Starting phenix.real_space_refine on Thu Jul 18 23:15:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8el8_28224/07_2024/8el8_28224.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8el8_28224/07_2024/8el8_28224.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8el8_28224/07_2024/8el8_28224.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8el8_28224/07_2024/8el8_28224.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8el8_28224/07_2024/8el8_28224.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8el8_28224/07_2024/8el8_28224.cif" } resolution = 3.2 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= -0.001 sd= 0.108 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 27 5.16 5 C 2868 2.51 5 N 778 2.21 5 O 792 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 68": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 4467 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1046 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 4, 'TRANS': 135} Chain breaks: 5 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 82 Chain: "B" Number of atoms: 3421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3421 Classifications: {'peptide': 457} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 15, 'TRANS': 441} Chain breaks: 2 Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 269 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TPO:plan-1': 1, 'ASP:plan': 15, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 14, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 154 Time building chain proxies: 3.26, per 1000 atoms: 0.73 Number of scatterers: 4467 At special positions: 0 Unit cell: (53.6823, 80.9495, 110.773, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 P 2 15.00 O 792 8.00 N 778 7.00 C 2868 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: 1.58 Conformation dependent library (CDL) restraints added in 823.5 milliseconds 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1148 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 1 sheets defined 67.2% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 252 through 265 Processing helix chain 'A' and resid 280 through 291 removed outlier: 3.680A pdb=" N LEU A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY A 291 " --> pdb=" O LYS A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 298 Processing helix chain 'A' and resid 299 through 303 removed outlier: 3.507A pdb=" N ALA A 303 " --> pdb=" O PRO A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 338 removed outlier: 3.962A pdb=" N THR A 322 " --> pdb=" O ASP A 318 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG A 323 " --> pdb=" O PRO A 319 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ALA A 324 " --> pdb=" O LYS A 320 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE A 332 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER A 336 " --> pdb=" O PHE A 332 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA A 338 " --> pdb=" O ARG A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 378 removed outlier: 3.674A pdb=" N TYR A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 13 removed outlier: 3.622A pdb=" N GLY B 13 " --> pdb=" O ILE B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 29 removed outlier: 3.615A pdb=" N GLU B 19 " --> pdb=" O ALA B 15 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG B 20 " --> pdb=" O GLY B 16 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG B 23 " --> pdb=" O GLU B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 38 No H-bonds generated for 'chain 'B' and resid 36 through 38' Processing helix chain 'B' and resid 39 through 54 removed outlier: 3.519A pdb=" N LEU B 54 " --> pdb=" O ILE B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 74 Processing helix chain 'B' and resid 80 through 84 removed outlier: 3.923A pdb=" N THR B 84 " --> pdb=" O VAL B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 97 removed outlier: 3.577A pdb=" N ILE B 91 " --> pdb=" O GLU B 87 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 92 " --> pdb=" O ASN B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 128 Processing helix chain 'B' and resid 129 through 139 removed outlier: 3.674A pdb=" N GLN B 133 " --> pdb=" O GLN B 129 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU B 136 " --> pdb=" O GLN B 132 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU B 137 " --> pdb=" O GLN B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 150 removed outlier: 3.909A pdb=" N LYS B 143 " --> pdb=" O ASN B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 175 Processing helix chain 'B' and resid 176 through 185 Processing helix chain 'B' and resid 187 through 201 removed outlier: 3.754A pdb=" N LEU B 191 " --> pdb=" O GLN B 187 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER B 201 " --> pdb=" O GLU B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 238 Processing helix chain 'B' and resid 249 through 264 removed outlier: 3.675A pdb=" N VAL B 255 " --> pdb=" O HIS B 251 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET B 256 " --> pdb=" O GLN B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 286 removed outlier: 4.137A pdb=" N GLU B 275 " --> pdb=" O GLU B 271 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER B 286 " --> pdb=" O VAL B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 298 removed outlier: 4.722A pdb=" N ASP B 294 " --> pdb=" O SER B 291 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL B 295 " --> pdb=" O CYS B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 355 removed outlier: 3.574A pdb=" N HIS B 343 " --> pdb=" O MET B 339 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP B 354 " --> pdb=" O GLU B 350 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LYS B 355 " --> pdb=" O LYS B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 377 removed outlier: 4.072A pdb=" N THR B 364 " --> pdb=" O ARG B 360 " (cutoff:3.500A) Proline residue: B 365 - end of helix removed outlier: 3.729A pdb=" N ALA B 376 " --> pdb=" O GLU B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 389 Processing helix chain 'B' and resid 404 through 412 Processing helix chain 'B' and resid 417 through 432 removed outlier: 3.708A pdb=" N LYS B 421 " --> pdb=" O ASP B 417 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA B 425 " --> pdb=" O LYS B 421 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU B 428 " --> pdb=" O ALA B 424 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU B 431 " --> pdb=" O PHE B 427 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N CYS B 432 " --> pdb=" O LEU B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 443 removed outlier: 3.596A pdb=" N LYS B 441 " --> pdb=" O ASP B 437 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 455 removed outlier: 5.193A pdb=" N GLY B 450 " --> pdb=" O GLY B 446 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N LEU B 451 " --> pdb=" O ASN B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 482 removed outlier: 3.500A pdb=" N LYS B 479 " --> pdb=" O THR B 475 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 210 removed outlier: 6.295A pdb=" N LEU A 46 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N VAL A 234 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE A 231 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N PHE A 277 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N TYR A 233 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ILE A 274 " --> pdb=" O TYR A 347 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N HIS A 349 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU A 276 " --> pdb=" O HIS A 349 " (cutoff:3.500A) 234 hydrogen bonds defined for protein. 675 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: 1.03 Time building geometry restraints manager: 1.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 853 1.33 - 1.45: 998 1.45 - 1.57: 2647 1.57 - 1.68: 2 1.68 - 1.80: 38 Bond restraints: 4538 Sorted by residual: bond pdb=" O3P SEP B 468 " pdb=" P SEP B 468 " ideal model delta sigma weight residual 1.610 1.476 0.134 2.00e-02 2.50e+03 4.48e+01 bond pdb=" O2P SEP B 468 " pdb=" P SEP B 468 " ideal model delta sigma weight residual 1.610 1.480 0.130 2.00e-02 2.50e+03 4.21e+01 bond pdb=" O1P SEP B 468 " pdb=" P SEP B 468 " ideal model delta sigma weight residual 1.610 1.481 0.129 2.00e-02 2.50e+03 4.17e+01 bond pdb=" OG1 TPO B 473 " pdb=" P TPO B 473 " ideal model delta sigma weight residual 1.717 1.598 0.119 2.00e-02 2.50e+03 3.55e+01 bond pdb=" CA LYS B 479 " pdb=" C LYS B 479 " ideal model delta sigma weight residual 1.523 1.468 0.055 1.35e-02 5.49e+03 1.67e+01 ... (remaining 4533 not shown) Histogram of bond angle deviations from ideal: 100.53 - 107.30: 132 107.30 - 114.06: 2677 114.06 - 120.82: 2104 120.82 - 127.59: 1219 127.59 - 134.35: 35 Bond angle restraints: 6167 Sorted by residual: angle pdb=" N ARG B 183 " pdb=" CA ARG B 183 " pdb=" C ARG B 183 " ideal model delta sigma weight residual 111.07 118.31 -7.24 1.07e+00 8.73e-01 4.58e+01 angle pdb=" N TYR B 442 " pdb=" CA TYR B 442 " pdb=" C TYR B 442 " ideal model delta sigma weight residual 111.36 117.49 -6.13 1.09e+00 8.42e-01 3.16e+01 angle pdb=" N THR B 443 " pdb=" CA THR B 443 " pdb=" C THR B 443 " ideal model delta sigma weight residual 112.68 119.02 -6.34 1.33e+00 5.65e-01 2.27e+01 angle pdb=" N GLY B 188 " pdb=" CA GLY B 188 " pdb=" C GLY B 188 " ideal model delta sigma weight residual 112.73 118.17 -5.44 1.20e+00 6.94e-01 2.06e+01 angle pdb=" C LYS B 482 " pdb=" N PRO B 483 " pdb=" CA PRO B 483 " ideal model delta sigma weight residual 119.05 114.40 4.65 1.11e+00 8.12e-01 1.75e+01 ... (remaining 6162 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 2477 16.84 - 33.67: 216 33.67 - 50.51: 38 50.51 - 67.34: 5 67.34 - 84.18: 3 Dihedral angle restraints: 2739 sinusoidal: 986 harmonic: 1753 Sorted by residual: dihedral pdb=" C TPO B 473 " pdb=" N TPO B 473 " pdb=" CA TPO B 473 " pdb=" CB TPO B 473 " ideal model delta harmonic sigma weight residual -122.60 -113.34 -9.26 0 2.50e+00 1.60e-01 1.37e+01 dihedral pdb=" CB GLU B 223 " pdb=" CG GLU B 223 " pdb=" CD GLU B 223 " pdb=" OE1 GLU B 223 " ideal model delta sinusoidal sigma weight residual 0.00 84.18 -84.18 1 3.00e+01 1.11e-03 9.59e+00 dihedral pdb=" CB LYS B 273 " pdb=" CG LYS B 273 " pdb=" CD LYS B 273 " pdb=" CE LYS B 273 " ideal model delta sinusoidal sigma weight residual -60.00 -114.69 54.69 3 1.50e+01 4.44e-03 9.30e+00 ... (remaining 2736 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 511 0.040 - 0.079: 197 0.079 - 0.119: 33 0.119 - 0.158: 11 0.158 - 0.198: 4 Chirality restraints: 756 Sorted by residual: chirality pdb=" CA TYR B 442 " pdb=" N TYR B 442 " pdb=" C TYR B 442 " pdb=" CB TYR B 442 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.76e-01 chirality pdb=" CB VAL B 83 " pdb=" CA VAL B 83 " pdb=" CG1 VAL B 83 " pdb=" CG2 VAL B 83 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.27e-01 chirality pdb=" CA TPO B 473 " pdb=" N TPO B 473 " pdb=" C TPO B 473 " pdb=" CB TPO B 473 " both_signs ideal model delta sigma weight residual False 2.53 2.70 -0.18 2.00e-01 2.50e+01 7.75e-01 ... (remaining 753 not shown) Planarity restraints: 771 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 478 " 0.010 2.00e-02 2.50e+03 2.04e-02 4.15e+00 pdb=" C TYR B 478 " -0.035 2.00e-02 2.50e+03 pdb=" O TYR B 478 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS B 479 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 81 " -0.031 5.00e-02 4.00e+02 4.61e-02 3.39e+00 pdb=" N PRO B 82 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 82 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 82 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 347 " -0.024 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO A 348 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 348 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 348 " -0.020 5.00e-02 4.00e+02 ... (remaining 768 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 1688 2.90 - 3.40: 4128 3.40 - 3.90: 6539 3.90 - 4.40: 6902 4.40 - 4.90: 12571 Nonbonded interactions: 31828 Sorted by model distance: nonbonded pdb=" OD1 ASP B 206 " pdb=" N GLU B 207 " model vdw 2.403 2.520 nonbonded pdb=" O LEU A 259 " pdb=" OG SER A 262 " model vdw 2.431 2.440 nonbonded pdb=" OE1 GLN A 281 " pdb=" NZ LYS A 325 " model vdw 2.449 2.520 nonbonded pdb=" O LEU B 300 " pdb=" OG1 THR B 301 " model vdw 2.459 2.440 nonbonded pdb=" N GLU B 185 " pdb=" O GLU B 185 " model vdw 2.473 2.496 ... (remaining 31823 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.240 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 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 : 0.007 0.134 4538 Z= 0.442 Angle : 0.704 9.354 6167 Z= 0.416 Chirality : 0.044 0.198 756 Planarity : 0.004 0.046 771 Dihedral : 13.199 84.180 1591 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % 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: 0.75 (0.35), residues: 573 helix: 1.29 (0.28), residues: 348 sheet: 1.88 (0.99), residues: 28 loop : -1.14 (0.42), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 268 HIS 0.007 0.001 HIS A 344 PHE 0.017 0.002 PHE B 163 TYR 0.008 0.001 TYR B 208 ARG 0.003 0.001 ARG B 435 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.543 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1713 time to fit residues: 13.0891 Evaluate side-chains 46 residues out of total 535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 24 optimal weight: 0.0010 chunk 15 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 34 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4538 Z= 0.139 Angle : 0.443 6.461 6167 Z= 0.232 Chirality : 0.036 0.125 756 Planarity : 0.003 0.040 771 Dihedral : 3.751 24.801 639 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.23 % Allowed : 7.22 % Favored : 92.55 % 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: 1.41 (0.37), residues: 573 helix: 1.94 (0.29), residues: 357 sheet: 1.10 (0.95), residues: 32 loop : -1.15 (0.46), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 466 HIS 0.004 0.001 HIS B 491 PHE 0.009 0.001 PHE B 163 TYR 0.005 0.001 TYR B 184 ARG 0.002 0.000 ARG B 154 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 49 time to evaluate : 0.544 Fit side-chains REVERT: B 339 MET cc_start: 0.8814 (mmt) cc_final: 0.8510 (mmt) outliers start: 1 outliers final: 1 residues processed: 50 average time/residue: 0.1725 time to fit residues: 11.3713 Evaluate side-chains 44 residues out of total 535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 29 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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: 0.8119 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4538 Z= 0.296 Angle : 0.496 5.633 6167 Z= 0.259 Chirality : 0.039 0.126 756 Planarity : 0.004 0.045 771 Dihedral : 3.732 17.743 639 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.45 % Allowed : 9.71 % Favored : 89.84 % 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: 1.31 (0.37), residues: 573 helix: 1.80 (0.29), residues: 361 sheet: 1.20 (0.98), residues: 32 loop : -1.17 (0.45), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 264 HIS 0.006 0.001 HIS A 344 PHE 0.015 0.002 PHE B 163 TYR 0.006 0.001 TYR B 208 ARG 0.002 0.000 ARG B 435 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.535 Fit side-chains REVERT: B 129 GLN cc_start: 0.8510 (tp40) cc_final: 0.8072 (tp40) outliers start: 2 outliers final: 1 residues processed: 42 average time/residue: 0.1552 time to fit residues: 8.8536 Evaluate side-chains 40 residues out of total 535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 27 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 47 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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: 0.8071 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4538 Z= 0.168 Angle : 0.418 5.316 6167 Z= 0.219 Chirality : 0.037 0.125 756 Planarity : 0.003 0.041 771 Dihedral : 3.508 16.504 639 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.90 % Allowed : 11.06 % Favored : 88.04 % 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: 1.49 (0.37), residues: 573 helix: 2.01 (0.29), residues: 357 sheet: 1.31 (0.98), residues: 32 loop : -1.16 (0.45), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 466 HIS 0.003 0.001 HIS A 344 PHE 0.010 0.001 PHE B 163 TYR 0.005 0.001 TYR B 184 ARG 0.001 0.000 ARG B 94 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 43 time to evaluate : 0.591 Fit side-chains REVERT: B 129 GLN cc_start: 0.8380 (tp40) cc_final: 0.7955 (tt0) outliers start: 4 outliers final: 3 residues processed: 46 average time/residue: 0.1602 time to fit residues: 9.9486 Evaluate side-chains 43 residues out of total 535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 40 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain B residue 339 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 11 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 486 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 4538 Z= 0.236 Angle : 0.448 5.357 6167 Z= 0.233 Chirality : 0.038 0.125 756 Planarity : 0.004 0.042 771 Dihedral : 3.547 17.472 639 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.81 % Allowed : 11.74 % Favored : 86.46 % 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: 1.37 (0.37), residues: 573 helix: 1.91 (0.29), residues: 357 sheet: 1.31 (0.97), residues: 32 loop : -1.23 (0.45), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 264 HIS 0.004 0.001 HIS A 344 PHE 0.014 0.001 PHE B 163 TYR 0.005 0.001 TYR B 184 ARG 0.001 0.000 ARG B 375 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 40 time to evaluate : 0.554 Fit side-chains REVERT: B 129 GLN cc_start: 0.8460 (tp40) cc_final: 0.8027 (tt0) REVERT: B 154 ARG cc_start: 0.8158 (ttm110) cc_final: 0.7881 (ttm110) outliers start: 8 outliers final: 4 residues processed: 47 average time/residue: 0.1538 time to fit residues: 9.8319 Evaluate side-chains 43 residues out of total 535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 395 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 14 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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: 0.8096 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4538 Z= 0.212 Angle : 0.442 5.653 6167 Z= 0.227 Chirality : 0.037 0.125 756 Planarity : 0.004 0.041 771 Dihedral : 3.502 17.642 639 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.03 % Allowed : 13.09 % Favored : 84.88 % 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: 1.39 (0.37), residues: 573 helix: 1.93 (0.29), residues: 357 sheet: 1.37 (0.97), residues: 32 loop : -1.24 (0.45), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 466 HIS 0.004 0.001 HIS A 344 PHE 0.012 0.001 PHE B 163 TYR 0.005 0.001 TYR B 184 ARG 0.001 0.000 ARG B 435 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 42 time to evaluate : 0.478 Fit side-chains REVERT: B 129 GLN cc_start: 0.8466 (tp40) cc_final: 0.8002 (tt0) REVERT: B 154 ARG cc_start: 0.8193 (ttm110) cc_final: 0.7873 (ttm110) outliers start: 9 outliers final: 6 residues processed: 50 average time/residue: 0.1443 time to fit residues: 9.8296 Evaluate side-chains 47 residues out of total 535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 395 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 32 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 35 optimal weight: 0.0970 chunk 34 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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: 0.8059 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 4538 Z= 0.143 Angle : 0.408 5.728 6167 Z= 0.209 Chirality : 0.036 0.125 756 Planarity : 0.003 0.040 771 Dihedral : 3.353 15.790 639 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.13 % Allowed : 14.22 % Favored : 84.65 % 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: 1.54 (0.37), residues: 573 helix: 2.11 (0.29), residues: 357 sheet: 1.11 (1.10), residues: 28 loop : -1.20 (0.45), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 466 HIS 0.003 0.001 HIS A 344 PHE 0.010 0.001 PHE B 163 TYR 0.004 0.001 TYR A 233 ARG 0.001 0.000 ARG B 261 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 44 time to evaluate : 0.479 Fit side-chains REVERT: B 129 GLN cc_start: 0.8369 (tp40) cc_final: 0.7913 (tt0) REVERT: B 154 ARG cc_start: 0.8138 (ttm110) cc_final: 0.7850 (ttm110) outliers start: 5 outliers final: 5 residues processed: 48 average time/residue: 0.1441 time to fit residues: 9.3909 Evaluate side-chains 48 residues out of total 535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 395 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 28 optimal weight: 0.0770 chunk 5 optimal weight: 0.0770 chunk 44 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 54 optimal weight: 0.0670 chunk 49 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.8438 ------------------------------------------------------------------------------- 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: 0.8057 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 4538 Z= 0.144 Angle : 0.404 5.636 6167 Z= 0.207 Chirality : 0.036 0.125 756 Planarity : 0.003 0.040 771 Dihedral : 3.278 14.438 639 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.81 % Allowed : 14.22 % Favored : 83.97 % 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: 1.64 (0.37), residues: 573 helix: 2.18 (0.29), residues: 356 sheet: 1.20 (1.11), residues: 28 loop : -1.14 (0.44), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 264 HIS 0.003 0.001 HIS A 344 PHE 0.011 0.001 PHE B 163 TYR 0.004 0.001 TYR B 184 ARG 0.001 0.000 ARG B 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.567 Fit side-chains REVERT: B 129 GLN cc_start: 0.8365 (tp40) cc_final: 0.7489 (tm-30) REVERT: B 154 ARG cc_start: 0.8107 (ttm110) cc_final: 0.7800 (ttm110) outliers start: 8 outliers final: 5 residues processed: 52 average time/residue: 0.1501 time to fit residues: 10.7227 Evaluate side-chains 48 residues out of total 535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 395 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 23 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 chunk 34 optimal weight: 0.0030 chunk 56 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 58 optimal weight: 0.4980 overall best weight: 1.0594 ------------------------------------------------------------------------------- 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: 0.8070 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 4538 Z= 0.170 Angle : 0.417 6.381 6167 Z= 0.213 Chirality : 0.036 0.125 756 Planarity : 0.003 0.042 771 Dihedral : 3.295 14.787 639 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.58 % Allowed : 14.45 % Favored : 83.97 % 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 (0.37), residues: 573 helix: 2.13 (0.29), residues: 357 sheet: 1.29 (1.11), residues: 28 loop : -1.19 (0.44), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 264 HIS 0.003 0.001 HIS A 344 PHE 0.011 0.001 PHE B 163 TYR 0.004 0.001 TYR B 184 ARG 0.001 0.000 ARG B 435 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 42 time to evaluate : 0.518 Fit side-chains REVERT: B 129 GLN cc_start: 0.8385 (tp40) cc_final: 0.7499 (tm-30) REVERT: B 154 ARG cc_start: 0.8138 (ttm110) cc_final: 0.7838 (ttm110) outliers start: 7 outliers final: 7 residues processed: 48 average time/residue: 0.1465 time to fit residues: 9.5696 Evaluate side-chains 48 residues out of total 535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 395 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 4 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 0.3980 chunk 37 optimal weight: 2.9990 chunk 49 optimal weight: 0.0050 chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 overall best weight: 0.8796 ------------------------------------------------------------------------------- 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: 0.8055 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 4538 Z= 0.146 Angle : 0.403 6.274 6167 Z= 0.206 Chirality : 0.036 0.126 756 Planarity : 0.003 0.043 771 Dihedral : 3.242 14.683 639 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.58 % Allowed : 14.67 % Favored : 83.75 % 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: 1.69 (0.37), residues: 573 helix: 2.20 (0.29), residues: 357 sheet: 1.03 (1.10), residues: 29 loop : -1.07 (0.45), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 466 HIS 0.003 0.001 HIS A 344 PHE 0.010 0.001 PHE B 163 TYR 0.004 0.001 TYR B 184 ARG 0.001 0.000 ARG B 406 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 42 time to evaluate : 0.502 Fit side-chains REVERT: B 129 GLN cc_start: 0.8369 (tp40) cc_final: 0.7488 (tm-30) REVERT: B 154 ARG cc_start: 0.8129 (ttm110) cc_final: 0.7814 (ttm110) outliers start: 7 outliers final: 7 residues processed: 48 average time/residue: 0.1484 time to fit residues: 9.7142 Evaluate side-chains 49 residues out of total 535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 42 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 395 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 0.6980 chunk 19 optimal weight: 0.0570 chunk 48 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.133279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.097508 restraints weight = 5607.486| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.51 r_work: 0.2927 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 4538 Z= 0.155 Angle : 0.406 6.110 6167 Z= 0.208 Chirality : 0.036 0.125 756 Planarity : 0.003 0.043 771 Dihedral : 3.240 14.822 639 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.58 % Allowed : 14.67 % Favored : 83.75 % 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: 1.68 (0.37), residues: 573 helix: 2.19 (0.29), residues: 358 sheet: 1.14 (1.11), residues: 29 loop : -1.10 (0.45), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 264 HIS 0.003 0.001 HIS A 344 PHE 0.011 0.001 PHE B 163 TYR 0.004 0.001 TYR B 184 ARG 0.001 0.000 ARG B 435 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1181.35 seconds wall clock time: 21 minutes 44.11 seconds (1304.11 seconds total)