Starting phenix.real_space_refine on Sat Jul 20 15:44:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p0g_17333/07_2024/8p0g_17333_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p0g_17333/07_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_17333/07_2024/8p0g_17333.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p0g_17333/07_2024/8p0g_17333.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p0g_17333/07_2024/8p0g_17333_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p0g_17333/07_2024/8p0g_17333_neut.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 Residue "B PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 7.98, per 1000 atoms: 0.70 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.27 Conformation dependent library (CDL) restraints added in 2.1 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: 3.65 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: 3.85 Time building geometry restraints manager: 5.12 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: 100.42 - 107.14: 516 107.14 - 113.87: 6610 113.87 - 120.59: 4544 120.59 - 127.32: 3948 127.32 - 134.04: 192 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 2.440 nonbonded pdb=" OE1 GLU C 74 " pdb=" OG SER C 112 " model vdw 2.144 2.440 nonbonded pdb=" OE1 GLU A 369 " pdb=" NH2 ARG B 527 " model vdw 2.168 2.520 nonbonded pdb=" OG1 THR B 62 " pdb=" OD2 ASP B 312 " model vdw 2.220 2.440 ... (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 ========== 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: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 37.030 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.260 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 2 poor density : 127 time to evaluate : 1.328 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: 0.3318 time to fit residues: 56.6379 Evaluate side-chains 72 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 70 time to evaluate : 1.383 ------------------------------------------------------------------------------- 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: 0.7980 chunk 103 optimal weight: 8.9990 chunk 57 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 69 optimal weight: 0.1980 chunk 55 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 chunk 41 optimal weight: 0.3980 chunk 64 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 123 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 582 HIS C 131 GLN C 242 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11617 Z= 0.180 Angle : 0.510 6.336 15810 Z= 0.260 Chirality : 0.038 0.175 1774 Planarity : 0.004 0.055 1953 Dihedral : 9.735 73.390 1771 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.35 % Favored : 96.50 % Rotamer: Outliers : 1.90 % Allowed : 13.94 % 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: 1.05 (0.24), residues: 1345 helix: 2.28 (0.22), residues: 613 sheet: -0.56 (0.44), residues: 127 loop : -0.71 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 253 HIS 0.003 0.000 HIS B 291 PHE 0.026 0.001 PHE C 41 TYR 0.018 0.001 TYR B 533 ARG 0.008 0.000 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 100 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 77 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 8 residues processed: 95 average time/residue: 0.2335 time to fit residues: 32.7151 Evaluate side-chains 76 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 68 time to evaluate : 1.262 ------------------------------------------------------------------------------- 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 491 VAL Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 695 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 102 optimal weight: 0.1980 chunk 84 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 123 optimal weight: 0.9990 chunk 133 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 453 ASN C 214 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11617 Z= 0.235 Angle : 0.507 6.186 15810 Z= 0.258 Chirality : 0.039 0.193 1774 Planarity : 0.003 0.037 1953 Dihedral : 9.636 73.307 1769 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.32 % Favored : 95.53 % Rotamer: Outliers : 2.81 % Allowed : 13.37 % Favored : 83.83 % 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 (0.24), residues: 1345 helix: 2.17 (0.21), residues: 613 sheet: -0.58 (0.44), residues: 125 loop : -0.74 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 253 HIS 0.004 0.000 HIS B 291 PHE 0.028 0.001 PHE C 41 TYR 0.021 0.001 TYR B 533 ARG 0.004 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 102 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 68 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 69 MET cc_start: 0.7413 (ptm) cc_final: 0.7091 (ptt) REVERT: C 101 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.8217 (tt) outliers start: 34 outliers final: 18 residues processed: 93 average time/residue: 0.2189 time to fit residues: 30.9133 Evaluate side-chains 86 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 67 time to evaluate : 1.369 ------------------------------------------------------------------------------- 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 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 407 SER Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 695 SER Chi-restraints excluded: chain C residue 73 LYS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 83 optimal weight: 0.0970 chunk 124 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 109 optimal weight: 10.0000 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1992 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= 0.227 Angle : 0.502 6.655 15810 Z= 0.253 Chirality : 0.038 0.158 1774 Planarity : 0.003 0.039 1953 Dihedral : 9.601 73.226 1768 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.84 % Favored : 95.01 % Rotamer: Outliers : 2.64 % Allowed : 14.27 % Favored : 83.09 % 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: 0.97 (0.23), residues: 1345 helix: 2.15 (0.21), residues: 613 sheet: -0.36 (0.44), residues: 121 loop : -0.71 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 336 HIS 0.004 0.001 HIS B 475 PHE 0.028 0.001 PHE C 41 TYR 0.021 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 101 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 69 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 69 MET cc_start: 0.7390 (ptm) cc_final: 0.7103 (ptt) REVERT: C 101 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.8225 (tt) outliers start: 32 outliers final: 18 residues processed: 93 average time/residue: 0.2130 time to fit residues: 30.6988 Evaluate side-chains 86 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 67 time to evaluate : 1.338 ------------------------------------------------------------------------------- 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 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 395 MET Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 495 THR Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 695 SER 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: 0.6980 chunk 1 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 chunk 90 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 453 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11617 Z= 0.163 Angle : 0.482 8.260 15810 Z= 0.241 Chirality : 0.038 0.282 1774 Planarity : 0.003 0.042 1953 Dihedral : 9.576 73.219 1768 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.40 % Favored : 95.53 % Rotamer: Outliers : 2.31 % Allowed : 15.43 % Favored : 82.26 % 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: 1.07 (0.23), residues: 1345 helix: 2.21 (0.21), residues: 614 sheet: -0.24 (0.44), residues: 121 loop : -0.66 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 336 HIS 0.004 0.000 HIS B 291 PHE 0.029 0.001 PHE C 41 TYR 0.018 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 fitting. rotamer outliers: 28 poor density : 70 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 MET cc_start: 0.8502 (tpp) cc_final: 0.8291 (ttm) REVERT: C 69 MET cc_start: 0.7315 (ptm) cc_final: 0.7074 (ptt) REVERT: C 101 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.8048 (tt) outliers start: 28 outliers final: 20 residues processed: 89 average time/residue: 0.2141 time to fit residues: 29.7713 Evaluate side-chains 91 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 70 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 THR 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 294 ILE Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain B residue 2 ASN Chi-restraints excluded: chain B residue 22 TYR 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 399 THR Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 695 SER Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 146 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 32 optimal weight: 0.7980 chunk 131 optimal weight: 5.9990 chunk 109 optimal weight: 8.9990 chunk 60 optimal weight: 6.9990 chunk 10 optimal weight: 0.4980 chunk 43 optimal weight: 3.9990 chunk 69 optimal weight: 0.4980 chunk 126 optimal weight: 5.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 453 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2210 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= 0.197 Angle : 0.501 9.180 15810 Z= 0.249 Chirality : 0.038 0.141 1774 Planarity : 0.003 0.041 1953 Dihedral : 9.576 73.210 1768 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.47 % Favored : 95.45 % Rotamer: Outliers : 2.31 % Allowed : 16.09 % Favored : 81.60 % 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: 1.05 (0.23), residues: 1345 helix: 2.17 (0.21), residues: 620 sheet: -0.19 (0.44), residues: 121 loop : -0.68 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 336 HIS 0.005 0.000 HIS B 291 PHE 0.027 0.001 PHE C 41 TYR 0.019 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 101 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 73 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 MET cc_start: 0.8494 (tpp) cc_final: 0.8279 (ttm) REVERT: B 636 ARG cc_start: 0.7359 (tpt170) cc_final: 0.7119 (tpt170) REVERT: C 69 MET cc_start: 0.7349 (ptm) cc_final: 0.7145 (ptt) outliers start: 28 outliers final: 22 residues processed: 91 average time/residue: 0.2116 time to fit residues: 29.4513 Evaluate side-chains 92 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 70 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 THR 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 483 PHE Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain B residue 2 ASN 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 683 SER Chi-restraints excluded: chain B residue 695 SER 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: 0.8980 chunk 96 optimal weight: 6.9990 chunk 110 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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: 0.8452 moved from start: 0.2308 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= 0.244 Angle : 0.520 8.892 15810 Z= 0.261 Chirality : 0.039 0.143 1774 Planarity : 0.003 0.040 1953 Dihedral : 9.622 73.140 1768 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.99 % Favored : 94.93 % Rotamer: Outliers : 2.23 % Allowed : 17.00 % Favored : 80.78 % 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: 0.98 (0.23), residues: 1345 helix: 2.10 (0.21), residues: 620 sheet: -0.16 (0.44), residues: 121 loop : -0.72 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 336 HIS 0.004 0.001 HIS B 291 PHE 0.029 0.002 PHE C 41 TYR 0.021 0.001 TYR B 533 ARG 0.002 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 99 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 72 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 MET cc_start: 0.8493 (tpp) cc_final: 0.8288 (ttm) REVERT: C 69 MET cc_start: 0.7352 (ptm) cc_final: 0.7135 (ptt) REVERT: C 101 ILE cc_start: 0.8466 (OUTLIER) cc_final: 0.8240 (tt) outliers start: 27 outliers final: 23 residues processed: 90 average time/residue: 0.2249 time to fit residues: 30.4624 Evaluate side-chains 94 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 70 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 THR 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 2 ASN 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 683 SER Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain B residue 695 SER 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: 2.9990 chunk 83 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 chunk 64 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 119 optimal weight: 0.4980 chunk 125 optimal weight: 0.0170 chunk 114 optimal weight: 3.9990 overall best weight: 1.5024 ------------------------------------------------------------------------------- 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: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11617 Z= 0.216 Angle : 0.520 10.116 15810 Z= 0.258 Chirality : 0.038 0.147 1774 Planarity : 0.003 0.041 1953 Dihedral : 9.623 73.107 1768 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.69 % Favored : 95.23 % Rotamer: Outliers : 2.39 % Allowed : 16.50 % Favored : 81.11 % 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: 0.99 (0.23), residues: 1345 helix: 2.05 (0.21), residues: 626 sheet: -0.14 (0.44), residues: 121 loop : -0.69 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 336 HIS 0.004 0.001 HIS B 291 PHE 0.028 0.001 PHE C 41 TYR 0.020 0.001 TYR B 533 ARG 0.002 0.000 ARG C 43 *********************** 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 99 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 70 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 101 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.8240 (tt) outliers start: 29 outliers final: 25 residues processed: 90 average time/residue: 0.2069 time to fit residues: 28.7827 Evaluate side-chains 95 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 69 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 194 THR 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 574 MET Chi-restraints excluded: chain B residue 2 ASN 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 495 THR Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 695 SER Chi-restraints excluded: chain C residue 73 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 110 optimal weight: 8.9990 chunk 115 optimal weight: 10.0000 chunk 121 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 129 optimal weight: 0.0370 overall best weight: 1.8066 ------------------------------------------------------------------------------- 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: 0.8463 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11617 Z= 0.248 Angle : 0.529 10.010 15810 Z= 0.264 Chirality : 0.039 0.145 1774 Planarity : 0.003 0.040 1953 Dihedral : 9.647 73.064 1768 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.07 % Favored : 94.86 % Rotamer: Outliers : 2.31 % Allowed : 16.67 % Favored : 81.02 % 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: 0.98 (0.23), residues: 1345 helix: 2.04 (0.21), residues: 626 sheet: -0.12 (0.44), residues: 121 loop : -0.70 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 336 HIS 0.004 0.001 HIS B 291 PHE 0.029 0.001 PHE C 41 TYR 0.021 0.001 TYR B 533 ARG 0.003 0.000 ARG C 198 *********************** 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 96 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 68 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 101 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8233 (tt) outliers start: 28 outliers final: 25 residues processed: 88 average time/residue: 0.1933 time to fit residues: 26.9660 Evaluate side-chains 94 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 68 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 194 THR 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 574 MET Chi-restraints excluded: chain B residue 2 ASN 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 495 THR Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 695 SER Chi-restraints excluded: chain C residue 73 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 135 optimal weight: 10.0000 chunk 124 optimal weight: 0.0570 chunk 107 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 overall best weight: 1.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 453 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11617 Z= 0.210 Angle : 0.534 10.360 15810 Z= 0.263 Chirality : 0.039 0.361 1774 Planarity : 0.003 0.041 1953 Dihedral : 9.644 73.056 1768 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.77 % Favored : 95.16 % Rotamer: Outliers : 2.39 % Allowed : 16.58 % Favored : 81.02 % 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: 0.99 (0.23), residues: 1345 helix: 2.06 (0.21), residues: 626 sheet: -0.10 (0.44), residues: 121 loop : -0.70 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 336 HIS 0.004 0.001 HIS B 291 PHE 0.028 0.001 PHE C 41 TYR 0.020 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 97 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 68 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 MET cc_start: 0.8455 (tpp) cc_final: 0.8195 (ttm) REVERT: C 101 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8207 (tt) outliers start: 29 outliers final: 25 residues processed: 88 average time/residue: 0.2117 time to fit residues: 29.2189 Evaluate side-chains 94 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 68 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 194 THR 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 574 MET Chi-restraints excluded: chain B residue 2 ASN Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 211 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 495 THR Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 695 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 2.9990 chunk 99 optimal weight: 8.9990 chunk 15 optimal weight: 0.3980 chunk 29 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 453 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.051082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.038674 restraints weight = 81445.405| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 4.29 r_work: 0.2567 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2574 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2574 r_free = 0.2574 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 = 0.2574 r_free = 0.2574 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2574 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11617 Z= 0.215 Angle : 0.523 10.402 15810 Z= 0.259 Chirality : 0.039 0.287 1774 Planarity : 0.003 0.041 1953 Dihedral : 9.659 73.051 1768 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.14 % Favored : 94.78 % Rotamer: Outliers : 2.23 % Allowed : 16.75 % Favored : 81.02 % 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: 0.97 (0.23), residues: 1345 helix: 2.05 (0.21), residues: 626 sheet: -0.14 (0.44), residues: 121 loop : -0.73 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 336 HIS 0.004 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 A 536 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2234.57 seconds wall clock time: 41 minutes 18.06 seconds (2478.06 seconds total)