Starting phenix.real_space_refine on Wed Feb 14 10:12:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ca1_16515/02_2024/8ca1_16515_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ca1_16515/02_2024/8ca1_16515.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ca1_16515/02_2024/8ca1_16515.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ca1_16515/02_2024/8ca1_16515.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ca1_16515/02_2024/8ca1_16515_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ca1_16515/02_2024/8ca1_16515_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.254 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 50 5.16 5 C 5708 2.51 5 N 1566 2.21 5 O 1708 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9036 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 4465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4465 Classifications: {'peptide': 589} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 570} Chain: "A" Number of atoms: 4465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4465 Classifications: {'peptide': 589} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 570} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.86, per 1000 atoms: 0.54 Number of scatterers: 9036 At special positions: 0 Unit cell: (85.176, 112.216, 86.528, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 50 16.00 P 4 15.00 O 1708 8.00 N 1566 7.00 C 5708 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: 4.10 Conformation dependent library (CDL) restraints added in 1.9 seconds 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2112 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 6 sheets defined 61.5% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.22 Creating SS restraints... Processing helix chain 'B' and resid 74 through 79 Processing helix chain 'B' and resid 85 through 87 No H-bonds generated for 'chain 'B' and resid 85 through 87' Processing helix chain 'B' and resid 97 through 116 removed outlier: 4.036A pdb=" N GLY B 108 " --> pdb=" O LYS B 104 " (cutoff:3.500A) Proline residue: B 109 - end of helix Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 131 through 139 removed outlier: 3.878A pdb=" N GLY B 136 " --> pdb=" O ASP B 132 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU B 137 " --> pdb=" O THR B 133 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS B 138 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU B 139 " --> pdb=" O GLN B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 144 No H-bonds generated for 'chain 'B' and resid 142 through 144' Processing helix chain 'B' and resid 149 through 151 No H-bonds generated for 'chain 'B' and resid 149 through 151' Processing helix chain 'B' and resid 158 through 170 Processing helix chain 'B' and resid 173 through 184 Processing helix chain 'B' and resid 188 through 192 Processing helix chain 'B' and resid 196 through 208 Proline residue: B 204 - end of helix removed outlier: 3.766A pdb=" N SER B 208 " --> pdb=" O PRO B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 228 No H-bonds generated for 'chain 'B' and resid 226 through 228' Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 320 through 322 No H-bonds generated for 'chain 'B' and resid 320 through 322' Processing helix chain 'B' and resid 330 through 366 removed outlier: 4.677A pdb=" N PHE B 343 " --> pdb=" O ASN B 339 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N GLY B 344 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N MET B 345 " --> pdb=" O GLY B 341 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA B 346 " --> pdb=" O ARG B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 376 No H-bonds generated for 'chain 'B' and resid 374 through 376' Processing helix chain 'B' and resid 378 through 407 removed outlier: 3.754A pdb=" N MET B 400 " --> pdb=" O SER B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 443 removed outlier: 3.681A pdb=" N TRP B 428 " --> pdb=" O SER B 424 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLY B 440 " --> pdb=" O GLN B 436 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N MET B 441 " --> pdb=" O ILE B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 456 Processing helix chain 'B' and resid 466 through 494 removed outlier: 4.856A pdb=" N ASP B 480 " --> pdb=" O GLN B 476 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LYS B 481 " --> pdb=" O GLY B 477 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY B 482 " --> pdb=" O CYS B 478 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS B 493 " --> pdb=" O GLY B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 514 removed outlier: 4.610A pdb=" N ARG B 513 " --> pdb=" O LEU B 510 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THR B 514 " --> pdb=" O ARG B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 561 removed outlier: 4.411A pdb=" N ARG B 532 " --> pdb=" O PRO B 528 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N SER B 533 " --> pdb=" O GLU B 529 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA B 537 " --> pdb=" O SER B 533 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL B 538 " --> pdb=" O GLY B 534 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LYS B 557 " --> pdb=" O VAL B 553 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N GLY B 558 " --> pdb=" O LYS B 554 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N VAL B 560 " --> pdb=" O LYS B 556 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ASN B 561 " --> pdb=" O LYS B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 592 removed outlier: 3.505A pdb=" N ARG B 568 " --> pdb=" O PHE B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 623 Processing helix chain 'B' and resid 626 through 645 Processing helix chain 'A' and resid 74 through 79 Processing helix chain 'A' and resid 85 through 87 No H-bonds generated for 'chain 'A' and resid 85 through 87' Processing helix chain 'A' and resid 97 through 116 removed outlier: 4.027A pdb=" N GLY A 108 " --> pdb=" O LYS A 104 " (cutoff:3.500A) Proline residue: A 109 - end of helix Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 131 through 139 removed outlier: 3.880A pdb=" N GLY A 136 " --> pdb=" O ASP A 132 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 137 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU A 139 " --> pdb=" O GLN A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 144 No H-bonds generated for 'chain 'A' and resid 142 through 144' Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 158 through 170 Processing helix chain 'A' and resid 173 through 184 Processing helix chain 'A' and resid 188 through 192 Processing helix chain 'A' and resid 196 through 208 Proline residue: A 204 - end of helix removed outlier: 3.766A pdb=" N SER A 208 " --> pdb=" O PRO A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 228 No H-bonds generated for 'chain 'A' and resid 226 through 228' Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 320 through 322 No H-bonds generated for 'chain 'A' and resid 320 through 322' Processing helix chain 'A' and resid 330 through 366 removed outlier: 4.677A pdb=" N PHE A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLY A 344 " --> pdb=" O ASN A 340 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N MET A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 346 " --> pdb=" O ARG A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 376 No H-bonds generated for 'chain 'A' and resid 374 through 376' Processing helix chain 'A' and resid 378 through 407 removed outlier: 3.739A pdb=" N MET A 400 " --> pdb=" O SER A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 443 removed outlier: 3.685A pdb=" N TRP A 428 " --> pdb=" O SER A 424 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N GLY A 440 " --> pdb=" O GLN A 436 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N MET A 441 " --> pdb=" O ILE A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 458 removed outlier: 4.359A pdb=" N ILE A 458 " --> pdb=" O ARG A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 494 removed outlier: 4.881A pdb=" N ASP A 480 " --> pdb=" O GLN A 476 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LYS A 481 " --> pdb=" O GLY A 477 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY A 482 " --> pdb=" O CYS A 478 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS A 493 " --> pdb=" O GLY A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 514 removed outlier: 4.611A pdb=" N ARG A 513 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THR A 514 " --> pdb=" O ARG A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 561 removed outlier: 4.414A pdb=" N ARG A 532 " --> pdb=" O PRO A 528 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N SER A 533 " --> pdb=" O GLU A 529 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 536 " --> pdb=" O ARG A 532 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA A 537 " --> pdb=" O SER A 533 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL A 538 " --> pdb=" O GLY A 534 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LYS A 557 " --> pdb=" O VAL A 553 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N GLY A 558 " --> pdb=" O LYS A 554 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N VAL A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N ASN A 561 " --> pdb=" O LYS A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 592 removed outlier: 3.506A pdb=" N ARG A 568 " --> pdb=" O PHE A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 623 Processing helix chain 'A' and resid 626 through 645 Processing sheet with id= A, first strand: chain 'B' and resid 213 through 216 removed outlier: 7.068A pdb=" N ILE B 259 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N CYS B 216 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N THR B 261 " --> pdb=" O CYS B 216 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 232 through 235 Processing sheet with id= C, first strand: chain 'B' and resid 246 through 248 removed outlier: 3.939A pdb=" N GLY B 246 " --> pdb=" O PHE B 313 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 213 through 216 removed outlier: 7.067A pdb=" N ILE A 259 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N CYS A 216 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N THR A 261 " --> pdb=" O CYS A 216 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 232 through 235 Processing sheet with id= F, first strand: chain 'A' and resid 246 through 248 removed outlier: 3.944A pdb=" N GLY A 246 " --> pdb=" O PHE A 313 " (cutoff:3.500A) 512 hydrogen bonds defined for protein. 1494 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.81 Time building geometry restraints manager: 4.32 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: 3002 1.34 - 1.46: 1931 1.46 - 1.58: 4172 1.58 - 1.70: 1 1.70 - 1.82: 86 Bond restraints: 9192 Sorted by residual: bond pdb=" O5B FAD B 701 " pdb=" PA FAD B 701 " ideal model delta sigma weight residual 1.634 1.528 0.106 2.00e-02 2.50e+03 2.79e+01 bond pdb=" O3P FAD B 701 " pdb=" P FAD B 701 " ideal model delta sigma weight residual 1.660 1.557 0.103 2.00e-02 2.50e+03 2.63e+01 bond pdb=" O3P FAD A 701 " pdb=" P FAD A 701 " ideal model delta sigma weight residual 1.660 1.566 0.094 2.00e-02 2.50e+03 2.23e+01 bond pdb=" O5B FAD A 701 " pdb=" PA FAD A 701 " ideal model delta sigma weight residual 1.634 1.541 0.093 2.00e-02 2.50e+03 2.18e+01 bond pdb=" O5' FAD B 701 " pdb=" P FAD B 701 " ideal model delta sigma weight residual 1.637 1.570 0.067 2.00e-02 2.50e+03 1.12e+01 ... (remaining 9187 not shown) Histogram of bond angle deviations from ideal: 98.35 - 105.49: 187 105.49 - 112.62: 4701 112.62 - 119.75: 3399 119.75 - 126.88: 4034 126.88 - 134.01: 79 Bond angle restraints: 12400 Sorted by residual: angle pdb=" CB MET B 301 " pdb=" CG MET B 301 " pdb=" SD MET B 301 " ideal model delta sigma weight residual 112.70 126.47 -13.77 3.00e+00 1.11e-01 2.11e+01 angle pdb=" N GLU B 450 " pdb=" CA GLU B 450 " pdb=" CB GLU B 450 " ideal model delta sigma weight residual 110.12 104.63 5.49 1.47e+00 4.63e-01 1.39e+01 angle pdb=" N GLU A 450 " pdb=" CA GLU A 450 " pdb=" CB GLU A 450 " ideal model delta sigma weight residual 110.12 104.94 5.18 1.47e+00 4.63e-01 1.24e+01 angle pdb=" C MET A 301 " pdb=" CA MET A 301 " pdb=" CB MET A 301 " ideal model delta sigma weight residual 110.32 103.14 7.18 2.11e+00 2.25e-01 1.16e+01 angle pdb=" CA GLU A 450 " pdb=" CB GLU A 450 " pdb=" CG GLU A 450 " ideal model delta sigma weight residual 114.10 120.60 -6.50 2.00e+00 2.50e-01 1.06e+01 ... (remaining 12395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.11: 5199 22.11 - 44.21: 310 44.21 - 66.32: 38 66.32 - 88.43: 15 88.43 - 110.53: 4 Dihedral angle restraints: 5566 sinusoidal: 2256 harmonic: 3310 Sorted by residual: dihedral pdb=" CA LYS B 493 " pdb=" C LYS B 493 " pdb=" N ASN B 494 " pdb=" CA ASN B 494 " ideal model delta harmonic sigma weight residual 180.00 152.20 27.80 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA LYS A 493 " pdb=" C LYS A 493 " pdb=" N ASN A 494 " pdb=" CA ASN A 494 " ideal model delta harmonic sigma weight residual 180.00 152.22 27.78 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA THR B 368 " pdb=" C THR B 368 " pdb=" N GLN B 369 " pdb=" CA GLN B 369 " ideal model delta harmonic sigma weight residual 180.00 153.15 26.85 0 5.00e+00 4.00e-02 2.88e+01 ... (remaining 5563 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1060 0.052 - 0.104: 262 0.104 - 0.156: 48 0.156 - 0.208: 14 0.208 - 0.259: 4 Chirality restraints: 1388 Sorted by residual: chirality pdb=" CA PHE B 496 " pdb=" N PHE B 496 " pdb=" C PHE B 496 " pdb=" CB PHE B 496 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA PHE A 496 " pdb=" N PHE A 496 " pdb=" C PHE A 496 " pdb=" CB PHE A 496 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA ILE A 303 " pdb=" N ILE A 303 " pdb=" C ILE A 303 " pdb=" CB ILE A 303 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 1385 not shown) Planarity restraints: 1596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 549 " -0.020 2.00e-02 2.50e+03 3.99e-02 1.59e+01 pdb=" C GLU B 549 " 0.069 2.00e-02 2.50e+03 pdb=" O GLU B 549 " -0.026 2.00e-02 2.50e+03 pdb=" N ALA B 550 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 549 " -0.020 2.00e-02 2.50e+03 3.98e-02 1.59e+01 pdb=" C GLU A 549 " 0.069 2.00e-02 2.50e+03 pdb=" O GLU A 549 " -0.026 2.00e-02 2.50e+03 pdb=" N ALA A 550 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 548 " 0.015 2.00e-02 2.50e+03 3.05e-02 9.30e+00 pdb=" C VAL B 548 " -0.053 2.00e-02 2.50e+03 pdb=" O VAL B 548 " 0.020 2.00e-02 2.50e+03 pdb=" N GLU B 549 " 0.018 2.00e-02 2.50e+03 ... (remaining 1593 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 144 2.61 - 3.18: 9482 3.18 - 3.76: 14261 3.76 - 4.33: 20304 4.33 - 4.90: 31771 Nonbonded interactions: 75962 Sorted by model distance: nonbonded pdb=" OG SER B 222 " pdb=" OE1 GLN A 369 " model vdw 2.041 2.440 nonbonded pdb=" OD2 ASP A 467 " pdb=" O2B FAD A 701 " model vdw 2.061 2.440 nonbonded pdb=" OH TYR A 202 " pdb=" OD1 ASN A 322 " model vdw 2.126 2.440 nonbonded pdb=" OH TYR B 202 " pdb=" OD1 ASN B 322 " model vdw 2.133 2.440 nonbonded pdb=" NZ LYS A 420 " pdb=" OD1 ASN A 466 " model vdw 2.154 2.520 ... (remaining 75957 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.500 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: 19.990 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 29.310 Find NCS groups from input model: 0.490 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 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 : 0.006 0.110 9192 Z= 0.394 Angle : 0.892 13.771 12400 Z= 0.505 Chirality : 0.050 0.259 1388 Planarity : 0.011 0.088 1596 Dihedral : 14.977 110.531 3454 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.45 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.92 (0.23), residues: 1174 helix: -1.38 (0.17), residues: 668 sheet: -1.29 (0.54), residues: 72 loop : -0.76 (0.32), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.005 TRP A 250 HIS 0.014 0.003 HIS A 182 PHE 0.046 0.004 PHE A 496 TYR 0.016 0.005 TYR A 577 ARG 0.024 0.004 ARG B 163 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 LEU cc_start: 0.9019 (mm) cc_final: 0.8812 (mt) REVERT: A 382 GLU cc_start: 0.8364 (pp20) cc_final: 0.8022 (pp20) REVERT: A 410 LYS cc_start: 0.7663 (mmtt) cc_final: 0.7324 (tptt) REVERT: A 438 MET cc_start: 0.8767 (mmm) cc_final: 0.8060 (mmm) REVERT: A 479 MET cc_start: 0.8531 (mmp) cc_final: 0.8112 (mmt) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.2028 time to fit residues: 27.9701 Evaluate side-chains 68 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 59 optimal weight: 0.0670 chunk 46 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 105 optimal weight: 0.9990 overall best weight: 1.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 GLN B 336 ASN B 369 GLN B 599 HIS A 87 GLN A 599 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9192 Z= 0.185 Angle : 0.613 7.753 12400 Z= 0.319 Chirality : 0.041 0.151 1388 Planarity : 0.004 0.035 1596 Dihedral : 8.674 75.907 1346 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.62 % Favored : 98.21 % Rotamer: Outliers : 1.38 % Allowed : 5.63 % Favored : 92.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.10 (0.24), residues: 1174 helix: 1.26 (0.19), residues: 672 sheet: -0.21 (0.56), residues: 64 loop : 0.21 (0.33), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 250 HIS 0.005 0.001 HIS A 599 PHE 0.012 0.001 PHE A 187 TYR 0.008 0.001 TYR A 202 ARG 0.004 0.001 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 99 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 382 GLU cc_start: 0.8570 (pt0) cc_final: 0.7915 (pp20) REVERT: B 438 MET cc_start: 0.8893 (mmm) cc_final: 0.8296 (mmm) REVERT: B 503 MET cc_start: 0.5084 (mmt) cc_final: 0.2716 (tmm) REVERT: A 382 GLU cc_start: 0.8446 (pp20) cc_final: 0.8179 (pt0) REVERT: A 438 MET cc_start: 0.8975 (mmm) cc_final: 0.8073 (mmm) REVERT: A 479 MET cc_start: 0.8398 (mmp) cc_final: 0.8005 (mmt) outliers start: 13 outliers final: 5 residues processed: 102 average time/residue: 0.1868 time to fit residues: 28.1264 Evaluate side-chains 74 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 69 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 488 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 20.0000 chunk 32 optimal weight: 0.9990 chunk 87 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 chunk 93 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 369 GLN B 618 ASN ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 GLN ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9192 Z= 0.295 Angle : 0.664 14.293 12400 Z= 0.334 Chirality : 0.041 0.157 1388 Planarity : 0.004 0.034 1596 Dihedral : 8.500 70.548 1346 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.73 % Favored : 97.10 % Rotamer: Outliers : 1.91 % Allowed : 8.60 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.25), residues: 1174 helix: 1.69 (0.19), residues: 660 sheet: 0.16 (0.53), residues: 64 loop : 0.01 (0.32), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 250 HIS 0.012 0.002 HIS B 182 PHE 0.015 0.002 PHE A 422 TYR 0.013 0.002 TYR A 161 ARG 0.003 0.000 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 84 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 382 GLU cc_start: 0.8676 (pt0) cc_final: 0.8015 (pp20) REVERT: B 400 MET cc_start: 0.8939 (ttt) cc_final: 0.8661 (ttt) REVERT: B 503 MET cc_start: 0.5202 (mmt) cc_final: 0.3083 (tmm) REVERT: A 382 GLU cc_start: 0.8590 (pp20) cc_final: 0.8382 (pp20) REVERT: A 441 MET cc_start: 0.8694 (ttm) cc_final: 0.8458 (ttp) REVERT: A 479 MET cc_start: 0.8402 (mmp) cc_final: 0.7983 (mmt) outliers start: 18 outliers final: 11 residues processed: 91 average time/residue: 0.1924 time to fit residues: 26.0409 Evaluate side-chains 79 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 68 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 488 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 11 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 100 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 GLN B 375 HIS A 369 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9192 Z= 0.304 Angle : 0.637 12.734 12400 Z= 0.322 Chirality : 0.041 0.143 1388 Planarity : 0.004 0.032 1596 Dihedral : 8.628 71.576 1346 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.56 % Favored : 97.27 % Rotamer: Outliers : 2.34 % Allowed : 10.62 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.42 (0.25), residues: 1174 helix: 1.67 (0.20), residues: 672 sheet: 0.23 (0.53), residues: 64 loop : -0.00 (0.33), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 250 HIS 0.012 0.002 HIS B 182 PHE 0.015 0.002 PHE A 422 TYR 0.013 0.002 TYR B 161 ARG 0.003 0.000 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 82 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 382 GLU cc_start: 0.8736 (pt0) cc_final: 0.7975 (pp20) REVERT: B 400 MET cc_start: 0.9018 (ttt) cc_final: 0.8811 (ttt) REVERT: B 503 MET cc_start: 0.5451 (mmt) cc_final: 0.3588 (tmm) REVERT: B 628 HIS cc_start: 0.8740 (m90) cc_final: 0.7967 (m-70) REVERT: A 425 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7821 (mm-30) REVERT: A 438 MET cc_start: 0.9009 (mmm) cc_final: 0.8296 (mmm) REVERT: A 441 MET cc_start: 0.8664 (ttm) cc_final: 0.8356 (ttm) REVERT: A 479 MET cc_start: 0.8429 (mmp) cc_final: 0.8039 (mmt) REVERT: A 628 HIS cc_start: 0.8754 (m90) cc_final: 0.8043 (m-70) outliers start: 22 outliers final: 14 residues processed: 90 average time/residue: 0.1938 time to fit residues: 25.8579 Evaluate side-chains 88 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 74 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 488 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 1.9990 chunk 63 optimal weight: 0.0030 chunk 1 optimal weight: 0.6980 chunk 83 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 overall best weight: 1.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9192 Z= 0.179 Angle : 0.549 11.820 12400 Z= 0.275 Chirality : 0.039 0.143 1388 Planarity : 0.003 0.033 1596 Dihedral : 8.110 69.247 1346 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.55 % Allowed : 11.04 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.87 (0.25), residues: 1174 helix: 2.08 (0.20), residues: 660 sheet: 0.33 (0.55), residues: 64 loop : 0.20 (0.33), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 607 HIS 0.008 0.001 HIS B 182 PHE 0.012 0.001 PHE A 422 TYR 0.008 0.001 TYR B 399 ARG 0.002 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 89 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 382 GLU cc_start: 0.8703 (pt0) cc_final: 0.7910 (pp20) REVERT: B 438 MET cc_start: 0.8767 (mtm) cc_final: 0.8469 (ttp) REVERT: B 503 MET cc_start: 0.5320 (mmt) cc_final: 0.4017 (tmm) REVERT: B 628 HIS cc_start: 0.8634 (m90) cc_final: 0.8054 (m-70) REVERT: A 382 GLU cc_start: 0.8548 (pp20) cc_final: 0.8240 (pt0) REVERT: A 425 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7919 (mm-30) REVERT: A 438 MET cc_start: 0.8958 (mmm) cc_final: 0.8304 (mmm) REVERT: A 441 MET cc_start: 0.8630 (ttm) cc_final: 0.8325 (ttm) REVERT: A 479 MET cc_start: 0.8360 (mmp) cc_final: 0.7979 (mmt) outliers start: 24 outliers final: 12 residues processed: 101 average time/residue: 0.1829 time to fit residues: 28.0702 Evaluate side-chains 88 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 76 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 503 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 7.9990 chunk 100 optimal weight: 20.0000 chunk 22 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 58 optimal weight: 20.0000 chunk 108 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 9192 Z= 0.363 Angle : 0.673 10.870 12400 Z= 0.339 Chirality : 0.042 0.240 1388 Planarity : 0.004 0.031 1596 Dihedral : 7.962 70.339 1346 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.98 % Favored : 96.93 % Rotamer: Outliers : 2.65 % Allowed : 12.63 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.38 (0.25), residues: 1174 helix: 1.70 (0.19), residues: 672 sheet: 0.26 (0.57), residues: 64 loop : -0.13 (0.32), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 607 HIS 0.012 0.002 HIS B 182 PHE 0.015 0.002 PHE A 422 TYR 0.015 0.002 TYR B 161 ARG 0.004 0.001 ARG B 636 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 78 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 301 MET cc_start: 0.8291 (mmm) cc_final: 0.7920 (mmm) REVERT: B 438 MET cc_start: 0.8888 (mtm) cc_final: 0.8618 (ttp) REVERT: B 503 MET cc_start: 0.5460 (mmt) cc_final: 0.3642 (tmm) REVERT: B 628 HIS cc_start: 0.8745 (m90) cc_final: 0.8209 (m-70) REVERT: A 438 MET cc_start: 0.9040 (mmm) cc_final: 0.8263 (mmm) REVERT: A 441 MET cc_start: 0.8695 (ttm) cc_final: 0.8392 (ttm) REVERT: A 479 MET cc_start: 0.8485 (mmp) cc_final: 0.8177 (mmt) REVERT: A 628 HIS cc_start: 0.8704 (m90) cc_final: 0.8111 (m-70) outliers start: 25 outliers final: 19 residues processed: 91 average time/residue: 0.1824 time to fit residues: 25.2042 Evaluate side-chains 94 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 75 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 559 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 44 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 498 ASN A 87 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9192 Z= 0.149 Angle : 0.539 10.883 12400 Z= 0.268 Chirality : 0.039 0.256 1388 Planarity : 0.003 0.036 1596 Dihedral : 7.143 67.340 1346 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.34 % Allowed : 14.33 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 2.00 (0.25), residues: 1174 helix: 2.26 (0.19), residues: 658 sheet: 0.25 (0.56), residues: 60 loop : 0.14 (0.33), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 607 HIS 0.005 0.001 HIS B 182 PHE 0.011 0.001 PHE A 422 TYR 0.007 0.001 TYR B 399 ARG 0.004 0.000 ARG A 451 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 93 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 438 MET cc_start: 0.8751 (mtm) cc_final: 0.8447 (ttp) REVERT: B 503 MET cc_start: 0.5224 (mmt) cc_final: 0.4085 (tmm) REVERT: A 301 MET cc_start: 0.8490 (mmm) cc_final: 0.8198 (mmm) REVERT: A 382 GLU cc_start: 0.8597 (pp20) cc_final: 0.8207 (pt0) REVERT: A 438 MET cc_start: 0.8893 (mmm) cc_final: 0.8229 (mmm) REVERT: A 441 MET cc_start: 0.8482 (ttm) cc_final: 0.8185 (ttm) REVERT: A 479 MET cc_start: 0.8296 (mmp) cc_final: 0.7940 (mmt) REVERT: A 629 GLN cc_start: 0.9007 (mm-40) cc_final: 0.8790 (mp10) outliers start: 22 outliers final: 17 residues processed: 102 average time/residue: 0.1748 time to fit residues: 27.4357 Evaluate side-chains 96 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 79 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 87 GLN Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 503 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 101 optimal weight: 0.4980 chunk 107 optimal weight: 9.9990 chunk 97 optimal weight: 7.9990 chunk 104 optimal weight: 7.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9192 Z= 0.285 Angle : 0.623 11.644 12400 Z= 0.313 Chirality : 0.042 0.233 1388 Planarity : 0.003 0.033 1596 Dihedral : 7.118 67.391 1346 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.55 % Allowed : 14.97 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.76 (0.25), residues: 1174 helix: 2.09 (0.19), residues: 658 sheet: 0.23 (0.59), residues: 64 loop : -0.02 (0.32), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 607 HIS 0.010 0.002 HIS B 182 PHE 0.014 0.001 PHE A 422 TYR 0.011 0.001 TYR A 161 ARG 0.002 0.000 ARG B 614 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 82 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 382 GLU cc_start: 0.8722 (pt0) cc_final: 0.8167 (pp20) REVERT: B 438 MET cc_start: 0.8858 (mtm) cc_final: 0.8562 (ttp) REVERT: B 503 MET cc_start: 0.5462 (mmt) cc_final: 0.3978 (tmm) REVERT: A 382 GLU cc_start: 0.8626 (pp20) cc_final: 0.8275 (pt0) REVERT: A 438 MET cc_start: 0.8979 (mmm) cc_final: 0.8294 (mmm) REVERT: A 441 MET cc_start: 0.8583 (ttm) cc_final: 0.8373 (ttm) REVERT: A 479 MET cc_start: 0.8385 (mmp) cc_final: 0.8028 (mmt) REVERT: A 629 GLN cc_start: 0.9041 (mm-40) cc_final: 0.8732 (mp10) outliers start: 24 outliers final: 21 residues processed: 94 average time/residue: 0.1711 time to fit residues: 24.8940 Evaluate side-chains 99 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 78 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 503 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 81 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9192 Z= 0.180 Angle : 0.551 11.458 12400 Z= 0.277 Chirality : 0.040 0.219 1388 Planarity : 0.003 0.035 1596 Dihedral : 6.733 65.157 1346 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.44 % Allowed : 15.07 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.98 (0.25), residues: 1174 helix: 2.26 (0.19), residues: 658 sheet: 0.23 (0.63), residues: 56 loop : 0.12 (0.33), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 607 HIS 0.006 0.001 HIS B 182 PHE 0.013 0.001 PHE B 422 TYR 0.007 0.001 TYR A 399 ARG 0.002 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 81 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 438 MET cc_start: 0.8817 (mtm) cc_final: 0.8506 (ttp) REVERT: B 503 MET cc_start: 0.5180 (mmt) cc_final: 0.4150 (tmm) REVERT: A 301 MET cc_start: 0.8530 (mmm) cc_final: 0.8287 (mmm) REVERT: A 382 GLU cc_start: 0.8604 (pp20) cc_final: 0.8267 (pt0) REVERT: A 438 MET cc_start: 0.8893 (mmm) cc_final: 0.8217 (mmm) REVERT: A 479 MET cc_start: 0.8313 (mmp) cc_final: 0.7978 (mmt) REVERT: A 629 GLN cc_start: 0.8998 (mm-40) cc_final: 0.8719 (mp10) outliers start: 23 outliers final: 21 residues processed: 91 average time/residue: 0.1719 time to fit residues: 24.3152 Evaluate side-chains 98 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 77 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 87 GLN Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 503 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 0.2980 chunk 76 optimal weight: 9.9990 chunk 115 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 71 optimal weight: 0.2980 chunk 56 optimal weight: 2.9990 chunk 73 optimal weight: 0.0670 chunk 98 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9192 Z= 0.139 Angle : 0.525 11.331 12400 Z= 0.262 Chirality : 0.039 0.197 1388 Planarity : 0.003 0.038 1596 Dihedral : 6.247 63.305 1346 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.23 % Allowed : 15.29 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 2.28 (0.25), residues: 1174 helix: 2.48 (0.19), residues: 670 sheet: 0.33 (0.62), residues: 56 loop : 0.22 (0.33), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 250 HIS 0.004 0.001 HIS B 182 PHE 0.012 0.001 PHE A 422 TYR 0.006 0.001 TYR B 399 ARG 0.003 0.000 ARG B 532 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 84 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 438 MET cc_start: 0.8728 (mtm) cc_final: 0.8415 (ttp) REVERT: B 503 MET cc_start: 0.4770 (mmt) cc_final: 0.4363 (tmm) REVERT: A 301 MET cc_start: 0.8541 (mmm) cc_final: 0.8284 (mmm) REVERT: A 382 GLU cc_start: 0.8641 (pp20) cc_final: 0.8188 (pt0) REVERT: A 438 MET cc_start: 0.8812 (mmm) cc_final: 0.8202 (mmm) REVERT: A 629 GLN cc_start: 0.9011 (mm-40) cc_final: 0.8699 (mp10) outliers start: 21 outliers final: 13 residues processed: 94 average time/residue: 0.2062 time to fit residues: 28.1794 Evaluate side-chains 91 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 78 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 87 GLN Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 503 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.0000 chunk 80 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 363 HIS ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.077387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.067680 restraints weight = 31470.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.069714 restraints weight = 16689.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.071149 restraints weight = 10420.895| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9192 Z= 0.153 Angle : 0.557 10.994 12400 Z= 0.276 Chirality : 0.039 0.181 1388 Planarity : 0.003 0.038 1596 Dihedral : 6.185 62.556 1346 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.70 % Allowed : 16.03 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 2.30 (0.25), residues: 1174 helix: 2.50 (0.19), residues: 674 sheet: 0.37 (0.62), residues: 56 loop : 0.20 (0.33), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 250 HIS 0.005 0.001 HIS B 182 PHE 0.013 0.001 PHE A 422 TYR 0.006 0.001 TYR B 399 ARG 0.005 0.000 ARG B 532 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1751.24 seconds wall clock time: 33 minutes 18.10 seconds (1998.10 seconds total)