Starting phenix.real_space_refine on Fri Nov 15 05:31:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tu9_41620/11_2024/8tu9_41620.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tu9_41620/11_2024/8tu9_41620.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tu9_41620/11_2024/8tu9_41620.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tu9_41620/11_2024/8tu9_41620.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tu9_41620/11_2024/8tu9_41620.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tu9_41620/11_2024/8tu9_41620.cif" } resolution = 3.26 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= 0.006 sd= 0.047 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 6 5.49 5 S 38 5.16 5 C 5524 2.51 5 N 1348 2.21 5 O 1474 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8390 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4102 Classifications: {'peptide': 533} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 26, 'TRANS': 506} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 6, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 68 Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 93 Unusual residues: {'ACO': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: B Time building chain proxies: 7.69, per 1000 atoms: 0.92 Number of scatterers: 8390 At special positions: 0 Unit cell: (77.35, 121.55, 105.4, 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 38 16.00 P 6 15.00 O 1474 8.00 N 1348 7.00 C 5524 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 76 " - pdb=" SG CYS A 79 " distance=2.03 Simple disulfide: pdb=" SG CYS A 415 " - pdb=" SG CYS A 434 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 702 " - " ASN A 134 " " NAG A 703 " - " ASN A 433 " " NAG A 704 " - " ASN A 114 " " NAG B 702 " - " ASN B 134 " " NAG B 703 " - " ASN B 433 " " NAG B 704 " - " ASN B 114 " Time building additional restraints: 2.06 Conformation dependent library (CDL) restraints added in 1.0 seconds 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1968 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 4 sheets defined 50.7% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 163 through 182 removed outlier: 3.641A pdb=" N PHE A 182 " --> pdb=" O ILE A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 260 removed outlier: 3.836A pdb=" N ASP A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 279 No H-bonds generated for 'chain 'A' and resid 277 through 279' Processing helix chain 'A' and resid 280 through 302 removed outlier: 4.283A pdb=" N TRP A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE A 285 " --> pdb=" O VAL A 281 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL A 286 " --> pdb=" O PHE A 282 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 328 removed outlier: 3.989A pdb=" N GLY A 312 " --> pdb=" O PHE A 308 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS A 313 " --> pdb=" O ARG A 309 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE A 326 " --> pdb=" O ILE A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 366 removed outlier: 3.686A pdb=" N PHE A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 389 through 410 removed outlier: 4.165A pdb=" N LEU A 394 " --> pdb=" O TRP A 390 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU A 395 " --> pdb=" O PRO A 391 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE A 396 " --> pdb=" O GLN A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 430 removed outlier: 3.672A pdb=" N GLY A 429 " --> pdb=" O GLY A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 447 removed outlier: 3.523A pdb=" N ILE A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 446 " --> pdb=" O ILE A 442 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 447 " --> pdb=" O ASP A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 463 Processing helix chain 'A' and resid 475 through 496 Processing helix chain 'A' and resid 499 through 523 removed outlier: 3.982A pdb=" N ILE A 503 " --> pdb=" O ARG A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 558 removed outlier: 3.744A pdb=" N SER A 548 " --> pdb=" O THR A 544 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE A 549 " --> pdb=" O THR A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 578 removed outlier: 4.334A pdb=" N ASN A 578 " --> pdb=" O TYR A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 589 Processing helix chain 'A' and resid 604 through 629 removed outlier: 3.608A pdb=" N HIS A 608 " --> pdb=" O SER A 604 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR A 610 " --> pdb=" O LYS A 606 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLN A 611 " --> pdb=" O GLU A 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 182 removed outlier: 3.642A pdb=" N PHE B 182 " --> pdb=" O ILE B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 260 removed outlier: 3.836A pdb=" N ASP B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 279 No H-bonds generated for 'chain 'B' and resid 277 through 279' Processing helix chain 'B' and resid 280 through 302 removed outlier: 4.282A pdb=" N TRP B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE B 285 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL B 286 " --> pdb=" O PHE B 282 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER B 299 " --> pdb=" O LEU B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 328 removed outlier: 3.989A pdb=" N GLY B 312 " --> pdb=" O PHE B 308 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS B 313 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE B 326 " --> pdb=" O ILE B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 366 removed outlier: 3.686A pdb=" N PHE B 366 " --> pdb=" O LEU B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 389 through 410 removed outlier: 4.165A pdb=" N LEU B 394 " --> pdb=" O TRP B 390 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU B 395 " --> pdb=" O PRO B 391 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE B 396 " --> pdb=" O GLN B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 430 removed outlier: 3.672A pdb=" N GLY B 429 " --> pdb=" O GLY B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 447 removed outlier: 3.524A pdb=" N ILE B 442 " --> pdb=" O ALA B 438 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 446 " --> pdb=" O ILE B 442 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 447 " --> pdb=" O ASP B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 463 Processing helix chain 'B' and resid 475 through 496 Processing helix chain 'B' and resid 499 through 523 removed outlier: 3.982A pdb=" N ILE B 503 " --> pdb=" O ARG B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 558 removed outlier: 3.745A pdb=" N SER B 548 " --> pdb=" O THR B 544 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE B 549 " --> pdb=" O THR B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 578 removed outlier: 4.335A pdb=" N ASN B 578 " --> pdb=" O TYR B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 589 Processing helix chain 'B' and resid 604 through 629 removed outlier: 3.608A pdb=" N HIS B 608 " --> pdb=" O SER B 604 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR B 610 " --> pdb=" O LYS B 606 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLN B 611 " --> pdb=" O GLU B 607 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 104 removed outlier: 3.600A pdb=" N LEU A 57 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 150 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU A 148 " --> pdb=" O ILE A 142 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 85 removed outlier: 3.506A pdb=" N GLN A 82 " --> pdb=" O TRP A 71 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL A 69 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N CYS A 123 " --> pdb=" O LEU A 113 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 104 removed outlier: 3.600A pdb=" N LEU B 57 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA B 150 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU B 148 " --> pdb=" O ILE B 142 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 82 through 85 removed outlier: 3.506A pdb=" N GLN B 82 " --> pdb=" O TRP B 71 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL B 69 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N CYS B 123 " --> pdb=" O LEU B 113 " (cutoff:3.500A) 418 hydrogen bonds defined for protein. 1230 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: 2.10 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.13: 2 1.13 - 1.31: 1266 1.31 - 1.49: 3704 1.49 - 1.66: 3602 1.66 - 1.84: 52 Bond restraints: 8626 Sorted by residual: bond pdb=" CB PRO A 371 " pdb=" CG PRO A 371 " ideal model delta sigma weight residual 1.492 0.953 0.539 5.00e-02 4.00e+02 1.16e+02 bond pdb=" CB PRO B 371 " pdb=" CG PRO B 371 " ideal model delta sigma weight residual 1.492 0.953 0.539 5.00e-02 4.00e+02 1.16e+02 bond pdb=" CG PRO A 371 " pdb=" CD PRO A 371 " ideal model delta sigma weight residual 1.503 1.232 0.271 3.40e-02 8.65e+02 6.34e+01 bond pdb=" CG PRO B 371 " pdb=" CD PRO B 371 " ideal model delta sigma weight residual 1.503 1.233 0.270 3.40e-02 8.65e+02 6.33e+01 bond pdb=" C1 NAG A 703 " pdb=" O5 NAG A 703 " ideal model delta sigma weight residual 1.406 1.466 -0.060 2.00e-02 2.50e+03 9.11e+00 ... (remaining 8621 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.77: 11792 14.77 - 29.54: 4 29.54 - 44.31: 0 44.31 - 59.08: 0 59.08 - 73.85: 2 Bond angle restraints: 11798 Sorted by residual: angle pdb=" CB PRO A 371 " pdb=" CG PRO A 371 " pdb=" CD PRO A 371 " ideal model delta sigma weight residual 106.10 179.95 -73.85 3.20e+00 9.77e-02 5.33e+02 angle pdb=" CB PRO B 371 " pdb=" CG PRO B 371 " pdb=" CD PRO B 371 " ideal model delta sigma weight residual 106.10 179.93 -73.83 3.20e+00 9.77e-02 5.32e+02 angle pdb=" N PRO B 371 " pdb=" CD PRO B 371 " pdb=" CG PRO B 371 " ideal model delta sigma weight residual 103.20 77.97 25.23 1.50e+00 4.44e-01 2.83e+02 angle pdb=" N PRO A 371 " pdb=" CD PRO A 371 " pdb=" CG PRO A 371 " ideal model delta sigma weight residual 103.20 77.99 25.21 1.50e+00 4.44e-01 2.82e+02 angle pdb=" CA PRO A 371 " pdb=" CB PRO A 371 " pdb=" CG PRO A 371 " ideal model delta sigma weight residual 104.50 75.99 28.51 1.90e+00 2.77e-01 2.25e+02 ... (remaining 11793 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 4531 17.01 - 34.02: 429 34.02 - 51.02: 84 51.02 - 68.03: 26 68.03 - 85.04: 8 Dihedral angle restraints: 5078 sinusoidal: 2000 harmonic: 3078 Sorted by residual: dihedral pdb=" CA LYS A 600 " pdb=" C LYS A 600 " pdb=" N ASP A 601 " pdb=" CA ASP A 601 " ideal model delta harmonic sigma weight residual 180.00 158.53 21.47 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA LYS B 600 " pdb=" C LYS B 600 " pdb=" N ASP B 601 " pdb=" CA ASP B 601 " ideal model delta harmonic sigma weight residual 180.00 158.54 21.46 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA LYS B 564 " pdb=" C LYS B 564 " pdb=" N GLY B 565 " pdb=" CA GLY B 565 " ideal model delta harmonic sigma weight residual -180.00 -158.77 -21.23 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 5075 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 1300 0.144 - 0.289: 60 0.289 - 0.433: 6 0.433 - 0.577: 2 0.577 - 0.721: 2 Chirality restraints: 1370 Sorted by residual: chirality pdb=" C1 NAG B 704 " pdb=" ND2 ASN B 114 " pdb=" C2 NAG B 704 " pdb=" O5 NAG B 704 " both_signs ideal model delta sigma weight residual False -2.40 -1.68 -0.72 2.00e-01 2.50e+01 1.30e+01 chirality pdb=" C1 NAG A 704 " pdb=" ND2 ASN A 114 " pdb=" C2 NAG A 704 " pdb=" O5 NAG A 704 " both_signs ideal model delta sigma weight residual False -2.40 -1.68 -0.72 2.00e-01 2.50e+01 1.29e+01 chirality pdb=" C1 NAG B 703 " pdb=" ND2 ASN B 433 " pdb=" C2 NAG B 703 " pdb=" O5 NAG B 703 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.29e+00 ... (remaining 1367 not shown) Planarity restraints: 1440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 531 " -0.111 5.00e-02 4.00e+02 1.65e-01 4.37e+01 pdb=" N PRO B 532 " 0.286 5.00e-02 4.00e+02 pdb=" CA PRO B 532 " -0.093 5.00e-02 4.00e+02 pdb=" CD PRO B 532 " -0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 531 " 0.111 5.00e-02 4.00e+02 1.65e-01 4.36e+01 pdb=" N PRO A 532 " -0.286 5.00e-02 4.00e+02 pdb=" CA PRO A 532 " 0.093 5.00e-02 4.00e+02 pdb=" CD PRO A 532 " 0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 506 " -0.519 9.50e-02 1.11e+02 2.33e-01 3.63e+01 pdb=" NE ARG A 506 " 0.041 2.00e-02 2.50e+03 pdb=" CZ ARG A 506 " -0.025 2.00e-02 2.50e+03 pdb=" NH1 ARG A 506 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG A 506 " -0.007 2.00e-02 2.50e+03 ... (remaining 1437 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 24 2.60 - 3.17: 6474 3.17 - 3.75: 12013 3.75 - 4.32: 15516 4.32 - 4.90: 27408 Nonbonded interactions: 61435 Sorted by model distance: nonbonded pdb=" SG CYS B 415 " pdb=" SG CYS B 434 " model vdw 2.023 3.760 nonbonded pdb=" SG CYS B 76 " pdb=" SG CYS B 79 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS A 334 " pdb=" SG CYS B 334 " model vdw 2.047 3.760 nonbonded pdb=" OG1 THR A 568 " pdb=" OG1 THR A 570 " model vdw 2.275 3.040 nonbonded pdb=" OG1 THR B 568 " pdb=" OG1 THR B 570 " model vdw 2.275 3.040 ... (remaining 61430 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' 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 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: 3.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.320 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 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 : 0.011 0.539 8626 Z= 0.717 Angle : 1.677 73.855 11798 Z= 0.825 Chirality : 0.078 0.721 1370 Planarity : 0.017 0.233 1434 Dihedral : 14.551 85.038 3104 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.24), residues: 1058 helix: 1.05 (0.21), residues: 482 sheet: 0.88 (0.53), residues: 114 loop : -2.58 (0.24), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 403 HIS 0.016 0.004 HIS A 586 PHE 0.043 0.003 PHE B 246 TYR 0.052 0.003 TYR A 127 ARG 0.030 0.005 ARG A 506 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.972 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.1563 time to fit residues: 16.0024 Evaluate side-chains 50 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS A 258 ASN A 605 HIS B 59 HIS B 258 ASN B 605 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 8626 Z= 0.395 Angle : 0.784 8.806 11798 Z= 0.424 Chirality : 0.052 0.378 1370 Planarity : 0.007 0.096 1434 Dihedral : 10.420 87.552 1368 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.83 % Allowed : 5.78 % Favored : 93.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.24), residues: 1058 helix: 1.66 (0.22), residues: 482 sheet: 0.56 (0.46), residues: 126 loop : -2.55 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 403 HIS 0.007 0.002 HIS B 608 PHE 0.040 0.003 PHE A 246 TYR 0.034 0.002 TYR A 453 ARG 0.005 0.001 ARG A 506 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.917 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 70 average time/residue: 0.1873 time to fit residues: 19.5789 Evaluate side-chains 61 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 104 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS B 59 HIS B 586 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8626 Z= 0.325 Angle : 0.687 7.925 11798 Z= 0.368 Chirality : 0.049 0.259 1370 Planarity : 0.006 0.062 1434 Dihedral : 9.564 82.642 1368 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.65 % Allowed : 7.90 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.25), residues: 1058 helix: 1.90 (0.22), residues: 480 sheet: 1.13 (0.46), residues: 122 loop : -2.49 (0.24), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 403 HIS 0.005 0.001 HIS A 608 PHE 0.027 0.002 PHE B 573 TYR 0.026 0.002 TYR B 453 ARG 0.003 0.001 ARG A 344 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.929 Fit side-chains outliers start: 14 outliers final: 11 residues processed: 81 average time/residue: 0.1671 time to fit residues: 20.4501 Evaluate side-chains 70 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 79 CYS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 533 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 chunk 96 optimal weight: 0.5980 chunk 102 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 27 optimal weight: 8.9990 chunk 85 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS A 586 HIS B 59 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8626 Z= 0.166 Angle : 0.565 7.436 11798 Z= 0.298 Chirality : 0.044 0.226 1370 Planarity : 0.004 0.042 1434 Dihedral : 9.135 84.626 1368 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.30 % Allowed : 12.03 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.25), residues: 1058 helix: 2.49 (0.23), residues: 480 sheet: 1.26 (0.44), residues: 124 loop : -2.34 (0.24), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 390 HIS 0.004 0.001 HIS B 78 PHE 0.018 0.001 PHE B 573 TYR 0.013 0.001 TYR A 542 ARG 0.001 0.000 ARG A 351 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.960 Fit side-chains REVERT: A 564 LYS cc_start: 0.8308 (ptmm) cc_final: 0.8064 (ptpt) REVERT: B 564 LYS cc_start: 0.8284 (ptmm) cc_final: 0.8047 (ptpt) outliers start: 11 outliers final: 7 residues processed: 70 average time/residue: 0.1501 time to fit residues: 16.5792 Evaluate side-chains 65 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 390 TRP Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 390 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 0.9990 chunk 1 optimal weight: 20.0000 chunk 76 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 34 optimal weight: 0.3980 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS B 59 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 8626 Z= 0.388 Angle : 0.694 6.393 11798 Z= 0.371 Chirality : 0.049 0.249 1370 Planarity : 0.005 0.040 1434 Dihedral : 8.884 64.628 1368 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.36 % Allowed : 11.91 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.25), residues: 1058 helix: 1.95 (0.22), residues: 480 sheet: 1.28 (0.45), residues: 122 loop : -2.42 (0.24), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 403 HIS 0.005 0.002 HIS B 608 PHE 0.026 0.002 PHE A 573 TYR 0.022 0.002 TYR B 453 ARG 0.002 0.000 ARG A 444 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 1.005 Fit side-chains outliers start: 20 outliers final: 15 residues processed: 77 average time/residue: 0.1687 time to fit residues: 19.8536 Evaluate side-chains 73 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 390 TRP Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 390 TRP Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 581 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 chunk 85 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 53 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS B 59 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8626 Z= 0.191 Angle : 0.569 6.625 11798 Z= 0.299 Chirality : 0.044 0.231 1370 Planarity : 0.004 0.036 1434 Dihedral : 8.404 60.698 1368 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.59 % Allowed : 12.26 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.25), residues: 1058 helix: 2.46 (0.23), residues: 480 sheet: 1.41 (0.45), residues: 122 loop : -2.31 (0.24), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 390 HIS 0.004 0.001 HIS A 59 PHE 0.018 0.001 PHE B 573 TYR 0.016 0.001 TYR B 542 ARG 0.002 0.000 ARG A 444 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 57 time to evaluate : 0.899 Fit side-chains outliers start: 22 outliers final: 15 residues processed: 76 average time/residue: 0.1396 time to fit residues: 17.1146 Evaluate side-chains 70 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 586 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 0.6980 chunk 58 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 102 optimal weight: 0.0270 chunk 63 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.5442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS B 59 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8626 Z= 0.263 Angle : 0.606 6.267 11798 Z= 0.321 Chirality : 0.046 0.237 1370 Planarity : 0.004 0.036 1434 Dihedral : 8.249 52.567 1368 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.89 % Allowed : 13.56 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.25), residues: 1058 helix: 2.35 (0.23), residues: 480 sheet: 1.46 (0.45), residues: 122 loop : -2.32 (0.25), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 390 HIS 0.004 0.001 HIS A 608 PHE 0.022 0.002 PHE B 573 TYR 0.017 0.001 TYR B 542 ARG 0.002 0.000 ARG B 351 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.870 Fit side-chains REVERT: A 139 VAL cc_start: 0.7776 (p) cc_final: 0.7503 (m) outliers start: 16 outliers final: 14 residues processed: 73 average time/residue: 0.1823 time to fit residues: 19.8213 Evaluate side-chains 70 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 533 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 69 optimal weight: 0.4980 chunk 50 optimal weight: 5.9990 chunk 9 optimal weight: 30.0000 chunk 80 optimal weight: 20.0000 chunk 92 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS B 59 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8626 Z= 0.231 Angle : 0.582 6.237 11798 Z= 0.307 Chirality : 0.045 0.232 1370 Planarity : 0.004 0.035 1434 Dihedral : 8.079 52.665 1368 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.12 % Allowed : 13.92 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.26), residues: 1058 helix: 2.39 (0.23), residues: 488 sheet: 1.52 (0.45), residues: 122 loop : -2.27 (0.25), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 403 HIS 0.005 0.001 HIS A 586 PHE 0.019 0.001 PHE B 573 TYR 0.017 0.001 TYR A 542 ARG 0.002 0.000 ARG B 444 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.895 Fit side-chains outliers start: 18 outliers final: 16 residues processed: 72 average time/residue: 0.1811 time to fit residues: 19.5233 Evaluate side-chains 73 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 533 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 57 optimal weight: 0.0670 chunk 41 optimal weight: 0.3980 chunk 74 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 62 optimal weight: 20.0000 chunk 100 optimal weight: 0.9980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS A 463 HIS B 59 HIS B 463 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8626 Z= 0.159 Angle : 0.530 6.369 11798 Z= 0.276 Chirality : 0.042 0.218 1370 Planarity : 0.004 0.033 1434 Dihedral : 7.735 52.361 1368 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.89 % Allowed : 14.86 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.26), residues: 1058 helix: 2.63 (0.23), residues: 488 sheet: 1.68 (0.46), residues: 118 loop : -2.10 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 403 HIS 0.004 0.001 HIS A 586 PHE 0.015 0.001 PHE B 573 TYR 0.016 0.001 TYR B 77 ARG 0.001 0.000 ARG B 241 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 1.027 Fit side-chains outliers start: 16 outliers final: 15 residues processed: 67 average time/residue: 0.1332 time to fit residues: 15.0660 Evaluate side-chains 65 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 586 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 64 optimal weight: 0.2980 chunk 51 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS B 59 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8626 Z= 0.166 Angle : 0.535 6.150 11798 Z= 0.279 Chirality : 0.043 0.216 1370 Planarity : 0.004 0.033 1434 Dihedral : 7.696 52.584 1368 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.77 % Allowed : 15.21 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.26), residues: 1058 helix: 2.71 (0.23), residues: 488 sheet: 1.74 (0.45), residues: 114 loop : -2.01 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 403 HIS 0.004 0.001 HIS B 586 PHE 0.016 0.001 PHE B 573 TYR 0.014 0.001 TYR B 542 ARG 0.001 0.000 ARG A 241 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.918 Fit side-chains outliers start: 15 outliers final: 15 residues processed: 64 average time/residue: 0.1487 time to fit residues: 15.6314 Evaluate side-chains 66 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 586 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 84 optimal weight: 0.0980 chunk 35 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS B 59 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.164206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.132900 restraints weight = 10447.696| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.92 r_work: 0.3473 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8626 Z= 0.198 Angle : 0.552 6.078 11798 Z= 0.290 Chirality : 0.044 0.223 1370 Planarity : 0.004 0.034 1434 Dihedral : 7.781 53.330 1368 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.89 % Allowed : 14.98 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.26), residues: 1058 helix: 2.62 (0.23), residues: 488 sheet: 1.73 (0.46), residues: 114 loop : -2.02 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 403 HIS 0.005 0.001 HIS A 586 PHE 0.019 0.001 PHE B 573 TYR 0.015 0.001 TYR B 542 ARG 0.002 0.000 ARG A 351 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1765.10 seconds wall clock time: 32 minutes 59.25 seconds (1979.25 seconds total)