Starting phenix.real_space_refine on Sat Nov 16 14:38:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p0g_17333/11_2024/8p0g_17333.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p0g_17333/11_2024/8p0g_17333.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p0g_17333/11_2024/8p0g_17333.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p0g_17333/11_2024/8p0g_17333.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p0g_17333/11_2024/8p0g_17333.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p0g_17333/11_2024/8p0g_17333.cif" } resolution = 3.17 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= 0.002 sd= 0.018 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: 6 Type Number sf(0) Gaussians P 19 5.49 5 Mg 1 5.21 5 S 68 5.16 5 C 7119 2.51 5 N 1979 2.21 5 O 2145 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 11331 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3644 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 426} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 5307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5307 Classifications: {'peptide': 662} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 628} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 1966 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 241, 1954 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 16, 'TRANS': 224} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 241, 1954 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 16, 'TRANS': 224} Chain breaks: 1 bond proxies already assigned to first conformer: 1989 Chain: "V" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 307 Classifications: {'RNA': 14} Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 8, 'rna3p_pyr': 3} Link IDs: {'rna2p': 3, 'rna3p': 10} Chain: "R" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 106 Classifications: {'RNA': 5} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 3} Link IDs: {'rna3p': 4} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR C 59 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR C 59 " occ=0.50 Time building chain proxies: 8.54, per 1000 atoms: 0.75 Number of scatterers: 11331 At special positions: 0 Unit cell: (102.548, 110.818, 95.932, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 68 16.00 P 19 15.00 Mg 1 11.99 O 2145 8.00 N 1979 7.00 C 7119 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: 2.80 Conformation dependent library (CDL) restraints added in 1.7 seconds 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2588 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 16 sheets defined 50.9% alpha, 10.2% beta 5 base pairs and 12 stacking pairs defined. Time for finding SS restraints: 3.71 Creating SS restraints... Processing helix chain 'A' and resid 176 through 184 Processing helix chain 'A' and resid 246 through 257 Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 273 through 286 removed outlier: 3.706A pdb=" N LEU A 277 " --> pdb=" O VAL A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 301 Processing helix chain 'A' and resid 304 through 316 removed outlier: 3.715A pdb=" N GLU A 308 " --> pdb=" O ASN A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 345 removed outlier: 4.215A pdb=" N GLU A 339 " --> pdb=" O PRO A 335 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG A 345 " --> pdb=" O MET A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 381 removed outlier: 4.555A pdb=" N ARG A 381 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 401 Processing helix chain 'A' and resid 485 through 493 Processing helix chain 'A' and resid 494 through 497 Processing helix chain 'A' and resid 498 through 515 removed outlier: 3.615A pdb=" N ILE A 504 " --> pdb=" O GLN A 500 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU A 515 " --> pdb=" O SER A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 557 Processing helix chain 'A' and resid 559 through 581 removed outlier: 4.356A pdb=" N ARG A 571 " --> pdb=" O ALA A 567 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU A 572 " --> pdb=" O ASN A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 599 removed outlier: 3.532A pdb=" N GLU A 599 " --> pdb=" O ASP A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 617 Processing helix chain 'B' and resid 13 through 20 removed outlier: 4.024A pdb=" N GLU B 17 " --> pdb=" O THR B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 49 Proline residue: B 44 - end of helix removed outlier: 4.453A pdb=" N TYR B 49 " --> pdb=" O TYR B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 58 removed outlier: 3.609A pdb=" N ALA B 57 " --> pdb=" O ASN B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 80 through 95 Processing helix chain 'B' and resid 95 through 108 Processing helix chain 'B' and resid 109 through 113 Processing helix chain 'B' and resid 114 through 121 Processing helix chain 'B' and resid 134 through 151 Processing helix chain 'B' and resid 157 through 171 removed outlier: 3.843A pdb=" N GLU B 170 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU B 171 " --> pdb=" O ASP B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 225 Processing helix chain 'B' and resid 247 through 249 No H-bonds generated for 'chain 'B' and resid 247 through 249' Processing helix chain 'B' and resid 250 through 266 Processing helix chain 'B' and resid 277 through 287 Processing helix chain 'B' and resid 310 through 326 removed outlier: 3.655A pdb=" N MET B 314 " --> pdb=" O ASP B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 344 Proline residue: B 338 - end of helix Processing helix chain 'B' and resid 373 through 380 removed outlier: 4.454A pdb=" N ARG B 378 " --> pdb=" O ASP B 375 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL B 380 " --> pdb=" O VAL B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 409 removed outlier: 3.710A pdb=" N SER B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE B 408 " --> pdb=" O ALA B 404 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU B 409 " --> pdb=" O LEU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 451 Processing helix chain 'B' and resid 496 through 514 Processing helix chain 'B' and resid 518 through 537 Processing helix chain 'B' and resid 543 through 552 Processing helix chain 'B' and resid 558 through 562 Processing helix chain 'B' and resid 575 through 583 Processing helix chain 'B' and resid 587 through 596 Processing helix chain 'B' and resid 646 through 666 removed outlier: 4.143A pdb=" N ASN B 650 " --> pdb=" O LYS B 646 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LYS B 651 " --> pdb=" O ALA B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 694 Processing helix chain 'B' and resid 698 through 708 removed outlier: 3.510A pdb=" N ARG B 708 " --> pdb=" O ARG B 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 27 Processing helix chain 'C' and resid 27 through 32 removed outlier: 3.667A pdb=" N SER C 32 " --> pdb=" O PRO C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 35 No H-bonds generated for 'chain 'C' and resid 33 through 35' Processing helix chain 'C' and resid 36 through 42 removed outlier: 4.136A pdb=" N THR C 40 " --> pdb=" O THR C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 62 removed outlier: 3.706A pdb=" N ARG C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL C 58 " --> pdb=" O GLN C 54 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ATYR C 59 " --> pdb=" O MET C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 108 removed outlier: 4.303A pdb=" N ASP C 105 " --> pdb=" O ILE C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 123 Processing helix chain 'C' and resid 123 through 135 Processing helix chain 'C' and resid 163 through 165 No H-bonds generated for 'chain 'C' and resid 163 through 165' Processing helix chain 'C' and resid 166 through 176 Processing helix chain 'C' and resid 177 through 180 removed outlier: 3.834A pdb=" N THR C 180 " --> pdb=" O PRO C 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 177 through 180' Processing helix chain 'C' and resid 181 through 186 Processing helix chain 'C' and resid 189 through 200 Processing helix chain 'C' and resid 208 through 221 removed outlier: 3.816A pdb=" N HIS C 214 " --> pdb=" O GLU C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 245 removed outlier: 4.077A pdb=" N MET C 240 " --> pdb=" O ARG C 236 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N HIS C 242 " --> pdb=" O ALA C 238 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N PHE C 243 " --> pdb=" O GLU C 239 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU C 244 " --> pdb=" O MET C 240 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N CYS C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 240 through 242 removed outlier: 7.585A pdb=" N TRP A 426 " --> pdb=" O ILE A 450 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LEU A 475 " --> pdb=" O MET A 451 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL A 464 " --> pdb=" O ILE A 263 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 240 through 242 removed outlier: 6.840A pdb=" N ILE A 414 " --> pdb=" O TRP A 426 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N MET A 428 " --> pdb=" O CYS A 412 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N CYS A 412 " --> pdb=" O MET A 428 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU A 430 " --> pdb=" O THR A 410 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N THR A 410 " --> pdb=" O LEU A 430 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 322 through 323 removed outlier: 3.531A pdb=" N LYS A 322 " --> pdb=" O THR B 356 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 442 through 445 Processing sheet with id=AA5, first strand: chain 'A' and resid 526 through 528 Processing sheet with id=AA6, first strand: chain 'A' and resid 584 through 586 Processing sheet with id=AA7, first strand: chain 'B' and resid 124 through 126 removed outlier: 3.648A pdb=" N ARG B 131 " --> pdb=" O SER B 126 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 173 through 178 Processing sheet with id=AA9, first strand: chain 'B' and resid 227 through 230 Processing sheet with id=AB1, first strand: chain 'B' and resid 302 through 303 removed outlier: 4.712A pdb=" N ASN B 453 " --> pdb=" O GLU B 303 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 345 through 348 removed outlier: 3.619A pdb=" N LYS B 345 " --> pdb=" O CYS B 387 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 467 through 470 Processing sheet with id=AB4, first strand: chain 'C' and resid 67 through 69 Processing sheet with id=AB5, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AB6, first strand: chain 'C' and resid 142 through 143 Processing sheet with id=AB7, first strand: chain 'C' and resid 150 through 154 523 hydrogen bonds defined for protein. 1441 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 14 hydrogen bonds 28 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 12 stacking parallelities Total time for adding SS restraints: 3.81 Time building geometry restraints manager: 3.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3620 1.34 - 1.46: 1723 1.46 - 1.57: 6124 1.57 - 1.69: 36 1.69 - 1.81: 114 Bond restraints: 11617 Sorted by residual: bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.91e+00 bond pdb=" CB PRO B 464 " pdb=" CG PRO B 464 " ideal model delta sigma weight residual 1.506 1.477 0.029 3.90e-02 6.57e+02 5.35e-01 bond pdb=" C LEU A 171 " pdb=" N GLN A 172 " ideal model delta sigma weight residual 1.332 1.322 0.010 1.40e-02 5.10e+03 5.21e-01 bond pdb=" C GLU C 201 " pdb=" N PRO C 202 " ideal model delta sigma weight residual 1.334 1.350 -0.016 2.34e-02 1.83e+03 4.85e-01 bond pdb=" CB PRO B 274 " pdb=" CG PRO B 274 " ideal model delta sigma weight residual 1.492 1.526 -0.034 5.00e-02 4.00e+02 4.59e-01 ... (remaining 11612 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.98: 15402 0.98 - 1.96: 298 1.96 - 2.94: 51 2.94 - 3.92: 51 3.92 - 4.89: 8 Bond angle restraints: 15810 Sorted by residual: angle pdb=" N GLU C 201 " pdb=" CA GLU C 201 " pdb=" C GLU C 201 " ideal model delta sigma weight residual 109.81 114.70 -4.89 2.21e+00 2.05e-01 4.89e+00 angle pdb=" C ASP A 405 " pdb=" N ARG A 406 " pdb=" CA ARG A 406 " ideal model delta sigma weight residual 121.54 125.43 -3.89 1.91e+00 2.74e-01 4.15e+00 angle pdb=" O4' A V 7 " pdb=" C1' A V 7 " pdb=" N9 A V 7 " ideal model delta sigma weight residual 108.20 110.89 -2.69 1.50e+00 4.44e-01 3.21e+00 angle pdb=" N GLU B 668 " pdb=" CA GLU B 668 " pdb=" C GLU B 668 " ideal model delta sigma weight residual 114.75 112.71 2.04 1.26e+00 6.30e-01 2.62e+00 angle pdb=" C PHE B 666 " pdb=" N PRO B 667 " pdb=" CA PRO B 667 " ideal model delta sigma weight residual 121.91 119.80 2.11 1.35e+00 5.49e-01 2.44e+00 ... (remaining 15805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.71: 6162 16.71 - 33.42: 698 33.42 - 50.13: 177 50.13 - 66.84: 68 66.84 - 83.55: 18 Dihedral angle restraints: 7123 sinusoidal: 3138 harmonic: 3985 Sorted by residual: dihedral pdb=" CA GLU C 201 " pdb=" C GLU C 201 " pdb=" N PRO C 202 " pdb=" CA PRO C 202 " ideal model delta harmonic sigma weight residual 180.00 -157.62 -22.38 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CG ARG B 581 " pdb=" CD ARG B 581 " pdb=" NE ARG B 581 " pdb=" CZ ARG B 581 " ideal model delta sinusoidal sigma weight residual 180.00 135.06 44.94 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CG ARG A 323 " pdb=" CD ARG A 323 " pdb=" NE ARG A 323 " pdb=" CZ ARG A 323 " ideal model delta sinusoidal sigma weight residual 180.00 135.58 44.42 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 7120 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1165 0.028 - 0.055: 423 0.055 - 0.083: 90 0.083 - 0.110: 73 0.110 - 0.138: 23 Chirality restraints: 1774 Sorted by residual: chirality pdb=" CA VAL B 491 " pdb=" N VAL B 491 " pdb=" C VAL B 491 " pdb=" CB VAL B 491 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA ILE A 192 " pdb=" N ILE A 192 " pdb=" C ILE A 192 " pdb=" CB ILE A 192 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.66e-01 chirality pdb=" CA ILE A 527 " pdb=" N ILE A 527 " pdb=" C ILE A 527 " pdb=" CB ILE A 527 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.02e-01 ... (remaining 1771 not shown) Planarity restraints: 1953 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A V 7 " 0.017 2.00e-02 2.50e+03 7.91e-03 1.72e+00 pdb=" N9 A V 7 " -0.019 2.00e-02 2.50e+03 pdb=" C8 A V 7 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A V 7 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A V 7 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A V 7 " 0.002 2.00e-02 2.50e+03 pdb=" N6 A V 7 " 0.004 2.00e-02 2.50e+03 pdb=" N1 A V 7 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A V 7 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A V 7 " -0.002 2.00e-02 2.50e+03 pdb=" C4 A V 7 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU C 201 " -0.021 5.00e-02 4.00e+02 3.14e-02 1.58e+00 pdb=" N PRO C 202 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO C 202 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 202 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 96 " 0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO B 97 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO B 97 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 97 " 0.017 5.00e-02 4.00e+02 ... (remaining 1950 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 100 2.55 - 3.14: 8783 3.14 - 3.73: 17692 3.73 - 4.31: 24963 4.31 - 4.90: 42634 Nonbonded interactions: 94172 Sorted by model distance: nonbonded pdb=" OD1 ASP B 423 " pdb="MG MG B 801 " model vdw 1.965 2.170 nonbonded pdb=" OD1 ASN A 516 " pdb=" OG SER A 518 " model vdw 2.070 3.040 nonbonded pdb=" OE1 GLU C 74 " pdb=" OG SER C 112 " model vdw 2.144 3.040 nonbonded pdb=" OE1 GLU A 369 " pdb=" NH2 ARG B 527 " model vdw 2.168 3.120 nonbonded pdb=" OG1 THR B 62 " pdb=" OD2 ASP B 312 " model vdw 2.220 3.040 ... (remaining 94167 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 32.160 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11617 Z= 0.126 Angle : 0.417 4.895 15810 Z= 0.209 Chirality : 0.036 0.138 1774 Planarity : 0.003 0.031 1953 Dihedral : 16.061 83.552 4535 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.65 % Favored : 96.20 % Rotamer: Outliers : 0.17 % Allowed : 12.29 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 0.93 (0.24), residues: 1345 helix: 2.17 (0.22), residues: 625 sheet: -0.44 (0.44), residues: 127 loop : -0.87 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 336 HIS 0.002 0.000 HIS B 291 PHE 0.015 0.001 PHE C 41 TYR 0.013 0.001 TYR B 22 ARG 0.001 0.000 ARG C 198 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 127 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 101 ILE cc_start: 0.8204 (pt) cc_final: 0.7930 (tt) outliers start: 2 outliers final: 2 residues processed: 129 average time/residue: 0.3510 time to fit residues: 60.2376 Evaluate side-chains 72 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain B residue 289 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 57 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 chunk 69 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 106 optimal weight: 0.5980 chunk 41 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 453 ASN B 582 HIS C 131 GLN C 242 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11617 Z= 0.233 Angle : 0.540 6.170 15810 Z= 0.277 Chirality : 0.039 0.171 1774 Planarity : 0.004 0.052 1953 Dihedral : 9.745 73.367 1771 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.58 % Favored : 96.27 % Rotamer: Outliers : 1.73 % Allowed : 14.11 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 0.96 (0.24), residues: 1345 helix: 2.21 (0.22), residues: 616 sheet: -0.59 (0.44), residues: 127 loop : -0.77 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 253 HIS 0.005 0.001 HIS B 291 PHE 0.026 0.001 PHE C 41 TYR 0.019 0.001 TYR B 533 ARG 0.007 0.001 ARG B 681 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 9 residues processed: 90 average time/residue: 0.2492 time to fit residues: 33.0704 Evaluate side-chains 77 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain C residue 73 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 102 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 chunk 34 optimal weight: 0.0770 chunk 123 optimal weight: 0.9980 chunk 133 optimal weight: 8.9990 chunk 110 optimal weight: 8.9990 chunk 122 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 overall best weight: 1.3540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 214 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11617 Z= 0.210 Angle : 0.511 6.980 15810 Z= 0.262 Chirality : 0.039 0.174 1774 Planarity : 0.004 0.040 1953 Dihedral : 9.638 73.278 1769 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.02 % Favored : 95.83 % Rotamer: Outliers : 2.56 % Allowed : 13.78 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 0.90 (0.24), residues: 1345 helix: 2.09 (0.21), residues: 620 sheet: -0.50 (0.44), residues: 121 loop : -0.77 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 336 HIS 0.006 0.001 HIS B 291 PHE 0.032 0.001 PHE C 41 TYR 0.019 0.001 TYR B 533 ARG 0.005 0.000 ARG C 43 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 67 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 652 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7942 (tt0) outliers start: 31 outliers final: 16 residues processed: 91 average time/residue: 0.2316 time to fit residues: 31.6034 Evaluate side-chains 81 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 395 MET Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 652 GLU Chi-restraints excluded: chain C residue 73 LYS Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 181 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 131 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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: 0.8397 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11617 Z= 0.169 Angle : 0.499 8.450 15810 Z= 0.252 Chirality : 0.038 0.152 1774 Planarity : 0.003 0.043 1953 Dihedral : 9.588 73.278 1768 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.87 % Favored : 95.98 % Rotamer: Outliers : 2.64 % Allowed : 13.94 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 0.92 (0.24), residues: 1345 helix: 2.09 (0.21), residues: 621 sheet: -0.55 (0.44), residues: 125 loop : -0.72 (0.26), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 336 HIS 0.006 0.001 HIS B 291 PHE 0.029 0.001 PHE C 41 TYR 0.019 0.001 TYR B 533 ARG 0.004 0.000 ARG C 43 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 66 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 652 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7987 (tt0) REVERT: C 101 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.8192 (tt) outliers start: 32 outliers final: 21 residues processed: 86 average time/residue: 0.2017 time to fit residues: 27.6185 Evaluate side-chains 88 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 65 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 395 MET Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 652 GLU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 181 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 90 optimal weight: 0.0020 chunk 0 optimal weight: 4.9990 chunk 67 optimal weight: 0.1980 chunk 117 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.4394 ------------------------------------------------------------------------------- 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: 0.8425 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11617 Z= 0.214 Angle : 0.501 7.608 15810 Z= 0.252 Chirality : 0.039 0.183 1774 Planarity : 0.004 0.042 1953 Dihedral : 9.589 73.230 1768 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.40 % Favored : 95.53 % Rotamer: Outliers : 2.64 % Allowed : 14.85 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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 (0.23), residues: 1345 helix: 2.10 (0.21), residues: 620 sheet: -0.43 (0.43), residues: 121 loop : -0.73 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 336 HIS 0.006 0.001 HIS B 291 PHE 0.028 0.001 PHE C 41 TYR 0.020 0.001 TYR B 533 ARG 0.003 0.000 ARG C 43 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 66 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 617 MET cc_start: 0.8564 (mtm) cc_final: 0.8308 (mtm) REVERT: B 652 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7935 (tt0) REVERT: C 101 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8246 (tt) outliers start: 32 outliers final: 23 residues processed: 88 average time/residue: 0.2019 time to fit residues: 27.9525 Evaluate side-chains 92 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 67 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 395 MET Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 652 GLU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 181 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 0.0870 chunk 25 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 131 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 10 optimal weight: 0.2980 chunk 43 optimal weight: 3.9990 chunk 69 optimal weight: 0.0970 chunk 126 optimal weight: 0.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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: 0.8377 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11617 Z= 0.140 Angle : 0.490 7.784 15810 Z= 0.244 Chirality : 0.038 0.146 1774 Planarity : 0.003 0.045 1953 Dihedral : 9.572 73.223 1768 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.73 % Favored : 96.20 % Rotamer: Outliers : 1.90 % Allowed : 15.68 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 1.01 (0.24), residues: 1345 helix: 2.16 (0.21), residues: 621 sheet: -0.43 (0.43), residues: 125 loop : -0.68 (0.26), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 336 HIS 0.006 0.001 HIS B 291 PHE 0.030 0.001 PHE C 41 TYR 0.017 0.001 TYR B 533 ARG 0.003 0.000 ARG C 43 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 617 MET cc_start: 0.8493 (mtm) cc_final: 0.8255 (mtm) REVERT: B 652 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7926 (tt0) REVERT: C 101 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8041 (tt) outliers start: 23 outliers final: 16 residues processed: 84 average time/residue: 0.2069 time to fit residues: 27.8032 Evaluate side-chains 86 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 395 MET Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 652 GLU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 181 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 110 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 131 optimal weight: 8.9990 chunk 82 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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: 0.8441 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11617 Z= 0.243 Angle : 0.521 8.694 15810 Z= 0.261 Chirality : 0.039 0.146 1774 Planarity : 0.004 0.042 1953 Dihedral : 9.613 73.185 1768 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.47 % Favored : 95.45 % Rotamer: Outliers : 2.15 % Allowed : 15.76 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 0.96 (0.23), residues: 1345 helix: 2.04 (0.21), residues: 627 sheet: -0.26 (0.43), residues: 121 loop : -0.69 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 330 HIS 0.006 0.001 HIS B 291 PHE 0.029 0.001 PHE C 41 TYR 0.020 0.001 TYR B 533 ARG 0.003 0.000 ARG B 686 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 68 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 101 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8209 (tt) outliers start: 26 outliers final: 21 residues processed: 82 average time/residue: 0.1982 time to fit residues: 26.2270 Evaluate side-chains 89 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 395 MET Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 652 GLU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 181 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 114 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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: 0.8526 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 11617 Z= 0.472 Angle : 0.647 8.713 15810 Z= 0.328 Chirality : 0.043 0.167 1774 Planarity : 0.004 0.042 1953 Dihedral : 9.757 72.918 1768 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.31 % Allowed : 15.92 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 0.61 (0.23), residues: 1345 helix: 1.73 (0.21), residues: 625 sheet: -0.46 (0.42), residues: 121 loop : -0.83 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 614 HIS 0.005 0.001 HIS B 291 PHE 0.030 0.002 PHE C 41 TYR 0.027 0.002 TYR B 533 ARG 0.004 0.000 ARG A 571 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 64 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 20 residues processed: 81 average time/residue: 0.1979 time to fit residues: 25.8420 Evaluate side-chains 83 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 395 MET Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 652 GLU Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 181 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.8980 chunk 125 optimal weight: 9.9990 chunk 73 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 110 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 80 optimal weight: 0.4980 chunk 129 optimal weight: 2.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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: 0.8447 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11617 Z= 0.190 Angle : 0.519 8.892 15810 Z= 0.263 Chirality : 0.039 0.146 1774 Planarity : 0.004 0.043 1953 Dihedral : 9.680 73.007 1768 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.90 % Allowed : 16.58 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 0.85 (0.23), residues: 1345 helix: 1.94 (0.21), residues: 626 sheet: -0.39 (0.43), residues: 121 loop : -0.72 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 336 HIS 0.006 0.001 HIS B 291 PHE 0.033 0.001 PHE C 41 TYR 0.019 0.001 TYR B 533 ARG 0.003 0.000 ARG C 43 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 65 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 652 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7912 (tt0) outliers start: 23 outliers final: 20 residues processed: 79 average time/residue: 0.2046 time to fit residues: 25.8330 Evaluate side-chains 86 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 395 MET Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 538 MET Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 652 GLU Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 181 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 135 optimal weight: 8.9990 chunk 124 optimal weight: 0.6980 chunk 107 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 83 optimal weight: 0.3980 chunk 66 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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: 0.8455 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11617 Z= 0.218 Angle : 0.539 9.735 15810 Z= 0.270 Chirality : 0.039 0.147 1774 Planarity : 0.004 0.043 1953 Dihedral : 9.668 73.054 1768 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.82 % Allowed : 16.67 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 0.86 (0.23), residues: 1345 helix: 1.95 (0.21), residues: 626 sheet: -0.39 (0.42), residues: 121 loop : -0.72 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 336 HIS 0.006 0.001 HIS B 291 PHE 0.032 0.001 PHE C 41 TYR 0.019 0.001 TYR B 533 ARG 0.002 0.000 ARG C 43 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 18 residues processed: 78 average time/residue: 0.2114 time to fit residues: 26.3995 Evaluate side-chains 83 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 395 MET Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 652 GLU Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 181 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 110 optimal weight: 20.0000 chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 = 0.3143 r_free = 0.3143 target = 0.051231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.038912 restraints weight = 82118.372| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 4.31 r_work: 0.2581 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2586 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2586 r_free = 0.2586 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2586 r_free = 0.2586 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2586 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11617 Z= 0.189 Angle : 0.516 9.609 15810 Z= 0.259 Chirality : 0.039 0.154 1774 Planarity : 0.004 0.044 1953 Dihedral : 9.666 73.077 1768 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.82 % Allowed : 16.75 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 0.91 (0.23), residues: 1345 helix: 1.99 (0.21), residues: 626 sheet: -0.35 (0.43), residues: 121 loop : -0.69 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 336 HIS 0.006 0.001 HIS B 291 PHE 0.032 0.001 PHE C 41 TYR 0.018 0.001 TYR B 533 ARG 0.002 0.000 ARG C 43 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2231.78 seconds wall clock time: 42 minutes 1.71 seconds (2521.71 seconds total)