Starting phenix.real_space_refine on Wed Feb 14 04:52:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3b_35148/02_2024/8i3b_35148_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3b_35148/02_2024/8i3b_35148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3b_35148/02_2024/8i3b_35148.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3b_35148/02_2024/8i3b_35148.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3b_35148/02_2024/8i3b_35148_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3b_35148/02_2024/8i3b_35148_updated.pdb" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.052 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 52 5.16 5 C 5624 2.51 5 N 1446 2.21 5 O 1518 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 44": "OD1" <-> "OD2" Residue "A TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 81": "NH1" <-> "NH2" Residue "A GLU 95": "OE1" <-> "OE2" Residue "A ASP 276": "OD1" <-> "OD2" Residue "A ASP 294": "OD1" <-> "OD2" Residue "A PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 346": "OD1" <-> "OD2" Residue "A PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 401": "NH1" <-> "NH2" Residue "A TYR 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 469": "OE1" <-> "OE2" Residue "A TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 543": "OD1" <-> "OD2" Residue "A TYR 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 632": "OD1" <-> "OD2" Residue "A PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 650": "NH1" <-> "NH2" Residue "B PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 44": "OD1" <-> "OD2" Residue "B TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 81": "NH1" <-> "NH2" Residue "B GLU 95": "OE1" <-> "OE2" Residue "B ASP 276": "OD1" <-> "OD2" Residue "B ASP 294": "OD1" <-> "OD2" Residue "B PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 346": "OD1" <-> "OD2" Residue "B PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 401": "NH1" <-> "NH2" Residue "B TYR 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 469": "OE1" <-> "OE2" Residue "B TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 543": "OD1" <-> "OD2" Residue "B TYR 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 632": "OD1" <-> "OD2" Residue "B PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 650": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8646 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4292 Classifications: {'peptide': 550} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 530} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 4292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4292 Classifications: {'peptide': 550} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 530} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.29, per 1000 atoms: 0.61 Number of scatterers: 8646 At special positions: 0 Unit cell: (80.51, 93.79, 122.01, 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 52 16.00 P 6 15.00 O 1518 8.00 N 1446 7.00 C 5624 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.33 Conformation dependent library (CDL) restraints added in 1.7 seconds 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2028 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 8 sheets defined 47.1% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'A' and resid 107 through 114 Processing helix chain 'A' and resid 138 through 140 No H-bonds generated for 'chain 'A' and resid 138 through 140' Processing helix chain 'A' and resid 157 through 168 Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 186 through 189 No H-bonds generated for 'chain 'A' and resid 186 through 189' Processing helix chain 'A' and resid 211 through 221 removed outlier: 4.183A pdb=" N SER A 216 " --> pdb=" O ARG A 212 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 218 " --> pdb=" O ARG A 214 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLU A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 251 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 337 through 346 Processing helix chain 'A' and resid 351 through 356 Processing helix chain 'A' and resid 382 through 400 removed outlier: 3.594A pdb=" N LEU A 393 " --> pdb=" O GLN A 389 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 424 Processing helix chain 'A' and resid 434 through 457 removed outlier: 3.800A pdb=" N LEU A 439 " --> pdb=" O ASP A 435 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) Proline residue: A 451 - end of helix removed outlier: 4.126A pdb=" N VAL A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N PHE A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 472 removed outlier: 3.656A pdb=" N ARG A 463 " --> pdb=" O PRO A 460 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ALA A 464 " --> pdb=" O GLN A 461 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A 465 " --> pdb=" O GLU A 462 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N THR A 467 " --> pdb=" O ALA A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 488 removed outlier: 3.756A pdb=" N ALA A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS A 484 " --> pdb=" O TYR A 480 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU A 486 " --> pdb=" O MET A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 removed outlier: 3.931A pdb=" N PHE A 502 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N TRP A 505 " --> pdb=" O THR A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 539 removed outlier: 3.540A pdb=" N GLY A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLY A 538 " --> pdb=" O GLY A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 548 Processing helix chain 'A' and resid 551 through 560 Processing helix chain 'A' and resid 574 through 579 Processing helix chain 'A' and resid 582 through 594 Processing helix chain 'A' and resid 599 through 603 Processing helix chain 'A' and resid 640 through 655 removed outlier: 3.549A pdb=" N LEU A 644 " --> pdb=" O GLY A 640 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG A 650 " --> pdb=" O PHE A 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 114 Processing helix chain 'B' and resid 138 through 140 No H-bonds generated for 'chain 'B' and resid 138 through 140' Processing helix chain 'B' and resid 157 through 168 Processing helix chain 'B' and resid 175 through 180 Processing helix chain 'B' and resid 186 through 189 No H-bonds generated for 'chain 'B' and resid 186 through 189' Processing helix chain 'B' and resid 211 through 221 removed outlier: 4.182A pdb=" N SER B 216 " --> pdb=" O ARG B 212 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B 218 " --> pdb=" O ARG B 214 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLU B 220 " --> pdb=" O SER B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 251 Processing helix chain 'B' and resid 298 through 300 No H-bonds generated for 'chain 'B' and resid 298 through 300' Processing helix chain 'B' and resid 312 through 318 Processing helix chain 'B' and resid 337 through 346 Processing helix chain 'B' and resid 351 through 356 Processing helix chain 'B' and resid 382 through 400 removed outlier: 3.594A pdb=" N LEU B 393 " --> pdb=" O GLN B 389 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU B 397 " --> pdb=" O LEU B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 424 Processing helix chain 'B' and resid 434 through 457 removed outlier: 3.799A pdb=" N LEU B 439 " --> pdb=" O ASP B 435 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) Proline residue: B 451 - end of helix removed outlier: 4.126A pdb=" N VAL B 456 " --> pdb=" O SER B 452 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N PHE B 457 " --> pdb=" O PHE B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 472 removed outlier: 3.656A pdb=" N ARG B 463 " --> pdb=" O PRO B 460 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ALA B 464 " --> pdb=" O GLN B 461 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE B 465 " --> pdb=" O GLU B 462 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N THR B 467 " --> pdb=" O ALA B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 488 removed outlier: 3.756A pdb=" N ALA B 483 " --> pdb=" O SER B 479 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS B 484 " --> pdb=" O TYR B 480 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU B 486 " --> pdb=" O MET B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 505 removed outlier: 3.932A pdb=" N PHE B 502 " --> pdb=" O SER B 498 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TRP B 505 " --> pdb=" O THR B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 539 removed outlier: 3.540A pdb=" N GLY B 532 " --> pdb=" O LEU B 528 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU B 533 " --> pdb=" O ALA B 529 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY B 534 " --> pdb=" O SER B 530 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLY B 538 " --> pdb=" O GLY B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 548 Processing helix chain 'B' and resid 551 through 560 Processing helix chain 'B' and resid 574 through 579 Processing helix chain 'B' and resid 582 through 594 Processing helix chain 'B' and resid 599 through 603 Processing helix chain 'B' and resid 640 through 655 removed outlier: 3.548A pdb=" N LEU B 644 " --> pdb=" O GLY B 640 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG B 650 " --> pdb=" O PHE B 646 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 126 through 129 removed outlier: 5.552A pdb=" N VAL A 87 " --> pdb=" O ASP A 44 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 97 through 101 removed outlier: 6.778A pdb=" N THR A 277 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LEU A 100 " --> pdb=" O THR A 277 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU A 279 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N SER A 282 " --> pdb=" O CYS A 286 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N CYS A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 142 through 145 removed outlier: 6.477A pdb=" N LEU A 227 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N VAL A 145 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL A 229 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR A 259 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N LEU A 230 " --> pdb=" O THR A 259 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL A 261 " --> pdb=" O LEU A 230 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 46 through 50 removed outlier: 7.064A pdb=" N VAL A 49 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N THR A 82 " --> pdb=" O VAL A 49 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 126 through 129 removed outlier: 5.552A pdb=" N VAL B 87 " --> pdb=" O ASP B 44 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 97 through 101 removed outlier: 6.778A pdb=" N THR B 277 " --> pdb=" O ALA B 98 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N LEU B 100 " --> pdb=" O THR B 277 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU B 279 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N SER B 282 " --> pdb=" O CYS B 286 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N CYS B 286 " --> pdb=" O SER B 282 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 142 through 145 removed outlier: 6.477A pdb=" N LEU B 227 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N VAL B 145 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL B 229 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N THR B 259 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N LEU B 230 " --> pdb=" O THR B 259 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL B 261 " --> pdb=" O LEU B 230 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 46 through 50 removed outlier: 7.064A pdb=" N VAL B 49 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N THR B 82 " --> pdb=" O VAL B 49 " (cutoff:3.500A) 308 hydrogen bonds defined for protein. 858 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: 2.29 Time building geometry restraints manager: 3.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2103 1.33 - 1.45: 1737 1.45 - 1.57: 4894 1.57 - 1.69: 10 1.69 - 1.81: 86 Bond restraints: 8830 Sorted by residual: bond pdb=" C4 ATP B 701 " pdb=" C5 ATP B 701 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.51e+01 bond pdb=" C4 ATP A 701 " pdb=" C5 ATP A 701 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.33e+01 bond pdb=" C5 ATP A 701 " pdb=" C6 ATP A 701 " ideal model delta sigma weight residual 1.409 1.474 -0.065 1.00e-02 1.00e+04 4.17e+01 bond pdb=" C5 ATP B 701 " pdb=" C6 ATP B 701 " ideal model delta sigma weight residual 1.409 1.473 -0.064 1.00e-02 1.00e+04 4.13e+01 bond pdb=" C5 ATP B 701 " pdb=" N7 ATP B 701 " ideal model delta sigma weight residual 1.387 1.338 0.049 1.00e-02 1.00e+04 2.39e+01 ... (remaining 8825 not shown) Histogram of bond angle deviations from ideal: 98.49 - 105.98: 191 105.98 - 113.47: 5033 113.47 - 120.95: 4334 120.95 - 128.44: 2344 128.44 - 135.93: 78 Bond angle restraints: 11980 Sorted by residual: angle pdb=" PB ATP B 701 " pdb=" O3B ATP B 701 " pdb=" PG ATP B 701 " ideal model delta sigma weight residual 139.87 120.71 19.16 1.00e+00 1.00e+00 3.67e+02 angle pdb=" PB ATP A 701 " pdb=" O3B ATP A 701 " pdb=" PG ATP A 701 " ideal model delta sigma weight residual 139.87 120.72 19.15 1.00e+00 1.00e+00 3.67e+02 angle pdb=" PA ATP A 701 " pdb=" O3A ATP A 701 " pdb=" PB ATP A 701 " ideal model delta sigma weight residual 136.83 120.55 16.28 1.00e+00 1.00e+00 2.65e+02 angle pdb=" PA ATP B 701 " pdb=" O3A ATP B 701 " pdb=" PB ATP B 701 " ideal model delta sigma weight residual 136.83 120.55 16.28 1.00e+00 1.00e+00 2.65e+02 angle pdb=" C5 ATP B 701 " pdb=" C4 ATP B 701 " pdb=" N3 ATP B 701 " ideal model delta sigma weight residual 126.80 118.78 8.02 1.00e+00 1.00e+00 6.43e+01 ... (remaining 11975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 4683 18.00 - 36.00: 473 36.00 - 53.99: 48 53.99 - 71.99: 18 71.99 - 89.99: 4 Dihedral angle restraints: 5226 sinusoidal: 2074 harmonic: 3152 Sorted by residual: dihedral pdb=" CA GLY B 104 " pdb=" C GLY B 104 " pdb=" N SER B 105 " pdb=" CA SER B 105 " ideal model delta harmonic sigma weight residual -180.00 -154.46 -25.54 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA GLY A 104 " pdb=" C GLY A 104 " pdb=" N SER A 105 " pdb=" CA SER A 105 " ideal model delta harmonic sigma weight residual -180.00 -154.47 -25.53 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA GLY B 631 " pdb=" C GLY B 631 " pdb=" N ASP B 632 " pdb=" CA ASP B 632 " ideal model delta harmonic sigma weight residual 180.00 -156.31 -23.69 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 5223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1136 0.069 - 0.138: 247 0.138 - 0.208: 31 0.208 - 0.277: 8 0.277 - 0.346: 4 Chirality restraints: 1426 Sorted by residual: chirality pdb=" CB ILE A 129 " pdb=" CA ILE A 129 " pdb=" CG1 ILE A 129 " pdb=" CG2 ILE A 129 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CB ILE B 129 " pdb=" CA ILE B 129 " pdb=" CG1 ILE B 129 " pdb=" CG2 ILE B 129 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CB VAL B 199 " pdb=" CA VAL B 199 " pdb=" CG1 VAL B 199 " pdb=" CG2 VAL B 199 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.72e+00 ... (remaining 1423 not shown) Planarity restraints: 1452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 51 " -0.016 2.00e-02 2.50e+03 3.17e-02 1.00e+01 pdb=" C ILE A 51 " 0.055 2.00e-02 2.50e+03 pdb=" O ILE A 51 " -0.021 2.00e-02 2.50e+03 pdb=" N HIS A 52 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 51 " -0.016 2.00e-02 2.50e+03 3.15e-02 9.95e+00 pdb=" C ILE B 51 " 0.055 2.00e-02 2.50e+03 pdb=" O ILE B 51 " -0.021 2.00e-02 2.50e+03 pdb=" N HIS B 52 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 169 " 0.043 5.00e-02 4.00e+02 6.59e-02 6.94e+00 pdb=" N PRO A 170 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 170 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 170 " 0.036 5.00e-02 4.00e+02 ... (remaining 1449 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1981 2.78 - 3.31: 7642 3.31 - 3.84: 13661 3.84 - 4.37: 16720 4.37 - 4.90: 28814 Nonbonded interactions: 68818 Sorted by model distance: nonbonded pdb=" OG1 THR A 156 " pdb=" OE1 GLU A 159 " model vdw 2.249 2.440 nonbonded pdb=" OG1 THR B 156 " pdb=" OE1 GLU B 159 " model vdw 2.250 2.440 nonbonded pdb=" OH TYR A 578 " pdb=" OD2 ASP A 632 " model vdw 2.295 2.440 nonbonded pdb=" OH TYR B 578 " pdb=" OD2 ASP B 632 " model vdw 2.296 2.440 nonbonded pdb=" OE1 GLU B 469 " pdb=" OH TYR B 475 " model vdw 2.330 2.440 ... (remaining 68813 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 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: 5.930 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 26.760 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 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 : 0.008 0.075 8830 Z= 0.521 Angle : 1.189 19.156 11980 Z= 0.754 Chirality : 0.062 0.346 1426 Planarity : 0.007 0.066 1452 Dihedral : 14.311 89.989 3198 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 1.50 % Allowed : 6.94 % Favored : 91.56 % 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: -5.42 (0.18), residues: 1076 helix: -3.50 (0.13), residues: 614 sheet: -2.64 (0.44), residues: 80 loop : -3.65 (0.24), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 426 HIS 0.013 0.002 HIS B 52 PHE 0.020 0.002 PHE A 499 TYR 0.014 0.002 TYR A 594 ARG 0.003 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 124 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 ASP cc_start: 0.8413 (t0) cc_final: 0.8055 (t70) REVERT: A 462 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7553 (mm-30) REVERT: B 231 ASP cc_start: 0.8421 (t0) cc_final: 0.8062 (t70) REVERT: B 462 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7430 (mm-30) REVERT: B 546 LYS cc_start: 0.7629 (mttt) cc_final: 0.7397 (mttm) outliers start: 14 outliers final: 7 residues processed: 137 average time/residue: 0.2386 time to fit residues: 43.7809 Evaluate side-chains 94 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 87 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 342 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 8.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 0.4980 chunk 64 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 112 ASN A 395 HIS A 427 HIS B 52 HIS B 427 HIS B 567 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8830 Z= 0.193 Angle : 0.596 7.707 11980 Z= 0.314 Chirality : 0.041 0.191 1426 Planarity : 0.005 0.056 1452 Dihedral : 8.422 81.994 1264 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 0.75 % Allowed : 13.68 % Favored : 85.58 % 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: -3.60 (0.22), residues: 1076 helix: -2.00 (0.18), residues: 590 sheet: -2.66 (0.54), residues: 60 loop : -2.77 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 447 HIS 0.006 0.001 HIS A 52 PHE 0.012 0.001 PHE B 453 TYR 0.017 0.001 TYR B 152 ARG 0.004 0.000 ARG A 401 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 100 time to evaluate : 1.061 Fit side-chains REVERT: A 148 ASP cc_start: 0.8399 (OUTLIER) cc_final: 0.8192 (p0) REVERT: A 152 TYR cc_start: 0.8614 (m-80) cc_final: 0.7842 (m-80) REVERT: A 231 ASP cc_start: 0.8374 (t0) cc_final: 0.8036 (t70) REVERT: A 293 ARG cc_start: 0.6562 (mmt-90) cc_final: 0.6006 (mmp80) REVERT: A 315 PHE cc_start: 0.7316 (t80) cc_final: 0.6794 (t80) REVERT: A 462 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7121 (mm-30) REVERT: A 492 GLU cc_start: 0.7244 (tp30) cc_final: 0.6251 (tp30) REVERT: A 573 MET cc_start: 0.8510 (ttm) cc_final: 0.8226 (ttm) REVERT: B 152 TYR cc_start: 0.8690 (m-80) cc_final: 0.7957 (m-80) REVERT: B 231 ASP cc_start: 0.8393 (t0) cc_final: 0.8095 (t70) REVERT: B 462 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7133 (mm-30) REVERT: B 492 GLU cc_start: 0.7285 (tp30) cc_final: 0.6238 (tp30) REVERT: B 508 TYR cc_start: 0.7386 (t80) cc_final: 0.7062 (t80) REVERT: B 573 MET cc_start: 0.8436 (ttm) cc_final: 0.8162 (ttm) REVERT: B 645 MET cc_start: 0.7500 (mtt) cc_final: 0.7294 (mtt) outliers start: 7 outliers final: 4 residues processed: 106 average time/residue: 0.2227 time to fit residues: 32.9756 Evaluate side-chains 95 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 197 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 chunk 27 optimal weight: 20.0000 chunk 100 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 HIS ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 HIS B 273 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 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 : 0.009 0.066 8830 Z= 0.563 Angle : 0.778 7.798 11980 Z= 0.396 Chirality : 0.049 0.183 1426 Planarity : 0.005 0.055 1452 Dihedral : 8.970 81.558 1256 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 3.31 % Allowed : 14.74 % Favored : 81.94 % 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: -3.68 (0.22), residues: 1076 helix: -2.04 (0.18), residues: 606 sheet: -2.51 (0.55), residues: 62 loop : -2.87 (0.26), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 447 HIS 0.007 0.001 HIS B 219 PHE 0.021 0.002 PHE A 446 TYR 0.015 0.002 TYR A 565 ARG 0.003 0.000 ARG B 470 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 92 time to evaluate : 1.175 Fit side-chains REVERT: A 152 TYR cc_start: 0.8775 (m-80) cc_final: 0.8499 (m-80) REVERT: A 286 CYS cc_start: 0.8098 (p) cc_final: 0.7684 (p) REVERT: A 492 GLU cc_start: 0.7441 (tp30) cc_final: 0.6494 (tp30) REVERT: A 573 MET cc_start: 0.8546 (ttm) cc_final: 0.8137 (ttm) REVERT: B 152 TYR cc_start: 0.8812 (m-80) cc_final: 0.8564 (m-80) REVERT: B 492 GLU cc_start: 0.7460 (tp30) cc_final: 0.6476 (tp30) outliers start: 31 outliers final: 19 residues processed: 114 average time/residue: 0.2142 time to fit residues: 35.0133 Evaluate side-chains 104 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 85 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain B residue 36 PHE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 514 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 51 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 67 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 9.9990 chunk 52 optimal weight: 0.4980 chunk 95 optimal weight: 0.7980 chunk 28 optimal weight: 10.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN A 224 ASN A 273 GLN B 147 GLN B 395 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8830 Z= 0.157 Angle : 0.551 7.349 11980 Z= 0.287 Chirality : 0.040 0.141 1426 Planarity : 0.004 0.050 1452 Dihedral : 8.116 83.744 1256 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 1.82 % Allowed : 16.88 % Favored : 81.30 % 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: -2.59 (0.24), residues: 1076 helix: -1.07 (0.21), residues: 590 sheet: -2.38 (0.58), residues: 60 loop : -2.45 (0.27), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 447 HIS 0.004 0.001 HIS A 219 PHE 0.021 0.001 PHE A 315 TYR 0.006 0.001 TYR A 152 ARG 0.004 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 102 time to evaluate : 0.911 Fit side-chains REVERT: A 152 TYR cc_start: 0.8623 (m-80) cc_final: 0.8307 (m-80) REVERT: A 231 ASP cc_start: 0.8337 (t0) cc_final: 0.7998 (t70) REVERT: A 286 CYS cc_start: 0.7941 (p) cc_final: 0.7598 (p) REVERT: A 492 GLU cc_start: 0.7201 (tp30) cc_final: 0.6275 (tp30) REVERT: A 645 MET cc_start: 0.7398 (mtt) cc_final: 0.7183 (mtt) REVERT: B 137 GLN cc_start: 0.8844 (mp10) cc_final: 0.8609 (mp10) REVERT: B 152 TYR cc_start: 0.8655 (m-80) cc_final: 0.8387 (m-80) REVERT: B 231 ASP cc_start: 0.8385 (t0) cc_final: 0.8046 (t70) REVERT: B 237 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7650 (mt) REVERT: B 492 GLU cc_start: 0.7200 (tp30) cc_final: 0.6250 (tp30) REVERT: B 645 MET cc_start: 0.7459 (mtt) cc_final: 0.7222 (mtt) outliers start: 17 outliers final: 10 residues processed: 113 average time/residue: 0.1924 time to fit residues: 31.1200 Evaluate side-chains 102 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 91 time to evaluate : 2.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain B residue 36 PHE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 514 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 26 optimal weight: 20.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 ASN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 8830 Z= 0.500 Angle : 0.738 8.614 11980 Z= 0.371 Chirality : 0.048 0.302 1426 Planarity : 0.005 0.052 1452 Dihedral : 8.714 81.919 1256 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 3.21 % Allowed : 16.77 % Favored : 80.02 % 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: -2.94 (0.23), residues: 1076 helix: -1.42 (0.20), residues: 606 sheet: -2.51 (0.57), residues: 60 loop : -2.53 (0.27), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 447 HIS 0.008 0.001 HIS B 219 PHE 0.018 0.002 PHE A 446 TYR 0.013 0.002 TYR B 565 ARG 0.003 0.000 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 94 time to evaluate : 1.026 Fit side-chains REVERT: A 137 GLN cc_start: 0.8797 (mp10) cc_final: 0.8544 (mp10) REVERT: A 152 TYR cc_start: 0.8718 (m-80) cc_final: 0.8511 (m-80) REVERT: A 231 ASP cc_start: 0.8458 (t0) cc_final: 0.8029 (t0) REVERT: A 286 CYS cc_start: 0.8051 (p) cc_final: 0.7706 (p) REVERT: A 492 GLU cc_start: 0.7375 (tp30) cc_final: 0.6347 (tp30) REVERT: B 97 MET cc_start: 0.6548 (tpt) cc_final: 0.6154 (tpt) REVERT: B 137 GLN cc_start: 0.8809 (mp10) cc_final: 0.8553 (mp10) REVERT: B 152 TYR cc_start: 0.8731 (m-80) cc_final: 0.8483 (m-80) REVERT: B 231 ASP cc_start: 0.8478 (t0) cc_final: 0.8067 (t0) REVERT: B 286 CYS cc_start: 0.7981 (p) cc_final: 0.7577 (p) REVERT: B 492 GLU cc_start: 0.7361 (tp30) cc_final: 0.6332 (tp30) REVERT: B 599 GLU cc_start: 0.5651 (OUTLIER) cc_final: 0.5374 (pm20) outliers start: 30 outliers final: 25 residues processed: 117 average time/residue: 0.1699 time to fit residues: 29.5521 Evaluate side-chains 117 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 91 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 573 MET Chi-restraints excluded: chain B residue 36 PHE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 600 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.5980 chunk 95 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 62 optimal weight: 0.0980 chunk 26 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 102 optimal weight: 0.0770 overall best weight: 0.5140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN A 273 GLN B 147 GLN B 273 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8830 Z= 0.143 Angle : 0.554 7.973 11980 Z= 0.284 Chirality : 0.040 0.155 1426 Planarity : 0.004 0.048 1452 Dihedral : 7.982 83.790 1256 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 2.35 % Allowed : 17.95 % Favored : 79.70 % 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: -2.06 (0.25), residues: 1076 helix: -0.70 (0.21), residues: 592 sheet: -1.87 (0.50), residues: 80 loop : -2.15 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 447 HIS 0.003 0.001 HIS A 219 PHE 0.022 0.001 PHE A 315 TYR 0.005 0.001 TYR B 564 ARG 0.003 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 102 time to evaluate : 1.090 Fit side-chains REVERT: A 137 GLN cc_start: 0.8832 (mp10) cc_final: 0.8585 (mp10) REVERT: A 152 TYR cc_start: 0.8642 (m-80) cc_final: 0.8382 (m-80) REVERT: A 231 ASP cc_start: 0.8337 (t0) cc_final: 0.7988 (t70) REVERT: A 286 CYS cc_start: 0.7895 (p) cc_final: 0.7572 (p) REVERT: A 492 GLU cc_start: 0.7228 (tp30) cc_final: 0.6266 (tp30) REVERT: B 137 GLN cc_start: 0.8833 (mp10) cc_final: 0.8592 (mp10) REVERT: B 152 TYR cc_start: 0.8644 (m-80) cc_final: 0.8398 (m-80) REVERT: B 231 ASP cc_start: 0.8405 (t0) cc_final: 0.8063 (t70) REVERT: B 286 CYS cc_start: 0.7859 (p) cc_final: 0.7548 (p) REVERT: B 492 GLU cc_start: 0.7298 (tp30) cc_final: 0.6292 (tp30) REVERT: B 645 MET cc_start: 0.7502 (mtt) cc_final: 0.7253 (mtt) outliers start: 22 outliers final: 17 residues processed: 120 average time/residue: 0.2222 time to fit residues: 39.8232 Evaluate side-chains 112 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 95 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain B residue 36 PHE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 600 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 106 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8830 Z= 0.204 Angle : 0.575 10.478 11980 Z= 0.290 Chirality : 0.041 0.148 1426 Planarity : 0.004 0.049 1452 Dihedral : 7.859 83.518 1256 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 2.46 % Allowed : 18.48 % Favored : 79.06 % 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: -1.76 (0.25), residues: 1076 helix: -0.46 (0.22), residues: 592 sheet: -1.74 (0.51), residues: 80 loop : -2.00 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 447 HIS 0.004 0.001 HIS A 219 PHE 0.025 0.001 PHE A 315 TYR 0.007 0.001 TYR A 584 ARG 0.003 0.000 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 99 time to evaluate : 1.003 Fit side-chains REVERT: A 137 GLN cc_start: 0.8825 (mp10) cc_final: 0.8577 (mp10) REVERT: A 152 TYR cc_start: 0.8664 (m-80) cc_final: 0.8416 (m-80) REVERT: A 226 SER cc_start: 0.7802 (t) cc_final: 0.7571 (t) REVERT: A 231 ASP cc_start: 0.8313 (t0) cc_final: 0.7983 (t70) REVERT: A 286 CYS cc_start: 0.7916 (p) cc_final: 0.7579 (p) REVERT: A 492 GLU cc_start: 0.7251 (tp30) cc_final: 0.6256 (tp30) REVERT: B 152 TYR cc_start: 0.8645 (m-80) cc_final: 0.8387 (m-80) REVERT: B 226 SER cc_start: 0.7960 (t) cc_final: 0.7738 (t) REVERT: B 231 ASP cc_start: 0.8368 (t0) cc_final: 0.8043 (t70) REVERT: B 286 CYS cc_start: 0.7858 (p) cc_final: 0.7498 (p) REVERT: B 492 GLU cc_start: 0.7246 (tp30) cc_final: 0.6258 (tp30) REVERT: B 645 MET cc_start: 0.7535 (mtt) cc_final: 0.7295 (mtt) outliers start: 23 outliers final: 21 residues processed: 118 average time/residue: 0.1740 time to fit residues: 30.3550 Evaluate side-chains 113 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 92 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain B residue 36 PHE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 600 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 72 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 GLN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 GLN B 403 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8830 Z= 0.331 Angle : 0.648 13.153 11980 Z= 0.322 Chirality : 0.044 0.156 1426 Planarity : 0.004 0.050 1452 Dihedral : 8.157 82.216 1256 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 2.99 % Allowed : 18.70 % Favored : 78.31 % 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: -1.88 (0.25), residues: 1076 helix: -0.61 (0.21), residues: 594 sheet: -1.87 (0.52), residues: 80 loop : -1.95 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 447 HIS 0.006 0.001 HIS B 219 PHE 0.021 0.001 PHE A 315 TYR 0.011 0.001 TYR A 584 ARG 0.002 0.000 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 93 time to evaluate : 1.063 Fit side-chains REVERT: A 152 TYR cc_start: 0.8671 (m-80) cc_final: 0.8404 (m-80) REVERT: A 226 SER cc_start: 0.7792 (t) cc_final: 0.7570 (t) REVERT: A 231 ASP cc_start: 0.8298 (t0) cc_final: 0.7989 (t70) REVERT: A 286 CYS cc_start: 0.7973 (p) cc_final: 0.7652 (p) REVERT: A 492 GLU cc_start: 0.7294 (tp30) cc_final: 0.6323 (tp30) REVERT: B 152 TYR cc_start: 0.8675 (m-80) cc_final: 0.8396 (m-80) REVERT: B 226 SER cc_start: 0.7929 (t) cc_final: 0.7697 (t) REVERT: B 231 ASP cc_start: 0.8312 (t0) cc_final: 0.8014 (t70) REVERT: B 286 CYS cc_start: 0.7869 (p) cc_final: 0.7512 (p) REVERT: B 492 GLU cc_start: 0.7301 (tp30) cc_final: 0.6301 (tp30) REVERT: B 573 MET cc_start: 0.8399 (ttt) cc_final: 0.8145 (ttt) outliers start: 28 outliers final: 26 residues processed: 116 average time/residue: 0.1723 time to fit residues: 29.6840 Evaluate side-chains 116 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 90 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain B residue 36 PHE Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 600 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 77 optimal weight: 0.2980 chunk 30 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 63 optimal weight: 8.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN A 273 GLN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8830 Z= 0.201 Angle : 0.571 11.881 11980 Z= 0.287 Chirality : 0.041 0.144 1426 Planarity : 0.004 0.048 1452 Dihedral : 7.861 83.159 1256 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 3.10 % Allowed : 18.80 % Favored : 78.10 % 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: -1.51 (0.26), residues: 1076 helix: -0.28 (0.22), residues: 590 sheet: -1.81 (0.53), residues: 80 loop : -1.78 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 447 HIS 0.004 0.001 HIS A 219 PHE 0.022 0.001 PHE A 315 TYR 0.009 0.001 TYR A 584 ARG 0.002 0.000 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 98 time to evaluate : 0.996 Fit side-chains REVERT: A 152 TYR cc_start: 0.8640 (m-80) cc_final: 0.8383 (m-80) REVERT: A 220 GLU cc_start: 0.6902 (OUTLIER) cc_final: 0.6135 (mp0) REVERT: A 226 SER cc_start: 0.7876 (t) cc_final: 0.7674 (t) REVERT: A 231 ASP cc_start: 0.8293 (t0) cc_final: 0.7973 (t70) REVERT: A 286 CYS cc_start: 0.7928 (p) cc_final: 0.7686 (p) REVERT: A 492 GLU cc_start: 0.7252 (tp30) cc_final: 0.6122 (tp30) REVERT: B 152 TYR cc_start: 0.8646 (m-80) cc_final: 0.8391 (m-80) REVERT: B 226 SER cc_start: 0.8002 (t) cc_final: 0.7783 (t) REVERT: B 231 ASP cc_start: 0.8309 (t0) cc_final: 0.7970 (t70) REVERT: B 286 CYS cc_start: 0.7855 (p) cc_final: 0.7540 (p) REVERT: B 492 GLU cc_start: 0.7249 (tp30) cc_final: 0.6230 (tp30) outliers start: 29 outliers final: 21 residues processed: 123 average time/residue: 0.1723 time to fit residues: 31.5726 Evaluate side-chains 119 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 97 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain B residue 36 PHE Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 600 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 109 optimal weight: 0.0470 chunk 100 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 69 optimal weight: 0.0070 chunk 92 optimal weight: 6.9990 chunk 26 optimal weight: 20.0000 overall best weight: 0.9500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8830 Z= 0.195 Angle : 0.576 12.022 11980 Z= 0.286 Chirality : 0.041 0.141 1426 Planarity : 0.004 0.048 1452 Dihedral : 7.702 83.070 1256 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 2.67 % Allowed : 19.34 % Favored : 77.99 % 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: -1.34 (0.26), residues: 1076 helix: -0.14 (0.22), residues: 590 sheet: -1.71 (0.53), residues: 80 loop : -1.71 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 447 HIS 0.004 0.001 HIS A 219 PHE 0.021 0.001 PHE A 315 TYR 0.009 0.001 TYR A 584 ARG 0.002 0.000 ARG A 180 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 95 time to evaluate : 1.037 Fit side-chains REVERT: A 152 TYR cc_start: 0.8632 (m-80) cc_final: 0.8379 (m-80) REVERT: A 220 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.6121 (mp0) REVERT: A 226 SER cc_start: 0.7819 (t) cc_final: 0.7585 (t) REVERT: A 231 ASP cc_start: 0.8238 (t0) cc_final: 0.7909 (t70) REVERT: A 492 GLU cc_start: 0.7180 (tp30) cc_final: 0.6265 (tp30) REVERT: B 152 TYR cc_start: 0.8637 (m-80) cc_final: 0.8397 (m-80) REVERT: B 226 SER cc_start: 0.8001 (t) cc_final: 0.7791 (t) REVERT: B 231 ASP cc_start: 0.8247 (t0) cc_final: 0.7927 (t70) REVERT: B 286 CYS cc_start: 0.7851 (p) cc_final: 0.7541 (p) REVERT: B 492 GLU cc_start: 0.7184 (tp30) cc_final: 0.6171 (tp30) outliers start: 25 outliers final: 22 residues processed: 116 average time/residue: 0.1775 time to fit residues: 30.3854 Evaluate side-chains 112 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 89 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain B residue 36 PHE Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 600 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 11 optimal weight: 0.0870 chunk 16 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.157408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.116899 restraints weight = 10677.751| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.91 r_work: 0.3317 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8830 Z= 0.167 Angle : 0.562 11.232 11980 Z= 0.279 Chirality : 0.040 0.138 1426 Planarity : 0.004 0.048 1452 Dihedral : 7.571 83.365 1256 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 2.56 % Allowed : 19.44 % Favored : 77.99 % 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: -1.17 (0.26), residues: 1076 helix: -0.00 (0.22), residues: 590 sheet: -1.72 (0.54), residues: 80 loop : -1.63 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 447 HIS 0.004 0.000 HIS B 219 PHE 0.020 0.001 PHE A 315 TYR 0.008 0.001 TYR A 584 ARG 0.002 0.000 ARG A 180 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1977.04 seconds wall clock time: 36 minutes 52.07 seconds (2212.07 seconds total)