERT: B 216 GLU cc_start: 0.5222 (mp0) cc_final: 0.5004 (mp0) REVERT: B 263 MET cc_start: 0.0595 (mmp) cc_final: -0.0716 (mmm) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1927 time to fit residues: 28.5235 Evaluate side-chains 97 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.734 ------------------------------------------------------------------------------- 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: 1.9990 chunk 61 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 63 optimal weight: 0.3980 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 3 optimal weight: 0.0980 chunk 44 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- 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 = 0.5062 r_free = 0.5062 target = 0.260463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4840 r_free = 0.4840 target = 0.226501 restraints weight = 22714.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4867 r_free = 0.4867 target = 0.227492 restraints weight = 18392.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4881 r_free = 0.4881 target = 0.229136 restraints weight = 14972.897| |-----------------------------------------------------------------------------| r_work (final): 0.4827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4814 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6848 Z= 0.145 Angle : 0.549 7.226 9278 Z= 0.289 Chirality : 0.042 0.185 1024 Planarity : 0.004 0.069 1122 Dihedral : 4.582 20.857 872 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: 1.65 (0.31), residues: 772 helix: 1.64 (0.23), residues: 468 sheet: -0.42 (0.62), residues: 82 loop : 0.76 (0.48), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 201 HIS 0.007 0.001 HIS B 76 PHE 0.021 0.001 PHE B 173 TYR 0.014 0.001 TYR A 162 ARG 0.005 0.000 ARG A 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1606.78 seconds wall clock time: 29 minutes 54.88 seconds (1794.88 seconds total)