Starting phenix.real_space_refine on Sat Dec 28 02:43:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7en0_31197/12_2024/7en0_31197.cif Found real_map, /net/cci-nas-00/data/ceres_data/7en0_31197/12_2024/7en0_31197.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7en0_31197/12_2024/7en0_31197.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7en0_31197/12_2024/7en0_31197.map" model { file = "/net/cci-nas-00/data/ceres_data/7en0_31197/12_2024/7en0_31197.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7en0_31197/12_2024/7en0_31197.cif" } resolution = 2.97 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= 1.000 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 3 5.49 5 S 48 5.16 5 C 4878 2.51 5 N 1137 2.21 5 O 1173 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 7239 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2350 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 313, 2339 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 15, 'TRANS': 297} Chain breaks: 1 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 111 Planarities with less than four sites: {'ASP:plan': 1, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 88 Conformer: "B" Number of residues, atoms: 313, 2339 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 15, 'TRANS': 297} Chain breaks: 1 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 111 Planarities with less than four sites: {'ASP:plan': 1, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 88 bond proxies already assigned to first conformer: 2399 Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'PLC': 1, 'SPH': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: C, B Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AARG A 357 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 357 " occ=0.50 residue: pdb=" N AARG B 357 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 357 " occ=0.50 residue: pdb=" N AARG C 357 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 357 " occ=0.50 Time building chain proxies: 5.48, per 1000 atoms: 0.76 Number of scatterers: 7239 At special positions: 0 Unit cell: (106.845, 105.797, 62.85, 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 48 16.00 P 3 15.00 O 1173 8.00 N 1137 7.00 C 4878 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.92 Conformation dependent library (CDL) restraints added in 2.0 seconds 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1782 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 0 sheets defined 81.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 193 through 197 Processing helix chain 'A' and resid 198 through 200 No H-bonds generated for 'chain 'A' and resid 198 through 200' Processing helix chain 'A' and resid 201 through 221 removed outlier: 3.986A pdb=" N CYS A 205 " --> pdb=" O CYS A 201 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLN A 211 " --> pdb=" O GLY A 207 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE A 213 " --> pdb=" O GLY A 209 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 214 " --> pdb=" O SER A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 259 removed outlier: 4.409A pdb=" N ASN A 234 " --> pdb=" O THR A 230 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR A 252 " --> pdb=" O THR A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 268 removed outlier: 4.109A pdb=" N ILE A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG A 264 " --> pdb=" O PHE A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 276 Processing helix chain 'A' and resid 277 through 289 removed outlier: 4.227A pdb=" N ALA A 283 " --> pdb=" O PRO A 279 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY A 289 " --> pdb=" O PHE A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 328 removed outlier: 3.544A pdb=" N SER A 310 " --> pdb=" O VAL A 306 " (cutoff:3.500A) Proline residue: A 313 - end of helix removed outlier: 3.559A pdb=" N LEU A 317 " --> pdb=" O PRO A 313 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A 326 " --> pdb=" O TYR A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 336 Processing helix chain 'A' and resid 338 through 344 removed outlier: 3.710A pdb=" N HIS A 342 " --> pdb=" O PRO A 339 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 343 " --> pdb=" O SER A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 359 removed outlier: 3.731A pdb=" N PHE A 349 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 382 removed outlier: 3.890A pdb=" N HIS A 374 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 403 removed outlier: 3.553A pdb=" N SER A 401 " --> pdb=" O PRO A 398 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET A 402 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE A 403 " --> pdb=" O TYR A 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 398 through 403' Processing helix chain 'A' and resid 404 through 418 Processing helix chain 'A' and resid 423 through 443 removed outlier: 3.708A pdb=" N VAL A 441 " --> pdb=" O MET A 437 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 458 Processing helix chain 'A' and resid 459 through 476 removed outlier: 3.658A pdb=" N THR A 469 " --> pdb=" O ALA A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 507 removed outlier: 3.561A pdb=" N MET A 495 " --> pdb=" O MET A 491 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU A 505 " --> pdb=" O VAL A 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 197 Processing helix chain 'B' and resid 198 through 200 No H-bonds generated for 'chain 'B' and resid 198 through 200' Processing helix chain 'B' and resid 201 through 221 removed outlier: 3.985A pdb=" N CYS B 205 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLN B 211 " --> pdb=" O GLY B 207 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE B 213 " --> pdb=" O GLY B 209 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 214 " --> pdb=" O SER B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 259 removed outlier: 4.409A pdb=" N ASN B 234 " --> pdb=" O THR B 230 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR B 252 " --> pdb=" O THR B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 268 removed outlier: 4.109A pdb=" N ILE B 263 " --> pdb=" O TYR B 259 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG B 264 " --> pdb=" O PHE B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 276 Processing helix chain 'B' and resid 277 through 289 removed outlier: 4.227A pdb=" N ALA B 283 " --> pdb=" O PRO B 279 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY B 289 " --> pdb=" O PHE B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 328 removed outlier: 3.545A pdb=" N SER B 310 " --> pdb=" O VAL B 306 " (cutoff:3.500A) Proline residue: B 313 - end of helix removed outlier: 3.560A pdb=" N LEU B 317 " --> pdb=" O PRO B 313 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU B 326 " --> pdb=" O TYR B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 336 Processing helix chain 'B' and resid 338 through 344 removed outlier: 3.709A pdb=" N HIS B 342 " --> pdb=" O PRO B 339 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 343 " --> pdb=" O SER B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 359 removed outlier: 3.731A pdb=" N PHE B 349 " --> pdb=" O VAL B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 382 removed outlier: 3.890A pdb=" N HIS B 374 " --> pdb=" O ILE B 370 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 403 removed outlier: 3.553A pdb=" N SER B 401 " --> pdb=" O PRO B 398 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET B 402 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE B 403 " --> pdb=" O TYR B 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 398 through 403' Processing helix chain 'B' and resid 404 through 418 Processing helix chain 'B' and resid 423 through 443 removed outlier: 3.708A pdb=" N VAL B 441 " --> pdb=" O MET B 437 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ARG B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 458 Processing helix chain 'B' and resid 459 through 476 removed outlier: 3.658A pdb=" N THR B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 507 removed outlier: 3.561A pdb=" N MET B 495 " --> pdb=" O MET B 491 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 505 " --> pdb=" O VAL B 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 197 Processing helix chain 'C' and resid 198 through 200 No H-bonds generated for 'chain 'C' and resid 198 through 200' Processing helix chain 'C' and resid 201 through 221 removed outlier: 3.986A pdb=" N CYS C 205 " --> pdb=" O CYS C 201 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLN C 211 " --> pdb=" O GLY C 207 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA C 212 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE C 213 " --> pdb=" O GLY C 209 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU C 214 " --> pdb=" O SER C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 259 removed outlier: 4.409A pdb=" N ASN C 234 " --> pdb=" O THR C 230 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU C 235 " --> pdb=" O PRO C 231 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR C 252 " --> pdb=" O THR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 268 removed outlier: 4.110A pdb=" N ILE C 263 " --> pdb=" O TYR C 259 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG C 264 " --> pdb=" O PHE C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 276 Processing helix chain 'C' and resid 277 through 289 removed outlier: 4.226A pdb=" N ALA C 283 " --> pdb=" O PRO C 279 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY C 289 " --> pdb=" O PHE C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 328 removed outlier: 3.545A pdb=" N SER C 310 " --> pdb=" O VAL C 306 " (cutoff:3.500A) Proline residue: C 313 - end of helix removed outlier: 3.559A pdb=" N LEU C 317 " --> pdb=" O PRO C 313 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU C 326 " --> pdb=" O TYR C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 336 Processing helix chain 'C' and resid 338 through 344 removed outlier: 3.710A pdb=" N HIS C 342 " --> pdb=" O PRO C 339 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU C 343 " --> pdb=" O SER C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 359 removed outlier: 3.731A pdb=" N PHE C 349 " --> pdb=" O VAL C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 382 removed outlier: 3.889A pdb=" N HIS C 374 " --> pdb=" O ILE C 370 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL C 377 " --> pdb=" O ALA C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 403 removed outlier: 3.553A pdb=" N SER C 401 " --> pdb=" O PRO C 398 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET C 402 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE C 403 " --> pdb=" O TYR C 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 398 through 403' Processing helix chain 'C' and resid 404 through 418 Processing helix chain 'C' and resid 423 through 443 removed outlier: 3.708A pdb=" N VAL C 441 " --> pdb=" O MET C 437 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG C 442 " --> pdb=" O SER C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 458 Processing helix chain 'C' and resid 459 through 476 removed outlier: 3.658A pdb=" N THR C 469 " --> pdb=" O ALA C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 507 removed outlier: 3.561A pdb=" N MET C 495 " --> pdb=" O MET C 491 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU C 505 " --> pdb=" O VAL C 501 " (cutoff:3.500A) 483 hydrogen bonds defined for protein. 1362 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: 2.05 Time building geometry restraints manager: 2.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1008 1.31 - 1.43: 2194 1.43 - 1.56: 4166 1.56 - 1.68: 6 1.68 - 1.81: 78 Bond restraints: 7452 Sorted by residual: bond pdb=" C4 SPH A 602 " pdb=" C5 SPH A 602 " ideal model delta sigma weight residual 1.334 1.473 -0.139 2.00e-02 2.50e+03 4.80e+01 bond pdb=" C4 SPH C 602 " pdb=" C5 SPH C 602 " ideal model delta sigma weight residual 1.334 1.472 -0.138 2.00e-02 2.50e+03 4.79e+01 bond pdb=" C4 SPH B 602 " pdb=" C5 SPH B 602 " ideal model delta sigma weight residual 1.334 1.472 -0.138 2.00e-02 2.50e+03 4.79e+01 bond pdb=" CB PLC B 601 " pdb=" O3 PLC B 601 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" CB PLC C 601 " pdb=" O3 PLC C 601 " ideal model delta sigma weight residual 1.327 1.397 -0.070 2.00e-02 2.50e+03 1.23e+01 ... (remaining 7447 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.17: 9932 3.17 - 6.33: 208 6.33 - 9.50: 27 9.50 - 12.66: 3 12.66 - 15.83: 3 Bond angle restraints: 10173 Sorted by residual: angle pdb=" O3P PLC B 601 " pdb=" P PLC B 601 " pdb=" O4P PLC B 601 " ideal model delta sigma weight residual 93.62 109.45 -15.83 3.00e+00 1.11e-01 2.78e+01 angle pdb=" O3P PLC A 601 " pdb=" P PLC A 601 " pdb=" O4P PLC A 601 " ideal model delta sigma weight residual 93.62 109.44 -15.82 3.00e+00 1.11e-01 2.78e+01 angle pdb=" O3P PLC C 601 " pdb=" P PLC C 601 " pdb=" O4P PLC C 601 " ideal model delta sigma weight residual 93.62 109.43 -15.81 3.00e+00 1.11e-01 2.78e+01 angle pdb=" N LEU B 504 " pdb=" CA LEU B 504 " pdb=" C LEU B 504 " ideal model delta sigma weight residual 113.20 106.98 6.22 1.21e+00 6.83e-01 2.64e+01 angle pdb=" N LEU C 504 " pdb=" CA LEU C 504 " pdb=" C LEU C 504 " ideal model delta sigma weight residual 113.20 107.01 6.19 1.21e+00 6.83e-01 2.62e+01 ... (remaining 10168 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.40: 4059 28.40 - 56.80: 222 56.80 - 85.21: 6 85.21 - 113.61: 0 113.61 - 142.01: 9 Dihedral angle restraints: 4296 sinusoidal: 1545 harmonic: 2751 Sorted by residual: dihedral pdb=" C1B PLC A 601 " pdb=" CB PLC A 601 " pdb=" O3 PLC A 601 " pdb=" C3 PLC A 601 " ideal model delta sinusoidal sigma weight residual 181.23 39.22 142.01 1 3.00e+01 1.11e-03 1.91e+01 dihedral pdb=" C1B PLC B 601 " pdb=" CB PLC B 601 " pdb=" O3 PLC B 601 " pdb=" C3 PLC B 601 " ideal model delta sinusoidal sigma weight residual 181.23 39.22 142.01 1 3.00e+01 1.11e-03 1.91e+01 dihedral pdb=" C1B PLC C 601 " pdb=" CB PLC C 601 " pdb=" O3 PLC C 601 " pdb=" C3 PLC C 601 " ideal model delta sinusoidal sigma weight residual 181.23 39.26 141.97 1 3.00e+01 1.11e-03 1.91e+01 ... (remaining 4293 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 882 0.049 - 0.097: 230 0.097 - 0.146: 43 0.146 - 0.194: 15 0.194 - 0.243: 21 Chirality restraints: 1191 Sorted by residual: chirality pdb=" C3 SPH C 602 " pdb=" C2 SPH C 602 " pdb=" C4 SPH C 602 " pdb=" O3 SPH C 602 " both_signs ideal model delta sigma weight residual False 2.42 2.18 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" C3 SPH A 602 " pdb=" C2 SPH A 602 " pdb=" C4 SPH A 602 " pdb=" O3 SPH A 602 " both_signs ideal model delta sigma weight residual False 2.42 2.18 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" C3 SPH B 602 " pdb=" C2 SPH B 602 " pdb=" C4 SPH B 602 " pdb=" O3 SPH B 602 " both_signs ideal model delta sigma weight residual False 2.42 2.18 0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 1188 not shown) Planarity restraints: 1218 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 SPH B 602 " 0.043 2.00e-02 2.50e+03 4.38e-02 1.92e+01 pdb=" C4 SPH B 602 " -0.040 2.00e-02 2.50e+03 pdb=" C5 SPH B 602 " -0.047 2.00e-02 2.50e+03 pdb=" C6 SPH B 602 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 SPH C 602 " -0.043 2.00e-02 2.50e+03 4.37e-02 1.91e+01 pdb=" C4 SPH C 602 " 0.040 2.00e-02 2.50e+03 pdb=" C5 SPH C 602 " 0.047 2.00e-02 2.50e+03 pdb=" C6 SPH C 602 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 SPH A 602 " 0.043 2.00e-02 2.50e+03 4.37e-02 1.91e+01 pdb=" C4 SPH A 602 " -0.040 2.00e-02 2.50e+03 pdb=" C5 SPH A 602 " -0.047 2.00e-02 2.50e+03 pdb=" C6 SPH A 602 " 0.044 2.00e-02 2.50e+03 ... (remaining 1215 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2269 2.82 - 3.34: 6826 3.34 - 3.86: 12171 3.86 - 4.38: 14508 4.38 - 4.90: 24431 Nonbonded interactions: 60205 Sorted by model distance: nonbonded pdb=" O THR B 459 " pdb=" OG1 THR B 463 " model vdw 2.299 3.040 nonbonded pdb=" O THR A 459 " pdb=" OG1 THR A 463 " model vdw 2.300 3.040 nonbonded pdb=" O THR C 459 " pdb=" OG1 THR C 463 " model vdw 2.300 3.040 nonbonded pdb=" O SER C 340 " pdb=" OG SER C 340 " model vdw 2.324 3.040 nonbonded pdb=" O SER B 340 " pdb=" OG SER B 340 " model vdw 2.325 3.040 ... (remaining 60200 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 191 through 356 or resid 358 through 512 or resid 601 thro \ ugh 602)) selection = (chain 'B' and (resid 191 through 356 or resid 358 through 512 or resid 601 thro \ ugh 602)) selection = (chain 'C' and (resid 191 through 356 or resid 358 through 512 or resid 601 thro \ ugh 602)) } 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=0.38 max=1.00 mean=0.99 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: 0.340 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.000 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 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:15.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 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 0.139 7452 Z= 0.455 Angle : 1.079 15.827 10173 Z= 0.600 Chirality : 0.054 0.243 1191 Planarity : 0.005 0.044 1218 Dihedral : 17.393 142.011 2514 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.65 % Allowed : 4.21 % Favored : 95.15 % Rotamer: Outliers : 4.80 % Allowed : 15.72 % Favored : 79.48 % 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: -3.26 (0.25), residues: 936 helix: -2.04 (0.17), residues: 681 sheet: None (None), residues: 0 loop : -1.92 (0.42), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 215 HIS 0.005 0.001 HIS B 374 PHE 0.017 0.001 PHE A 421 TYR 0.007 0.001 TYR C 400 ARG 0.015 0.001 ARG A 225 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.792 Fit side-chains revert: symmetry clash REVERT: A 263 ILE cc_start: 0.7640 (OUTLIER) cc_final: 0.7285 (mt) REVERT: A 332 ARG cc_start: 0.6296 (ttp-110) cc_final: 0.5481 (ttt90) REVERT: A 482 ARG cc_start: 0.7212 (ttm170) cc_final: 0.6940 (mtm-85) REVERT: A 491 MET cc_start: 0.7328 (ttm) cc_final: 0.7032 (ttm) REVERT: A 505 LEU cc_start: 0.6536 (OUTLIER) cc_final: 0.6175 (mp) REVERT: B 263 ILE cc_start: 0.7505 (OUTLIER) cc_final: 0.7087 (mt) REVERT: B 264 ARG cc_start: 0.6791 (mtm-85) cc_final: 0.6534 (mtm180) REVERT: B 327 SER cc_start: 0.7766 (OUTLIER) cc_final: 0.7538 (p) REVERT: B 332 ARG cc_start: 0.6176 (ttp-110) cc_final: 0.5386 (ttt90) REVERT: B 491 MET cc_start: 0.7502 (ttm) cc_final: 0.7290 (ttm) REVERT: B 505 LEU cc_start: 0.6210 (OUTLIER) cc_final: 0.5963 (mp) REVERT: C 264 ARG cc_start: 0.6824 (mtm-85) cc_final: 0.6416 (ttp-110) REVERT: C 267 PHE cc_start: 0.7844 (t80) cc_final: 0.7499 (t80) REVERT: C 272 ARG cc_start: 0.7006 (mtt180) cc_final: 0.6666 (mtt180) REVERT: C 331 ARG cc_start: 0.7073 (mtm-85) cc_final: 0.5703 (mmm160) REVERT: C 332 ARG cc_start: 0.6126 (ttp-110) cc_final: 0.5264 (ttt90) REVERT: C 455 TRP cc_start: 0.6427 (t-100) cc_final: 0.6210 (t-100) REVERT: C 482 ARG cc_start: 0.7385 (ttm170) cc_final: 0.7153 (ttm-80) REVERT: C 505 LEU cc_start: 0.6321 (OUTLIER) cc_final: 0.6048 (mp) outliers start: 30 outliers final: 7 residues processed: 148 average time/residue: 1.1741 time to fit residues: 183.5745 Evaluate side-chains 118 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 442 ARG Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 505 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 39 optimal weight: 0.1980 chunk 24 optimal weight: 8.9990 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 HIS A 348 ASN A 374 HIS B 374 HIS C 374 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7452 Z= 0.186 Angle : 0.595 9.652 10173 Z= 0.293 Chirality : 0.038 0.119 1191 Planarity : 0.005 0.029 1218 Dihedral : 16.611 145.540 1195 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.33 % Allowed : 21.69 % Favored : 75.98 % 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: -1.17 (0.27), residues: 936 helix: -0.46 (0.19), residues: 681 sheet: None (None), residues: 0 loop : -1.27 (0.42), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 455 HIS 0.004 0.001 HIS C 374 PHE 0.021 0.001 PHE B 260 TYR 0.019 0.002 TYR B 259 ARG 0.004 0.001 ARG C 264 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.929 Fit side-chains revert: symmetry clash REVERT: A 264 ARG cc_start: 0.6182 (mtm-85) cc_final: 0.5891 (ttp-110) REVERT: A 332 ARG cc_start: 0.5847 (ttp-110) cc_final: 0.5082 (ttt90) REVERT: C 264 ARG cc_start: 0.6198 (mtm-85) cc_final: 0.5957 (mtm180) REVERT: C 272 ARG cc_start: 0.7024 (mtt180) cc_final: 0.6702 (mtt180) REVERT: C 482 ARG cc_start: 0.7407 (ttm170) cc_final: 0.7167 (ttm-80) REVERT: C 501 VAL cc_start: 0.7327 (m) cc_final: 0.7083 (t) REVERT: C 505 LEU cc_start: 0.6393 (OUTLIER) cc_final: 0.6143 (mp) outliers start: 13 outliers final: 3 residues processed: 104 average time/residue: 1.4338 time to fit residues: 156.5252 Evaluate side-chains 96 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 92 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain C residue 442 ARG Chi-restraints excluded: chain C residue 505 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 67 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7452 Z= 0.203 Angle : 0.574 10.350 10173 Z= 0.279 Chirality : 0.038 0.123 1191 Planarity : 0.004 0.030 1218 Dihedral : 15.503 149.579 1175 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.18 % Allowed : 23.29 % Favored : 74.53 % 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: -0.09 (0.28), residues: 936 helix: 0.24 (0.20), residues: 687 sheet: None (None), residues: 0 loop : -0.55 (0.45), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 455 HIS 0.002 0.001 HIS B 342 PHE 0.025 0.001 PHE C 267 TYR 0.015 0.001 TYR C 259 ARG 0.003 0.000 ARG B 331 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.755 Fit side-chains revert: symmetry clash REVERT: A 331 ARG cc_start: 0.7265 (mpp80) cc_final: 0.5873 (mmm160) REVERT: A 332 ARG cc_start: 0.5976 (ttp-110) cc_final: 0.5224 (ttt90) REVERT: A 505 LEU cc_start: 0.6660 (OUTLIER) cc_final: 0.6355 (mp) REVERT: B 249 SER cc_start: 0.8186 (t) cc_final: 0.7964 (m) REVERT: C 272 ARG cc_start: 0.7115 (mtt180) cc_final: 0.6740 (mtt180) REVERT: C 501 VAL cc_start: 0.7286 (m) cc_final: 0.7065 (t) REVERT: C 505 LEU cc_start: 0.6241 (OUTLIER) cc_final: 0.6033 (mp) outliers start: 12 outliers final: 1 residues processed: 104 average time/residue: 1.3284 time to fit residues: 145.7750 Evaluate side-chains 95 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 92 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain C residue 442 ARG Chi-restraints excluded: chain C residue 505 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.7236 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7452 Z= 0.196 Angle : 0.569 9.426 10173 Z= 0.276 Chirality : 0.038 0.124 1191 Planarity : 0.004 0.029 1218 Dihedral : 14.976 151.939 1175 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.46 % Allowed : 25.62 % Favored : 72.93 % 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: 0.42 (0.29), residues: 936 helix: 0.62 (0.20), residues: 687 sheet: None (None), residues: 0 loop : -0.39 (0.45), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 455 HIS 0.002 0.001 HIS B 342 PHE 0.023 0.001 PHE C 267 TYR 0.021 0.001 TYR A 259 ARG 0.007 0.000 ARG C 264 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.754 Fit side-chains revert: symmetry clash REVERT: A 331 ARG cc_start: 0.7262 (mpp80) cc_final: 0.6034 (mmm160) REVERT: A 332 ARG cc_start: 0.5979 (ttp-110) cc_final: 0.5261 (ttt90) REVERT: A 505 LEU cc_start: 0.6553 (OUTLIER) cc_final: 0.6230 (mp) REVERT: B 249 SER cc_start: 0.8167 (t) cc_final: 0.7962 (m) REVERT: B 331 ARG cc_start: 0.7225 (mpp80) cc_final: 0.5922 (mmm160) REVERT: C 264 ARG cc_start: 0.6190 (ttp-110) cc_final: 0.5859 (ttp-110) REVERT: C 272 ARG cc_start: 0.7115 (mtt180) cc_final: 0.6712 (mtt180) REVERT: C 482 ARG cc_start: 0.7335 (ttm170) cc_final: 0.7079 (ttm-80) outliers start: 7 outliers final: 1 residues processed: 99 average time/residue: 1.3046 time to fit residues: 136.2092 Evaluate side-chains 94 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 92 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain C residue 442 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 1.9990 chunk 51 optimal weight: 0.3980 chunk 1 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 76 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 0.4980 chunk 80 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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: 0.7241 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7452 Z= 0.202 Angle : 0.562 8.812 10173 Z= 0.273 Chirality : 0.038 0.125 1191 Planarity : 0.004 0.029 1218 Dihedral : 14.671 150.686 1173 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.60 % Allowed : 26.06 % Favored : 72.34 % 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 (0.29), residues: 936 helix: 0.86 (0.20), residues: 687 sheet: None (None), residues: 0 loop : -0.27 (0.45), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 455 HIS 0.002 0.001 HIS B 342 PHE 0.020 0.001 PHE C 267 TYR 0.020 0.001 TYR B 259 ARG 0.005 0.000 ARG C 264 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.766 Fit side-chains REVERT: A 331 ARG cc_start: 0.7243 (mpp80) cc_final: 0.6014 (mmm160) REVERT: A 332 ARG cc_start: 0.6056 (ttp-110) cc_final: 0.5283 (ttt90) REVERT: A 421 PHE cc_start: 0.8222 (OUTLIER) cc_final: 0.7251 (m-80) REVERT: A 505 LEU cc_start: 0.6546 (OUTLIER) cc_final: 0.6221 (mp) REVERT: B 224 MET cc_start: 0.7796 (OUTLIER) cc_final: 0.6363 (mtm) REVERT: B 249 SER cc_start: 0.8166 (t) cc_final: 0.7943 (m) REVERT: B 331 ARG cc_start: 0.7235 (mpp80) cc_final: 0.5991 (mmm160) REVERT: C 264 ARG cc_start: 0.6186 (ttp-110) cc_final: 0.5841 (ttp-110) REVERT: C 272 ARG cc_start: 0.6944 (mtt180) cc_final: 0.6517 (mtt180) REVERT: C 482 ARG cc_start: 0.7379 (ttm170) cc_final: 0.7121 (ttm-80) outliers start: 8 outliers final: 0 residues processed: 100 average time/residue: 1.3081 time to fit residues: 137.8718 Evaluate side-chains 96 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 93 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 224 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7452 Z= 0.212 Angle : 0.564 7.944 10173 Z= 0.275 Chirality : 0.038 0.126 1191 Planarity : 0.004 0.030 1218 Dihedral : 14.505 149.253 1173 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.60 % Allowed : 26.93 % Favored : 71.47 % 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: 0.94 (0.29), residues: 936 helix: 0.99 (0.20), residues: 687 sheet: None (None), residues: 0 loop : -0.15 (0.45), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 455 HIS 0.002 0.001 HIS A 374 PHE 0.024 0.001 PHE C 479 TYR 0.016 0.001 TYR A 259 ARG 0.005 0.000 ARG C 264 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.789 Fit side-chains REVERT: A 331 ARG cc_start: 0.7186 (mpp80) cc_final: 0.5901 (mmm160) REVERT: A 332 ARG cc_start: 0.6130 (ttp-110) cc_final: 0.5356 (ttt90) REVERT: A 421 PHE cc_start: 0.8250 (OUTLIER) cc_final: 0.7253 (m-80) REVERT: A 505 LEU cc_start: 0.6476 (OUTLIER) cc_final: 0.6139 (mp) REVERT: B 224 MET cc_start: 0.7809 (OUTLIER) cc_final: 0.6482 (mtm) REVERT: B 249 SER cc_start: 0.8192 (t) cc_final: 0.7933 (m) REVERT: B 331 ARG cc_start: 0.7207 (mpp80) cc_final: 0.6028 (mmm160) REVERT: B 332 ARG cc_start: 0.5989 (ttp-110) cc_final: 0.5249 (ttt90) REVERT: C 264 ARG cc_start: 0.6201 (ttp-110) cc_final: 0.5759 (ttp-110) REVERT: C 272 ARG cc_start: 0.6946 (mtt180) cc_final: 0.6518 (mtt180) outliers start: 8 outliers final: 1 residues processed: 99 average time/residue: 1.3462 time to fit residues: 140.5451 Evaluate side-chains 94 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 421 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 65 optimal weight: 0.0070 chunk 50 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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: 0.7215 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7452 Z= 0.168 Angle : 0.542 6.598 10173 Z= 0.265 Chirality : 0.037 0.124 1191 Planarity : 0.003 0.029 1218 Dihedral : 14.310 148.361 1173 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.46 % Allowed : 27.37 % Favored : 71.18 % 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: 1.25 (0.29), residues: 936 helix: 1.20 (0.20), residues: 687 sheet: None (None), residues: 0 loop : 0.01 (0.46), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 455 HIS 0.002 0.001 HIS B 303 PHE 0.020 0.001 PHE C 479 TYR 0.016 0.001 TYR A 259 ARG 0.004 0.000 ARG C 264 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.677 Fit side-chains REVERT: A 331 ARG cc_start: 0.7151 (mpp80) cc_final: 0.5869 (mmm160) REVERT: A 332 ARG cc_start: 0.6029 (ttp-110) cc_final: 0.5272 (ttt90) REVERT: A 421 PHE cc_start: 0.7934 (OUTLIER) cc_final: 0.7165 (m-80) REVERT: A 505 LEU cc_start: 0.6391 (OUTLIER) cc_final: 0.6040 (mp) REVERT: B 224 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.6441 (mtm) REVERT: B 249 SER cc_start: 0.8168 (t) cc_final: 0.7964 (m) REVERT: B 331 ARG cc_start: 0.7168 (mpp80) cc_final: 0.5902 (mmm160) REVERT: C 224 MET cc_start: 0.7986 (OUTLIER) cc_final: 0.6397 (mmm) REVERT: C 264 ARG cc_start: 0.6255 (ttp-110) cc_final: 0.5776 (ttp-110) REVERT: C 272 ARG cc_start: 0.6821 (mtt180) cc_final: 0.6406 (mtt180) REVERT: C 421 PHE cc_start: 0.7870 (OUTLIER) cc_final: 0.7185 (m-80) outliers start: 7 outliers final: 1 residues processed: 97 average time/residue: 1.2487 time to fit residues: 127.8718 Evaluate side-chains 100 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 94 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 421 PHE Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain C residue 421 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 81 optimal weight: 0.2980 chunk 85 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7452 Z= 0.186 Angle : 0.547 6.433 10173 Z= 0.268 Chirality : 0.038 0.124 1191 Planarity : 0.003 0.030 1218 Dihedral : 14.160 146.215 1173 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.89 % Allowed : 26.49 % Favored : 71.62 % 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: 1.35 (0.29), residues: 936 helix: 1.25 (0.20), residues: 687 sheet: None (None), residues: 0 loop : 0.10 (0.47), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 455 HIS 0.002 0.001 HIS A 374 PHE 0.025 0.001 PHE B 479 TYR 0.015 0.001 TYR A 259 ARG 0.004 0.000 ARG C 264 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.714 Fit side-chains REVERT: A 331 ARG cc_start: 0.7243 (mpp80) cc_final: 0.5964 (mmm160) REVERT: A 332 ARG cc_start: 0.6057 (ttp-110) cc_final: 0.5275 (ttt90) REVERT: A 421 PHE cc_start: 0.7951 (OUTLIER) cc_final: 0.7062 (m-80) REVERT: A 437 MET cc_start: 0.7567 (mtm) cc_final: 0.7282 (mtm) REVERT: A 505 LEU cc_start: 0.6378 (OUTLIER) cc_final: 0.5998 (mp) REVERT: B 249 SER cc_start: 0.8159 (t) cc_final: 0.7957 (m) REVERT: B 331 ARG cc_start: 0.7252 (mpp80) cc_final: 0.5955 (mmm160) REVERT: C 224 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.6413 (mmm) REVERT: C 264 ARG cc_start: 0.6268 (ttp-110) cc_final: 0.5774 (ttp-110) REVERT: C 272 ARG cc_start: 0.6764 (mtt180) cc_final: 0.6367 (mtt180) outliers start: 10 outliers final: 2 residues processed: 104 average time/residue: 1.3324 time to fit residues: 146.1214 Evaluate side-chains 98 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 421 PHE Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain C residue 294 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 50 optimal weight: 0.4980 chunk 36 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7452 Z= 0.173 Angle : 0.542 6.644 10173 Z= 0.267 Chirality : 0.037 0.123 1191 Planarity : 0.003 0.030 1218 Dihedral : 13.998 144.501 1173 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.60 % Allowed : 26.78 % Favored : 71.62 % 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 (0.29), residues: 936 helix: 1.32 (0.20), residues: 687 sheet: None (None), residues: 0 loop : 0.22 (0.47), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 455 HIS 0.002 0.001 HIS C 374 PHE 0.026 0.001 PHE C 479 TYR 0.015 0.001 TYR A 259 ARG 0.004 0.000 ARG C 264 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.718 Fit side-chains REVERT: A 331 ARG cc_start: 0.7227 (mpp80) cc_final: 0.5953 (mmm160) REVERT: A 332 ARG cc_start: 0.6031 (ttp-110) cc_final: 0.5278 (ttt90) REVERT: A 421 PHE cc_start: 0.7821 (OUTLIER) cc_final: 0.7042 (m-80) REVERT: B 331 ARG cc_start: 0.7247 (mpp80) cc_final: 0.6001 (mmm160) REVERT: C 225 ARG cc_start: 0.7901 (mpt-90) cc_final: 0.7600 (mpt-90) REVERT: C 264 ARG cc_start: 0.6225 (ttp-110) cc_final: 0.5727 (ttp-110) REVERT: C 272 ARG cc_start: 0.6755 (mtt180) cc_final: 0.6327 (mtt90) REVERT: C 498 LEU cc_start: 0.6939 (mp) cc_final: 0.6666 (pp) outliers start: 8 outliers final: 1 residues processed: 106 average time/residue: 1.2392 time to fit residues: 138.6705 Evaluate side-chains 99 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 97 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain B residue 421 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 2.9990 chunk 41 optimal weight: 0.1980 chunk 61 optimal weight: 7.9990 chunk 92 optimal weight: 0.2980 chunk 85 optimal weight: 0.9990 chunk 73 optimal weight: 0.0040 chunk 7 optimal weight: 8.9990 chunk 56 optimal weight: 0.0770 chunk 45 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 overall best weight: 0.3150 ------------------------------------------------------------------------------- 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: 0.7174 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7452 Z= 0.146 Angle : 0.530 6.596 10173 Z= 0.261 Chirality : 0.037 0.120 1191 Planarity : 0.003 0.029 1218 Dihedral : 13.814 143.476 1173 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.16 % Allowed : 27.80 % Favored : 71.03 % 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 (0.29), residues: 936 helix: 1.43 (0.20), residues: 687 sheet: None (None), residues: 0 loop : 0.34 (0.48), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 455 HIS 0.002 0.001 HIS B 303 PHE 0.028 0.001 PHE B 479 TYR 0.014 0.001 TYR A 259 ARG 0.004 0.000 ARG C 264 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 101 time to evaluate : 0.770 Fit side-chains REVERT: A 331 ARG cc_start: 0.7249 (mpp80) cc_final: 0.6003 (mmm160) REVERT: A 332 ARG cc_start: 0.5996 (ttp-110) cc_final: 0.5262 (ttt90) REVERT: A 421 PHE cc_start: 0.7451 (OUTLIER) cc_final: 0.6963 (m-80) REVERT: A 431 MET cc_start: 0.6963 (ttm) cc_final: 0.6537 (mtp) REVERT: B 331 ARG cc_start: 0.7184 (mpp80) cc_final: 0.5981 (mmm160) REVERT: C 225 ARG cc_start: 0.7897 (mpt-90) cc_final: 0.7601 (mpt-90) REVERT: C 272 ARG cc_start: 0.6666 (mtt180) cc_final: 0.6255 (mtt90) outliers start: 5 outliers final: 1 residues processed: 104 average time/residue: 1.2487 time to fit residues: 136.8999 Evaluate side-chains 100 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 98 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain B residue 421 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 10 optimal weight: 0.0970 chunk 20 optimal weight: 0.9990 chunk 73 optimal weight: 0.0010 chunk 30 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- 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 = 0.3784 r_free = 0.3784 target = 0.159481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.115874 restraints weight = 22851.004| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 4.86 r_work: 0.2842 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2768 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2731 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7452 Z= 0.160 Angle : 0.538 6.287 10173 Z= 0.265 Chirality : 0.037 0.120 1191 Planarity : 0.003 0.032 1218 Dihedral : 13.719 141.945 1173 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.16 % Allowed : 27.95 % Favored : 70.89 % 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 (0.29), residues: 936 helix: 1.46 (0.20), residues: 687 sheet: None (None), residues: 0 loop : 0.38 (0.48), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 455 HIS 0.002 0.001 HIS B 303 PHE 0.026 0.001 PHE C 479 TYR 0.015 0.001 TYR A 259 ARG 0.009 0.000 ARG C 264 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2797.62 seconds wall clock time: 50 minutes 57.12 seconds (3057.12 seconds total)