Starting phenix.real_space_refine on Fri Mar 15 22:23:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bgw_16041/03_2024/8bgw_16041_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bgw_16041/03_2024/8bgw_16041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bgw_16041/03_2024/8bgw_16041.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bgw_16041/03_2024/8bgw_16041.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bgw_16041/03_2024/8bgw_16041_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bgw_16041/03_2024/8bgw_16041_updated.pdb" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 Fe 6 7.16 5 P 1 5.49 5 S 48 5.16 5 C 8356 2.51 5 N 1999 2.21 5 O 2515 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 28": "OE1" <-> "OE2" Residue "A GLU 39": "OE1" <-> "OE2" Residue "A ASP 112": "OD1" <-> "OD2" Residue "A GLU 228": "OE1" <-> "OE2" Residue "A ASP 368": "OD1" <-> "OD2" Residue "A ASP 396": "OD1" <-> "OD2" Residue "A GLU 490": "OE1" <-> "OE2" Residue "A PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 584": "OE1" <-> "OE2" Residue "A PHE 722": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 38": "OE1" <-> "OE2" Residue "B GLU 39": "OE1" <-> "OE2" Residue "B ASP 112": "OD1" <-> "OD2" Residue "B GLU 228": "OE1" <-> "OE2" Residue "B ASP 368": "OD1" <-> "OD2" Residue "B ASP 396": "OD1" <-> "OD2" Residue "B GLU 490": "OE1" <-> "OE2" Residue "B PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 569": "OE1" <-> "OE2" Residue "B TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 691": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 705": "OE1" <-> "OE2" Residue "B PHE 722": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12927 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5921 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 750, 5902 Classifications: {'peptide': 750} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 713} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 750, 5902 Classifications: {'peptide': 750} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 713} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 6070 Chain: "B" Number of atoms: 5920 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 750, 5901 Classifications: {'peptide': 750} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 713} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 750, 5901 Classifications: {'peptide': 750} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 713} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 6069 Chain: "A" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 320 Unusual residues: {' CA': 1, ' FE': 1, '10M': 1, 'HEM': 2, 'LOP': 7, 'UQ1': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 176 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'LOP:plan-1': 4, 'LOP:plan-3': 5, 'LOP:plan-2': 2} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 317 Unusual residues: {' CA': 1, ' FE': 1, '10M': 1, 'HEM': 2, 'LOP': 6, 'UQ1': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'LOP:plan-1': 3, 'LOP:plan-3': 2, 'LOP:plan-2': 2} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 230 Classifications: {'water': 230} Link IDs: {None: 229} Chain: "B" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 219 Classifications: {'water': 219} Link IDs: {None: 218} Time building chain proxies: 12.42, per 1000 atoms: 0.96 Number of scatterers: 12927 At special positions: 0 Unit cell: (71.89, 111.93, 101.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 6 26.01 Ca 2 19.99 S 48 16.00 P 1 15.00 O 2515 8.00 N 1999 7.00 C 8356 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.58 Conformation dependent library (CDL) restraints added in 4.1 seconds 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2714 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 66 helices and 2 sheets defined 71.3% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.54 Creating SS restraints... Processing helix chain 'A' and resid 5 through 31 Processing helix chain 'A' and resid 51 through 64 Processing helix chain 'A' and resid 66 through 68 No H-bonds generated for 'chain 'A' and resid 66 through 68' Processing helix chain 'A' and resid 83 through 104 Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 113 through 128 Processing helix chain 'A' and resid 143 through 159 Processing helix chain 'A' and resid 164 through 172 removed outlier: 5.009A pdb=" N ARG A 168 " --> pdb=" O ALA A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 201 Processing helix chain 'A' and resid 219 through 221 No H-bonds generated for 'chain 'A' and resid 219 through 221' Processing helix chain 'A' and resid 227 through 254 Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 277 through 306 removed outlier: 4.023A pdb=" N LEU A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLY A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N LYS A 284 " --> pdb=" O ARG A 280 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N TYR A 285 " --> pdb=" O ALA A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 320 No H-bonds generated for 'chain 'A' and resid 318 through 320' Processing helix chain 'A' and resid 324 through 354 Proline residue: A 352 - end of helix Processing helix chain 'A' and resid 363 through 390 Processing helix chain 'A' and resid 398 through 401 No H-bonds generated for 'chain 'A' and resid 398 through 401' Processing helix chain 'A' and resid 413 through 439 removed outlier: 3.568A pdb=" N GLY A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Proline residue: A 436 - end of helix Processing helix chain 'A' and resid 446 through 461 Processing helix chain 'A' and resid 463 through 466 Processing helix chain 'A' and resid 474 through 487 Processing helix chain 'A' and resid 492 through 507 Processing helix chain 'A' and resid 514 through 538 removed outlier: 3.765A pdb=" N GLY A 530 " --> pdb=" O LEU A 526 " (cutoff:3.500A) Proline residue: A 533 - end of helix removed outlier: 5.021A pdb=" N PHE A 536 " --> pdb=" O ILE A 532 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N HIS A 537 " --> pdb=" O PRO A 533 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N HIS A 538 " --> pdb=" O GLY A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 578 removed outlier: 3.538A pdb=" N VAL A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Proline residue: A 562 - end of helix removed outlier: 3.593A pdb=" N VAL A 565 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU A 566 " --> pdb=" O PRO A 562 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N GLY A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N HIS A 568 " --> pdb=" O ILE A 564 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU A 569 " --> pdb=" O VAL A 565 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 576 " --> pdb=" O GLU A 572 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS A 577 " --> pdb=" O ASN A 573 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR A 578 " --> pdb=" O TRP A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 602 removed outlier: 5.124A pdb=" N TRP A 588 " --> pdb=" O ASN A 585 " (cutoff:3.500A) Proline residue: A 589 - end of helix removed outlier: 3.621A pdb=" N VAL A 596 " --> pdb=" O PHE A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 610 Processing helix chain 'A' and resid 614 through 620 removed outlier: 3.790A pdb=" N TYR A 619 " --> pdb=" O VAL A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 653 removed outlier: 4.272A pdb=" N PHE A 640 " --> pdb=" O GLY A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 681 Processing helix chain 'A' and resid 683 through 696 Processing helix chain 'A' and resid 699 through 702 No H-bonds generated for 'chain 'A' and resid 699 through 702' Processing helix chain 'A' and resid 705 through 708 No H-bonds generated for 'chain 'A' and resid 705 through 708' Processing helix chain 'A' and resid 711 through 744 removed outlier: 4.458A pdb=" N THR A 721 " --> pdb=" O ARG A 717 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N PHE A 722 " --> pdb=" O TRP A 718 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLY A 723 " --> pdb=" O GLY A 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 31 Processing helix chain 'B' and resid 51 through 64 Processing helix chain 'B' and resid 66 through 68 No H-bonds generated for 'chain 'B' and resid 66 through 68' Processing helix chain 'B' and resid 83 through 104 Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 113 through 128 Processing helix chain 'B' and resid 143 through 159 Processing helix chain 'B' and resid 164 through 172 removed outlier: 5.010A pdb=" N ARG B 168 " --> pdb=" O ALA B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 201 Processing helix chain 'B' and resid 219 through 221 No H-bonds generated for 'chain 'B' and resid 219 through 221' Processing helix chain 'B' and resid 227 through 254 Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'B' and resid 277 through 306 removed outlier: 4.022A pdb=" N LEU B 282 " --> pdb=" O SER B 278 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLY B 283 " --> pdb=" O GLN B 279 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N LYS B 284 " --> pdb=" O ARG B 280 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N TYR B 285 " --> pdb=" O ALA B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 320 No H-bonds generated for 'chain 'B' and resid 318 through 320' Processing helix chain 'B' and resid 324 through 354 Proline residue: B 352 - end of helix Processing helix chain 'B' and resid 363 through 390 Processing helix chain 'B' and resid 398 through 401 No H-bonds generated for 'chain 'B' and resid 398 through 401' Processing helix chain 'B' and resid 413 through 439 removed outlier: 3.568A pdb=" N GLY B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) Proline residue: B 436 - end of helix Processing helix chain 'B' and resid 446 through 461 Processing helix chain 'B' and resid 463 through 466 Processing helix chain 'B' and resid 474 through 487 Processing helix chain 'B' and resid 492 through 507 Processing helix chain 'B' and resid 514 through 538 removed outlier: 3.762A pdb=" N GLY B 530 " --> pdb=" O LEU B 526 " (cutoff:3.500A) Proline residue: B 533 - end of helix removed outlier: 5.020A pdb=" N PHE B 536 " --> pdb=" O ILE B 532 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N HIS B 537 " --> pdb=" O PRO B 533 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N HIS B 538 " --> pdb=" O GLY B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 578 removed outlier: 3.539A pdb=" N VAL B 561 " --> pdb=" O ALA B 557 " (cutoff:3.500A) Proline residue: B 562 - end of helix removed outlier: 3.593A pdb=" N VAL B 565 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU B 566 " --> pdb=" O PRO B 562 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N GLY B 567 " --> pdb=" O LEU B 563 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N HIS B 568 " --> pdb=" O ILE B 564 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU B 569 " --> pdb=" O VAL B 565 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU B 576 " --> pdb=" O GLU B 572 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LYS B 577 " --> pdb=" O ASN B 573 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N THR B 578 " --> pdb=" O TRP B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 602 removed outlier: 5.122A pdb=" N TRP B 588 " --> pdb=" O ASN B 585 " (cutoff:3.500A) Proline residue: B 589 - end of helix removed outlier: 3.623A pdb=" N VAL B 596 " --> pdb=" O PHE B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 610 Processing helix chain 'B' and resid 614 through 620 removed outlier: 3.791A pdb=" N TYR B 619 " --> pdb=" O VAL B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 653 removed outlier: 4.271A pdb=" N PHE B 640 " --> pdb=" O GLY B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 681 Processing helix chain 'B' and resid 683 through 696 Processing helix chain 'B' and resid 699 through 702 No H-bonds generated for 'chain 'B' and resid 699 through 702' Processing helix chain 'B' and resid 705 through 708 No H-bonds generated for 'chain 'B' and resid 705 through 708' Processing helix chain 'B' and resid 711 through 743 removed outlier: 4.461A pdb=" N THR B 721 " --> pdb=" O ARG B 717 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N PHE B 722 " --> pdb=" O TRP B 718 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLY B 723 " --> pdb=" O GLY B 719 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 138 through 141 removed outlier: 6.284A pdb=" N GLU A 39 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N LEU A 141 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA A 41 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N SER A 42 " --> pdb=" O ARG A 47 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N ARG A 47 " --> pdb=" O SER A 42 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 138 through 141 removed outlier: 6.282A pdb=" N GLU B 39 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N LEU B 141 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ALA B 41 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N SER B 42 " --> pdb=" O ARG B 47 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N ARG B 47 " --> pdb=" O SER B 42 " (cutoff:3.500A) 743 hydrogen bonds defined for protein. 2105 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: 4.24 Time building geometry restraints manager: 6.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.36: 3967 1.36 - 1.55: 8794 1.55 - 1.73: 11 1.73 - 1.92: 96 1.92 - 2.10: 12 Bond restraints: 12880 Sorted by residual: bond pdb=" C12 LOP B 812 " pdb=" C13 LOP B 812 " ideal model delta sigma weight residual 1.530 1.307 0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" C11 LOP B 810 " pdb=" C12 LOP B 810 " ideal model delta sigma weight residual 1.523 1.309 0.214 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C10 LOP A 812 " pdb=" C11 LOP A 812 " ideal model delta sigma weight residual 1.524 1.316 0.208 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C32 LOP B 811 " pdb=" C33 LOP B 811 " ideal model delta sigma weight residual 1.523 1.320 0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C13 LOP A 807 " pdb=" C14 LOP A 807 " ideal model delta sigma weight residual 1.497 1.301 0.196 2.00e-02 2.50e+03 9.63e+01 ... (remaining 12875 not shown) Histogram of bond angle deviations from ideal: 85.91 - 104.50: 296 104.50 - 123.08: 14383 123.08 - 141.67: 2830 141.67 - 160.25: 0 160.25 - 178.84: 8 Bond angle restraints: 17517 Sorted by residual: angle pdb=" CA ASP A 82 " pdb=" CB ASP A 82 " pdb=" CG ASP A 82 " ideal model delta sigma weight residual 112.60 104.60 8.00 1.00e+00 1.00e+00 6.40e+01 angle pdb=" CA ASP B 82 " pdb=" CB ASP B 82 " pdb=" CG ASP B 82 " ideal model delta sigma weight residual 112.60 104.69 7.91 1.00e+00 1.00e+00 6.26e+01 angle pdb=" CA PHE B 635 " pdb=" CB PHE B 635 " pdb=" CG PHE B 635 " ideal model delta sigma weight residual 113.80 106.77 7.03 1.00e+00 1.00e+00 4.95e+01 angle pdb=" CA PHE A 635 " pdb=" CB PHE A 635 " pdb=" CG PHE A 635 " ideal model delta sigma weight residual 113.80 106.78 7.02 1.00e+00 1.00e+00 4.93e+01 angle pdb=" CA PHE A 598 " pdb=" CB PHE A 598 " pdb=" CG PHE A 598 " ideal model delta sigma weight residual 113.80 107.56 6.24 1.00e+00 1.00e+00 3.89e+01 ... (remaining 17512 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.36: 6784 27.36 - 54.72: 431 54.72 - 82.08: 81 82.08 - 109.44: 23 109.44 - 136.80: 6 Dihedral angle restraints: 7325 sinusoidal: 3049 harmonic: 4276 Sorted by residual: dihedral pdb=" CA PRO B 81 " pdb=" C PRO B 81 " pdb=" N ASP B 82 " pdb=" CA ASP B 82 " ideal model delta harmonic sigma weight residual 180.00 151.34 28.66 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA PRO A 81 " pdb=" C PRO A 81 " pdb=" N ASP A 82 " pdb=" CA ASP A 82 " ideal model delta harmonic sigma weight residual 180.00 151.35 28.65 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA ILE A 679 " pdb=" C ILE A 679 " pdb=" N PHE A 680 " pdb=" CA PHE A 680 " ideal model delta harmonic sigma weight residual -180.00 -156.45 -23.55 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 7322 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 863 0.059 - 0.117: 621 0.117 - 0.176: 257 0.176 - 0.235: 61 0.235 - 0.293: 20 Chirality restraints: 1822 Sorted by residual: chirality pdb=" CA ILE B 620 " pdb=" N ILE B 620 " pdb=" C ILE B 620 " pdb=" CB ILE B 620 " both_signs ideal model delta sigma weight residual False 2.43 2.14 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA ILE A 620 " pdb=" N ILE A 620 " pdb=" C ILE A 620 " pdb=" CB ILE A 620 " both_signs ideal model delta sigma weight residual False 2.43 2.14 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA VAL B 628 " pdb=" N VAL B 628 " pdb=" C VAL B 628 " pdb=" CB VAL B 628 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.27 2.00e-01 2.50e+01 1.89e+00 ... (remaining 1819 not shown) Planarity restraints: 2145 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 UQ1 B 806 " 0.044 2.00e-02 2.50e+03 4.66e-01 6.51e+03 pdb=" C2 UQ1 B 806 " 0.270 2.00e-02 2.50e+03 pdb=" C3 UQ1 B 806 " -0.235 2.00e-02 2.50e+03 pdb=" C4 UQ1 B 806 " 0.044 2.00e-02 2.50e+03 pdb=" C5 UQ1 B 806 " 0.177 2.00e-02 2.50e+03 pdb=" C6 UQ1 B 806 " -0.114 2.00e-02 2.50e+03 pdb=" C7 UQ1 B 806 " -0.647 2.00e-02 2.50e+03 pdb=" CM5 UQ1 B 806 " 0.558 2.00e-02 2.50e+03 pdb=" O1 UQ1 B 806 " -0.091 2.00e-02 2.50e+03 pdb=" O2 UQ1 B 806 " 0.846 2.00e-02 2.50e+03 pdb=" O3 UQ1 B 806 " -0.977 2.00e-02 2.50e+03 pdb=" O4 UQ1 B 806 " 0.126 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 UQ1 A 806 " 0.121 2.00e-02 2.50e+03 2.51e-01 1.90e+03 pdb=" C2 UQ1 A 806 " -0.032 2.00e-02 2.50e+03 pdb=" C3 UQ1 A 806 " -0.089 2.00e-02 2.50e+03 pdb=" C4 UQ1 A 806 " 0.188 2.00e-02 2.50e+03 pdb=" C5 UQ1 A 806 " -0.021 2.00e-02 2.50e+03 pdb=" C6 UQ1 A 806 " -0.039 2.00e-02 2.50e+03 pdb=" C7 UQ1 A 806 " -0.249 2.00e-02 2.50e+03 pdb=" CM5 UQ1 A 806 " -0.240 2.00e-02 2.50e+03 pdb=" O1 UQ1 A 806 " 0.362 2.00e-02 2.50e+03 pdb=" O2 UQ1 A 806 " -0.115 2.00e-02 2.50e+03 pdb=" O3 UQ1 A 806 " -0.406 2.00e-02 2.50e+03 pdb=" O4 UQ1 A 806 " 0.519 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 UQ1 B 806 " 0.178 2.00e-02 2.50e+03 2.58e-01 8.33e+02 pdb=" C11 UQ1 B 806 " 0.043 2.00e-02 2.50e+03 pdb=" C7 UQ1 B 806 " 0.303 2.00e-02 2.50e+03 pdb=" C8 UQ1 B 806 " -0.449 2.00e-02 2.50e+03 pdb=" C9 UQ1 B 806 " -0.076 2.00e-02 2.50e+03 ... (remaining 2142 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 252 2.52 - 3.11: 11545 3.11 - 3.71: 25705 3.71 - 4.30: 37899 4.30 - 4.90: 59775 Nonbonded interactions: 135176 Sorted by model distance: nonbonded pdb=" NE2 HIS B 629 " pdb="FE HEM B 803 " model vdw 1.923 3.080 nonbonded pdb=" NE2 HIS A 629 " pdb="FE HEM A 802 " model vdw 1.924 3.080 nonbonded pdb=" NE2 HIS B 631 " pdb="FE HEM B 802 " model vdw 1.945 3.080 nonbonded pdb=" NE2 HIS A 631 " pdb="FE HEM A 801 " model vdw 1.945 3.080 nonbonded pdb=" OD2 ASP B 86 " pdb=" OH TYR B 156 " model vdw 2.038 2.440 ... (remaining 135171 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' and (resid 1 through 301 or resid 303 through 717 or resid 719 throug \ h 749 or (resid 750 and (name N or name CA or name C or name O )) or resid 802 o \ r resid 806 or (resid 807 and (name C10 or name C11 or name C12 or name C13 or n \ ame C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 \ or name C21 or name C22 or name C24 or name C25 or name C26 or name C27 or name \ C28 or name C29 or name C30 or name C31 or name C32 or name C6 or name C7 or nam \ e C8 or name C9 or name O6 )) or (resid 808 and (name C10 or name C11 or name C1 \ 2 or name C13 or name C14 or name C15 or name C24 or name C25 or name C26 or nam \ e C27 or name C28 or name C29 or name C30 or name C31 or name C32 or name C33 or \ name C34 or name C35 or name C4 or name C5 or name C6 or name C7 or name C8 or \ name C9 or name O5 or name O6 or name O7 or name O8 )) or resid 809 or (resid 81 \ 0 and (name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or n \ ame C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C30 \ or name C31 or name C32 or name C33 or name C34 or name C6 or name C7 or name C8 \ or name C9 )) or resid 812)) selection = (chain 'B' and (resid 1 through 301 or resid 303 through 717 or resid 719 throug \ h 750 or resid 802 or resid 806 or (resid 807 and (name C10 or name C11 or name \ C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or n \ ame C19 or name C20 or name C21 or name C22 or name C24 or name C25 or name C26 \ or name C27 or name C28 or name C29 or name C30 or name C31 or name C32 or name \ C6 or name C7 or name C8 or name C9 or name O6 )) or resid 808 through 809 or (r \ esid 810 and (name C10 or name C11 or name C12 or name C13 or name C14 or name C \ 15 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or na \ me C30 or name C31 or name C32 or name C33 or name C34 or name C6 or name C7 or \ name C8 or name C9 )) or (resid 812 and (name C10 or name C11 or name C12 or nam \ e C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or \ name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C3 \ 0 or name C31 or name C32 or name C33 or name C34 or name C6 or name C7 or name \ C8 or name C9 )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 13.310 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 47.220 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:12.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 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 : 0.016 0.237 12880 Z= 1.012 Angle : 2.058 15.221 17517 Z= 1.446 Chirality : 0.090 0.293 1822 Planarity : 0.021 0.466 2145 Dihedral : 19.296 136.796 4611 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.08 % Favored : 93.38 % Rotamer: Outliers : 3.84 % Allowed : 8.45 % Favored : 87.71 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.60 (0.18), residues: 1500 helix: -2.44 (0.12), residues: 1052 sheet: None (None), residues: 0 loop : -1.66 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.085 0.015 TRP B 215 HIS 0.027 0.009 HIS B 89 PHE 0.065 0.009 PHE B 635 TYR 0.073 0.012 TYR B 324 ARG 0.054 0.003 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 160 time to evaluate : 1.346 Fit side-chains REVERT: A 184 ASN cc_start: 0.7826 (m-40) cc_final: 0.7025 (t0) REVERT: A 187 ARG cc_start: 0.7725 (ttp-110) cc_final: 0.7499 (ttp-110) REVERT: A 228 GLU cc_start: 0.6307 (mm-30) cc_final: 0.5920 (mt-10) REVERT: A 273 PHE cc_start: 0.7934 (m-80) cc_final: 0.7603 (m-80) REVERT: A 280 ARG cc_start: 0.7529 (mtm-85) cc_final: 0.7295 (mtt90) REVERT: A 353 LEU cc_start: 0.8500 (tt) cc_final: 0.8290 (tp) REVERT: A 430 MET cc_start: 0.8730 (mmm) cc_final: 0.8277 (mmm) REVERT: A 513 ARG cc_start: 0.7377 (ttt90) cc_final: 0.6295 (ttt180) REVERT: A 515 MET cc_start: 0.7308 (OUTLIER) cc_final: 0.6973 (tpt) REVERT: A 571 TRP cc_start: 0.7553 (t60) cc_final: 0.7101 (t-100) REVERT: A 575 ARG cc_start: 0.6342 (mtp85) cc_final: 0.5917 (ttm110) REVERT: A 673 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.6798 (mt) REVERT: A 734 MET cc_start: 0.8304 (tpp) cc_final: 0.7967 (tpp) REVERT: B 5 ARG cc_start: 0.6045 (ttm110) cc_final: 0.5842 (ttm-80) REVERT: B 31 ARG cc_start: 0.6947 (mtm-85) cc_final: 0.6704 (mtm110) REVERT: B 38 GLU cc_start: 0.7424 (mm-30) cc_final: 0.6611 (mm-30) REVERT: B 184 ASN cc_start: 0.7820 (m-40) cc_final: 0.6933 (t0) REVERT: B 228 GLU cc_start: 0.6319 (mm-30) cc_final: 0.5945 (mt-10) REVERT: B 273 PHE cc_start: 0.7915 (m-80) cc_final: 0.7595 (m-80) REVERT: B 353 LEU cc_start: 0.8492 (tt) cc_final: 0.8285 (tp) REVERT: B 430 MET cc_start: 0.8719 (mmm) cc_final: 0.8255 (mmm) REVERT: B 513 ARG cc_start: 0.7379 (ttt90) cc_final: 0.6301 (ttt180) REVERT: B 515 MET cc_start: 0.7247 (OUTLIER) cc_final: 0.6943 (tpt) REVERT: B 546 THR cc_start: 0.7952 (t) cc_final: 0.7693 (m) REVERT: B 571 TRP cc_start: 0.7653 (t60) cc_final: 0.7120 (t-100) REVERT: B 572 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7048 (mt-10) REVERT: B 575 ARG cc_start: 0.6460 (mtp85) cc_final: 0.5924 (ttm110) REVERT: B 584 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7077 (pt0) REVERT: B 673 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.6796 (mt) REVERT: B 708 MET cc_start: 0.8792 (mmm) cc_final: 0.8583 (mmt) REVERT: B 734 MET cc_start: 0.8304 (tpp) cc_final: 0.7968 (tpp) outliers start: 45 outliers final: 15 residues processed: 191 average time/residue: 1.5200 time to fit residues: 312.9122 Evaluate side-chains 156 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 137 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 729 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 0.1980 chunk 113 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 chunk 38 optimal weight: 0.2980 chunk 76 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 117 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 136 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN A 224 HIS A 621 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 12880 Z= 0.298 Angle : 0.847 22.803 17517 Z= 0.377 Chirality : 0.044 0.192 1822 Planarity : 0.005 0.035 2145 Dihedral : 15.223 87.453 2115 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.71 % Allowed : 11.52 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 (0.21), residues: 1500 helix: 0.08 (0.15), residues: 1058 sheet: None (None), residues: 0 loop : -0.37 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A 338 HIS 0.007 0.002 HIS A 305 PHE 0.027 0.002 PHE B 194 TYR 0.024 0.003 TYR A 78 ARG 0.004 0.001 ARG B 187 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 150 time to evaluate : 1.304 Fit side-chains REVERT: A 184 ASN cc_start: 0.8062 (m-40) cc_final: 0.7316 (t0) REVERT: A 187 ARG cc_start: 0.7829 (ttp-110) cc_final: 0.7426 (ttp80) REVERT: A 358 ARG cc_start: 0.6670 (ppt170) cc_final: 0.6064 (ptt-90) REVERT: A 368 ASP cc_start: 0.8097 (m-30) cc_final: 0.7815 (m-30) REVERT: A 430 MET cc_start: 0.8549 (mmm) cc_final: 0.8229 (mmm) REVERT: A 513 ARG cc_start: 0.7492 (ttt90) cc_final: 0.7228 (ttt90) REVERT: A 514 ARG cc_start: 0.6301 (OUTLIER) cc_final: 0.5487 (ttp-110) REVERT: A 515 MET cc_start: 0.7184 (OUTLIER) cc_final: 0.6720 (tpt) REVERT: A 571 TRP cc_start: 0.7412 (t60) cc_final: 0.7203 (t-100) REVERT: A 673 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.6788 (mt) REVERT: B 101 ARG cc_start: 0.7442 (mmt180) cc_final: 0.7201 (mtp180) REVERT: B 184 ASN cc_start: 0.8075 (m-40) cc_final: 0.7315 (t0) REVERT: B 430 MET cc_start: 0.8557 (mmm) cc_final: 0.8206 (mmm) REVERT: B 494 GLU cc_start: 0.7362 (tp30) cc_final: 0.6468 (tp30) REVERT: B 513 ARG cc_start: 0.7497 (ttt90) cc_final: 0.7236 (ttt90) REVERT: B 514 ARG cc_start: 0.6315 (OUTLIER) cc_final: 0.5514 (ttp-110) REVERT: B 515 MET cc_start: 0.7128 (OUTLIER) cc_final: 0.6762 (tpt) REVERT: B 546 THR cc_start: 0.8301 (t) cc_final: 0.8054 (m) REVERT: B 571 TRP cc_start: 0.7525 (t60) cc_final: 0.7230 (t-100) REVERT: B 572 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7179 (mt-10) REVERT: B 584 GLU cc_start: 0.7680 (mm-30) cc_final: 0.6699 (pt0) REVERT: B 673 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.6777 (mt) REVERT: B 721 THR cc_start: 0.8399 (t) cc_final: 0.8091 (m) outliers start: 20 outliers final: 4 residues processed: 160 average time/residue: 1.4399 time to fit residues: 249.9704 Evaluate side-chains 142 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 132 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 673 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 113 optimal weight: 0.9990 chunk 92 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 136 optimal weight: 0.0980 chunk 147 optimal weight: 0.6980 chunk 121 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN A 710 GLN B 32 GLN B 320 GLN B 710 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 12880 Z= 0.316 Angle : 0.801 22.329 17517 Z= 0.355 Chirality : 0.043 0.169 1822 Planarity : 0.005 0.038 2145 Dihedral : 13.092 81.944 2091 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.62 % Allowed : 12.03 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.60 (0.21), residues: 1500 helix: 0.73 (0.15), residues: 1048 sheet: None (None), residues: 0 loop : -0.16 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 338 HIS 0.007 0.002 HIS B 629 PHE 0.026 0.002 PHE B 635 TYR 0.021 0.002 TYR B 78 ARG 0.005 0.001 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 140 time to evaluate : 1.358 Fit side-chains REVERT: A 184 ASN cc_start: 0.8076 (m-40) cc_final: 0.7312 (t0) REVERT: A 187 ARG cc_start: 0.7797 (ttp-110) cc_final: 0.7482 (ttp80) REVERT: A 358 ARG cc_start: 0.6708 (ppt170) cc_final: 0.6109 (ptt-90) REVERT: A 368 ASP cc_start: 0.8003 (m-30) cc_final: 0.7688 (m-30) REVERT: A 430 MET cc_start: 0.8598 (mmm) cc_final: 0.8211 (mmm) REVERT: A 477 MET cc_start: 0.8284 (tmm) cc_final: 0.7970 (tmm) REVERT: A 513 ARG cc_start: 0.7507 (ttt90) cc_final: 0.7179 (ttt90) REVERT: A 515 MET cc_start: 0.7190 (tmm) cc_final: 0.6989 (tpt) REVERT: A 571 TRP cc_start: 0.7333 (t60) cc_final: 0.7088 (t-100) REVERT: A 673 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.6911 (mt) REVERT: A 705 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8356 (pt0) REVERT: B 101 ARG cc_start: 0.7505 (mmt180) cc_final: 0.7285 (mtp180) REVERT: B 184 ASN cc_start: 0.8087 (m-40) cc_final: 0.7303 (t0) REVERT: B 430 MET cc_start: 0.8594 (mmm) cc_final: 0.8350 (mmm) REVERT: B 477 MET cc_start: 0.8282 (tmm) cc_final: 0.7969 (tmm) REVERT: B 513 ARG cc_start: 0.7507 (ttt90) cc_final: 0.7261 (ttt90) REVERT: B 514 ARG cc_start: 0.6228 (OUTLIER) cc_final: 0.5727 (tpt170) REVERT: B 546 THR cc_start: 0.8211 (t) cc_final: 0.7989 (m) REVERT: B 571 TRP cc_start: 0.7441 (t60) cc_final: 0.7157 (t-100) REVERT: B 572 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7138 (mt-10) REVERT: B 584 GLU cc_start: 0.7701 (mm-30) cc_final: 0.6683 (pt0) REVERT: B 673 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.6868 (mt) outliers start: 19 outliers final: 3 residues processed: 146 average time/residue: 1.4920 time to fit residues: 235.2265 Evaluate side-chains 137 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 130 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 728 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 91 optimal weight: 0.1980 chunk 136 optimal weight: 0.5980 chunk 144 optimal weight: 0.5980 chunk 71 optimal weight: 0.0980 chunk 129 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 HIS B 167 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12880 Z= 0.264 Angle : 0.753 20.531 17517 Z= 0.333 Chirality : 0.042 0.165 1822 Planarity : 0.005 0.040 2145 Dihedral : 12.522 81.928 2085 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.41 % Favored : 96.52 % Rotamer: Outliers : 1.71 % Allowed : 12.80 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.89 (0.21), residues: 1500 helix: 0.92 (0.15), residues: 1052 sheet: None (None), residues: 0 loop : 0.04 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 338 HIS 0.010 0.002 HIS A 167 PHE 0.021 0.002 PHE B 194 TYR 0.018 0.002 TYR B 78 ARG 0.004 0.001 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 133 time to evaluate : 1.425 Fit side-chains REVERT: A 184 ASN cc_start: 0.8070 (m-40) cc_final: 0.7266 (t0) REVERT: A 187 ARG cc_start: 0.7791 (ttp-110) cc_final: 0.7459 (ttp80) REVERT: A 358 ARG cc_start: 0.6673 (ppt170) cc_final: 0.6111 (ptt-90) REVERT: A 368 ASP cc_start: 0.7949 (m-30) cc_final: 0.7637 (m-30) REVERT: A 430 MET cc_start: 0.8542 (mmm) cc_final: 0.8202 (mmm) REVERT: A 460 LEU cc_start: 0.7185 (mm) cc_final: 0.6915 (mt) REVERT: A 477 MET cc_start: 0.8284 (tmm) cc_final: 0.8031 (tmm) REVERT: A 513 ARG cc_start: 0.7499 (ttt90) cc_final: 0.7215 (ttt90) REVERT: A 515 MET cc_start: 0.7207 (tmm) cc_final: 0.6920 (tpt) REVERT: A 673 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.6891 (mt) REVERT: B 184 ASN cc_start: 0.8067 (m-40) cc_final: 0.7311 (t0) REVERT: B 430 MET cc_start: 0.8525 (mmm) cc_final: 0.8161 (mmm) REVERT: B 460 LEU cc_start: 0.7061 (mm) cc_final: 0.6819 (mt) REVERT: B 477 MET cc_start: 0.8269 (tmm) cc_final: 0.8017 (tmm) REVERT: B 513 ARG cc_start: 0.7511 (ttt90) cc_final: 0.7208 (ttt90) REVERT: B 514 ARG cc_start: 0.6185 (OUTLIER) cc_final: 0.5708 (tpt170) REVERT: B 546 THR cc_start: 0.8206 (t) cc_final: 0.7992 (m) REVERT: B 571 TRP cc_start: 0.7374 (t60) cc_final: 0.7163 (t-100) REVERT: B 572 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7158 (mt-10) REVERT: B 584 GLU cc_start: 0.7702 (mm-30) cc_final: 0.6709 (pt0) REVERT: B 673 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.6880 (mt) outliers start: 20 outliers final: 4 residues processed: 142 average time/residue: 1.5129 time to fit residues: 232.3030 Evaluate side-chains 133 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 126 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 673 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 123 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 GLN B 167 HIS B 710 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 12880 Z= 0.378 Angle : 0.830 22.156 17517 Z= 0.366 Chirality : 0.045 0.176 1822 Planarity : 0.005 0.041 2145 Dihedral : 12.899 82.513 2085 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.54 % Allowed : 12.88 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.67 (0.21), residues: 1500 helix: 0.77 (0.15), residues: 1048 sheet: None (None), residues: 0 loop : -0.09 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 338 HIS 0.008 0.002 HIS B 305 PHE 0.027 0.002 PHE B 635 TYR 0.017 0.003 TYR A 324 ARG 0.006 0.001 ARG A 703 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 141 time to evaluate : 1.347 Fit side-chains REVERT: A 1 MET cc_start: 0.5847 (ttm) cc_final: 0.5376 (ttm) REVERT: A 184 ASN cc_start: 0.8127 (m-40) cc_final: 0.7315 (t0) REVERT: A 187 ARG cc_start: 0.7868 (ttp-110) cc_final: 0.7599 (ttp80) REVERT: A 358 ARG cc_start: 0.6705 (ppt170) cc_final: 0.6118 (ptt-90) REVERT: A 368 ASP cc_start: 0.8061 (m-30) cc_final: 0.7765 (m-30) REVERT: A 430 MET cc_start: 0.8640 (mmm) cc_final: 0.8283 (mmm) REVERT: A 460 LEU cc_start: 0.7112 (mm) cc_final: 0.6793 (mt) REVERT: A 477 MET cc_start: 0.8242 (tmm) cc_final: 0.7845 (tmm) REVERT: A 673 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.6942 (mt) REVERT: B 184 ASN cc_start: 0.8096 (m-40) cc_final: 0.7323 (t0) REVERT: B 430 MET cc_start: 0.8640 (mmm) cc_final: 0.8280 (mmm) REVERT: B 477 MET cc_start: 0.8239 (tmm) cc_final: 0.7840 (tmm) REVERT: B 514 ARG cc_start: 0.6177 (OUTLIER) cc_final: 0.5877 (tmm160) REVERT: B 515 MET cc_start: 0.6844 (tpt) cc_final: 0.6612 (tpt) REVERT: B 571 TRP cc_start: 0.7370 (t60) cc_final: 0.7162 (t-100) REVERT: B 572 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7200 (mt-10) REVERT: B 584 GLU cc_start: 0.7733 (mm-30) cc_final: 0.6683 (pt0) REVERT: B 673 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.6951 (mt) outliers start: 18 outliers final: 5 residues processed: 149 average time/residue: 1.4780 time to fit residues: 238.1423 Evaluate side-chains 148 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 140 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 728 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 0.5980 chunk 130 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 145 optimal weight: 0.5980 chunk 120 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 139 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN A 710 GLN B 32 GLN ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 12880 Z= 0.315 Angle : 0.783 21.734 17517 Z= 0.345 Chirality : 0.043 0.158 1822 Planarity : 0.005 0.041 2145 Dihedral : 12.450 81.607 2085 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.94 % Allowed : 13.74 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.80 (0.21), residues: 1500 helix: 0.84 (0.15), residues: 1052 sheet: None (None), residues: 0 loop : 0.03 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 338 HIS 0.007 0.002 HIS B 305 PHE 0.022 0.002 PHE B 635 TYR 0.017 0.002 TYR B 78 ARG 0.004 0.001 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 134 time to evaluate : 1.205 Fit side-chains REVERT: A 1 MET cc_start: 0.5814 (ttm) cc_final: 0.5298 (ttm) REVERT: A 184 ASN cc_start: 0.8113 (m-40) cc_final: 0.7269 (t0) REVERT: A 187 ARG cc_start: 0.7832 (ttp-110) cc_final: 0.7530 (ttp80) REVERT: A 358 ARG cc_start: 0.6699 (ppt170) cc_final: 0.6114 (ptt-90) REVERT: A 368 ASP cc_start: 0.8011 (m-30) cc_final: 0.7710 (m-30) REVERT: A 430 MET cc_start: 0.8605 (mmm) cc_final: 0.8331 (mmm) REVERT: A 477 MET cc_start: 0.8268 (tmm) cc_final: 0.7926 (tmm) REVERT: A 673 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.6882 (mt) REVERT: B 184 ASN cc_start: 0.8090 (m-40) cc_final: 0.7328 (t0) REVERT: B 430 MET cc_start: 0.8596 (mmm) cc_final: 0.8320 (mmm) REVERT: B 477 MET cc_start: 0.8245 (tmm) cc_final: 0.7903 (tmm) REVERT: B 514 ARG cc_start: 0.6139 (OUTLIER) cc_final: 0.5853 (tmm160) REVERT: B 515 MET cc_start: 0.6819 (tpt) cc_final: 0.6606 (tpt) REVERT: B 572 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7192 (mt-10) REVERT: B 584 GLU cc_start: 0.7685 (mm-30) cc_final: 0.6624 (pt0) REVERT: B 673 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.6889 (mt) outliers start: 11 outliers final: 5 residues processed: 139 average time/residue: 1.4906 time to fit residues: 223.7663 Evaluate side-chains 140 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 132 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 728 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 0.1980 chunk 82 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 144 optimal weight: 0.4980 chunk 90 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 89 HIS ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 12880 Z= 0.310 Angle : 0.775 21.314 17517 Z= 0.342 Chirality : 0.042 0.156 1822 Planarity : 0.005 0.042 2145 Dihedral : 12.200 81.639 2085 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.54 % Allowed : 13.99 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.88 (0.21), residues: 1500 helix: 0.88 (0.15), residues: 1052 sheet: None (None), residues: 0 loop : 0.12 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 338 HIS 0.007 0.002 HIS A 305 PHE 0.021 0.002 PHE B 194 TYR 0.016 0.002 TYR A 78 ARG 0.004 0.001 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 129 time to evaluate : 1.131 Fit side-chains REVERT: A 1 MET cc_start: 0.5854 (ttm) cc_final: 0.5395 (ttm) REVERT: A 184 ASN cc_start: 0.8120 (m-40) cc_final: 0.7262 (t0) REVERT: A 187 ARG cc_start: 0.7842 (ttp-110) cc_final: 0.7581 (ttp80) REVERT: A 358 ARG cc_start: 0.6697 (ppt170) cc_final: 0.6112 (ptt-90) REVERT: A 368 ASP cc_start: 0.7948 (m-30) cc_final: 0.7642 (m-30) REVERT: A 430 MET cc_start: 0.8589 (mmm) cc_final: 0.8318 (mmm) REVERT: A 460 LEU cc_start: 0.7182 (mm) cc_final: 0.6928 (mt) REVERT: A 477 MET cc_start: 0.8263 (tmm) cc_final: 0.7903 (tmm) REVERT: A 514 ARG cc_start: 0.6443 (tmm160) cc_final: 0.5805 (tpt170) REVERT: A 673 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.6898 (mt) REVERT: B 31 ARG cc_start: 0.6855 (mtm-85) cc_final: 0.6586 (mtm110) REVERT: B 32 GLN cc_start: 0.7352 (mm-40) cc_final: 0.6807 (mm-40) REVERT: B 184 ASN cc_start: 0.8093 (m-40) cc_final: 0.7302 (t0) REVERT: B 430 MET cc_start: 0.8581 (mmm) cc_final: 0.8289 (mmm) REVERT: B 477 MET cc_start: 0.8245 (tmm) cc_final: 0.7894 (tmm) REVERT: B 514 ARG cc_start: 0.6156 (OUTLIER) cc_final: 0.5876 (tmm160) REVERT: B 572 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7173 (mt-10) REVERT: B 584 GLU cc_start: 0.7702 (mm-30) cc_final: 0.6686 (pt0) REVERT: B 673 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.6886 (mt) outliers start: 18 outliers final: 7 residues processed: 135 average time/residue: 1.5425 time to fit residues: 225.0281 Evaluate side-chains 139 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 129 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 728 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 98 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 13 optimal weight: 0.2980 chunk 113 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 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 32 GLN A 89 HIS ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 12880 Z= 0.320 Angle : 0.786 21.837 17517 Z= 0.346 Chirality : 0.043 0.158 1822 Planarity : 0.005 0.042 2145 Dihedral : 12.147 81.413 2085 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.62 % Allowed : 14.16 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.21), residues: 1500 helix: 0.88 (0.15), residues: 1048 sheet: None (None), residues: 0 loop : 0.07 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 338 HIS 0.007 0.002 HIS A 305 PHE 0.022 0.002 PHE B 635 TYR 0.016 0.002 TYR A 78 ARG 0.005 0.001 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 127 time to evaluate : 1.323 Fit side-chains REVERT: A 1 MET cc_start: 0.5868 (ttm) cc_final: 0.5445 (ttm) REVERT: A 184 ASN cc_start: 0.8123 (m-40) cc_final: 0.7263 (t0) REVERT: A 187 ARG cc_start: 0.7828 (ttp-110) cc_final: 0.7584 (ttp80) REVERT: A 358 ARG cc_start: 0.6703 (ppt170) cc_final: 0.6118 (ptt-90) REVERT: A 368 ASP cc_start: 0.8008 (m-30) cc_final: 0.7709 (m-30) REVERT: A 430 MET cc_start: 0.8609 (mmm) cc_final: 0.8323 (mmm) REVERT: A 477 MET cc_start: 0.8251 (tmm) cc_final: 0.7873 (tmm) REVERT: A 514 ARG cc_start: 0.6604 (tmm160) cc_final: 0.5961 (tpt170) REVERT: A 673 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.6889 (mt) REVERT: B 184 ASN cc_start: 0.8093 (m-40) cc_final: 0.7305 (t0) REVERT: B 430 MET cc_start: 0.8600 (mmm) cc_final: 0.8311 (mmm) REVERT: B 477 MET cc_start: 0.8243 (tmm) cc_final: 0.7857 (tmm) REVERT: B 514 ARG cc_start: 0.6196 (OUTLIER) cc_final: 0.5910 (tmm160) REVERT: B 572 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7194 (mt-10) REVERT: B 584 GLU cc_start: 0.7707 (mm-30) cc_final: 0.6696 (pt0) REVERT: B 673 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.6882 (mt) outliers start: 19 outliers final: 9 residues processed: 134 average time/residue: 1.4909 time to fit residues: 216.5250 Evaluate side-chains 139 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 127 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 728 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.9990 chunk 138 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 chunk 58 optimal weight: 0.0050 chunk 105 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 121 optimal weight: 0.5980 chunk 127 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 142 optimal weight: 0.5980 chunk 86 optimal weight: 0.7980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN A 224 HIS B 32 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12880 Z= 0.282 Angle : 0.754 20.274 17517 Z= 0.333 Chirality : 0.042 0.148 1822 Planarity : 0.005 0.042 2145 Dihedral : 11.702 81.184 2085 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.19 % Allowed : 14.85 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.95 (0.21), residues: 1500 helix: 0.94 (0.15), residues: 1052 sheet: None (None), residues: 0 loop : 0.12 (0.32), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 338 HIS 0.006 0.001 HIS A 305 PHE 0.020 0.002 PHE B 194 TYR 0.025 0.002 TYR A 468 ARG 0.004 0.000 ARG B 187 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 127 time to evaluate : 1.414 Fit side-chains REVERT: A 1 MET cc_start: 0.5862 (ttm) cc_final: 0.5469 (ttm) REVERT: A 32 GLN cc_start: 0.7295 (mm-40) cc_final: 0.6756 (mm-40) REVERT: A 184 ASN cc_start: 0.8121 (m-40) cc_final: 0.7288 (t0) REVERT: A 187 ARG cc_start: 0.7812 (ttp-110) cc_final: 0.7514 (ttp80) REVERT: A 358 ARG cc_start: 0.6714 (ppt170) cc_final: 0.6118 (ptt-90) REVERT: A 368 ASP cc_start: 0.7946 (m-30) cc_final: 0.7645 (m-30) REVERT: A 430 MET cc_start: 0.8574 (mmm) cc_final: 0.8317 (mmm) REVERT: A 477 MET cc_start: 0.8240 (tmm) cc_final: 0.7914 (tmm) REVERT: A 514 ARG cc_start: 0.6638 (tmm160) cc_final: 0.5973 (tpt170) REVERT: A 673 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.6863 (mt) REVERT: B 31 ARG cc_start: 0.6926 (mtm-85) cc_final: 0.6702 (mtm110) REVERT: B 184 ASN cc_start: 0.8072 (m-40) cc_final: 0.7320 (t0) REVERT: B 430 MET cc_start: 0.8549 (mmm) cc_final: 0.8281 (mmm) REVERT: B 477 MET cc_start: 0.8246 (tmm) cc_final: 0.7907 (tmm) REVERT: B 514 ARG cc_start: 0.6217 (OUTLIER) cc_final: 0.5628 (tpt170) REVERT: B 572 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7179 (mt-10) REVERT: B 584 GLU cc_start: 0.7695 (mm-30) cc_final: 0.6711 (pt0) REVERT: B 673 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.6874 (mt) outliers start: 14 outliers final: 8 residues processed: 133 average time/residue: 1.6295 time to fit residues: 233.7753 Evaluate side-chains 136 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 125 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 673 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 137 optimal weight: 0.6980 chunk 118 optimal weight: 0.0060 chunk 12 optimal weight: 0.6980 chunk 91 optimal weight: 0.0170 chunk 72 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.4234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12880 Z= 0.264 Angle : 0.741 19.777 17517 Z= 0.329 Chirality : 0.041 0.146 1822 Planarity : 0.005 0.042 2145 Dihedral : 11.371 80.793 2085 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.19 % Allowed : 15.10 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 (0.22), residues: 1500 helix: 1.02 (0.15), residues: 1052 sheet: None (None), residues: 0 loop : 0.16 (0.32), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 338 HIS 0.006 0.001 HIS A 305 PHE 0.019 0.002 PHE A 194 TYR 0.025 0.002 TYR B 468 ARG 0.004 0.000 ARG B 187 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 126 time to evaluate : 1.365 Fit side-chains REVERT: A 1 MET cc_start: 0.5857 (ttm) cc_final: 0.5469 (ttm) REVERT: A 184 ASN cc_start: 0.8121 (m-40) cc_final: 0.7287 (t0) REVERT: A 187 ARG cc_start: 0.7809 (ttp-110) cc_final: 0.7510 (ttp80) REVERT: A 358 ARG cc_start: 0.6702 (ppt170) cc_final: 0.6111 (ptt-90) REVERT: A 368 ASP cc_start: 0.7938 (m-30) cc_final: 0.7637 (m-30) REVERT: A 430 MET cc_start: 0.8555 (mmm) cc_final: 0.8313 (mmm) REVERT: A 477 MET cc_start: 0.8240 (tmm) cc_final: 0.8021 (tmm) REVERT: A 514 ARG cc_start: 0.6574 (tmm160) cc_final: 0.5929 (tpt170) REVERT: A 673 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.6793 (mt) REVERT: B 31 ARG cc_start: 0.6927 (mtm-85) cc_final: 0.6651 (mtm110) REVERT: B 184 ASN cc_start: 0.8087 (m-40) cc_final: 0.7301 (t0) REVERT: B 430 MET cc_start: 0.8534 (mmm) cc_final: 0.8298 (mmm) REVERT: B 477 MET cc_start: 0.8226 (tmm) cc_final: 0.7910 (tmm) REVERT: B 514 ARG cc_start: 0.6263 (OUTLIER) cc_final: 0.5683 (tpt170) REVERT: B 572 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7181 (mt-10) REVERT: B 584 GLU cc_start: 0.7693 (mm-30) cc_final: 0.6721 (pt0) REVERT: B 673 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.6874 (mt) outliers start: 14 outliers final: 7 residues processed: 131 average time/residue: 1.5532 time to fit residues: 219.6013 Evaluate side-chains 134 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 124 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 673 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 122 optimal weight: 0.0980 chunk 15 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 86 optimal weight: 0.0050 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.137966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.114784 restraints weight = 20076.635| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.38 r_work: 0.3253 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12880 Z= 0.274 Angle : 0.748 20.015 17517 Z= 0.331 Chirality : 0.041 0.150 1822 Planarity : 0.005 0.042 2145 Dihedral : 11.293 80.639 2085 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.02 % Allowed : 15.27 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 (0.22), residues: 1500 helix: 1.03 (0.15), residues: 1050 sheet: None (None), residues: 0 loop : 0.15 (0.32), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 338 HIS 0.006 0.001 HIS A 305 PHE 0.019 0.002 PHE A 194 TYR 0.029 0.002 TYR B 468 ARG 0.004 0.001 ARG B 187 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4795.56 seconds wall clock time: 85 minutes 45.07 seconds (5145.07 seconds total)