Starting phenix.real_space_refine on Sun Jul 21 06:38:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ai5_11791/07_2024/7ai5_11791.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ai5_11791/07_2024/7ai5_11791.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ai5_11791/07_2024/7ai5_11791.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ai5_11791/07_2024/7ai5_11791.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ai5_11791/07_2024/7ai5_11791.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ai5_11791/07_2024/7ai5_11791.cif" } resolution = 4.4 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= 0.016 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 50 5.49 5 S 58 5.16 5 C 8258 2.51 5 N 2382 2.21 5 O 2628 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 193": "NH1" <-> "NH2" Residue "A PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 261": "OE1" <-> "OE2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 454": "OE1" <-> "OE2" Residue "A GLU 505": "OE1" <-> "OE2" Residue "A TYR 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 582": "OE1" <-> "OE2" Residue "A PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 693": "OD1" <-> "OD2" Residue "A PHE 725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 730": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 193": "NH1" <-> "NH2" Residue "B PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 261": "OE1" <-> "OE2" Residue "B PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "B TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 454": "OE1" <-> "OE2" Residue "B GLU 505": "OE1" <-> "OE2" Residue "B GLU 582": "OE1" <-> "OE2" Residue "B PHE 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 693": "OD1" <-> "OD2" Residue "B GLU 694": "OE1" <-> "OE2" Residue "B ASP 703": "OD1" <-> "OD2" Residue "B PHE 725": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 13376 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 788, 6206 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 35, 'TRANS': 752} Chain breaks: 1 Chain: "B" Number of atoms: 6206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 788, 6206 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 35, 'TRANS': 752} Chain breaks: 1 Chain: "C" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 457 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "D" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 445 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} 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: 7.79, per 1000 atoms: 0.58 Number of scatterers: 13376 At special positions: 0 Unit cell: (127.53, 128.7, 115.83, 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 58 16.00 P 50 15.00 O 2628 8.00 N 2382 7.00 C 8258 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.32 Conformation dependent library (CDL) restraints added in 2.4 seconds 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2952 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 14 sheets defined 51.3% alpha, 13.0% beta 22 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 4.72 Creating SS restraints... Processing helix chain 'A' and resid 11 through 24 removed outlier: 3.682A pdb=" N HIS A 24 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 51 Processing helix chain 'A' and resid 75 through 86 removed outlier: 3.824A pdb=" N TYR A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 125 Processing helix chain 'A' and resid 162 through 174 Processing helix chain 'A' and resid 186 through 191 removed outlier: 4.257A pdb=" N ILE A 190 " --> pdb=" O GLU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 204 Processing helix chain 'A' and resid 205 through 218 removed outlier: 3.646A pdb=" N ALA A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 226 Processing helix chain 'A' and resid 230 through 249 removed outlier: 3.597A pdb=" N LEU A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA A 236 " --> pdb=" O ARG A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 266 Processing helix chain 'A' and resid 270 through 277 Processing helix chain 'A' and resid 290 through 296 removed outlier: 3.843A pdb=" N VAL A 294 " --> pdb=" O THR A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 313 Processing helix chain 'A' and resid 317 through 332 removed outlier: 3.889A pdb=" N LEU A 321 " --> pdb=" O ASP A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 344 Proline residue: A 340 - end of helix removed outlier: 3.927A pdb=" N GLN A 344 " --> pdb=" O PRO A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 357 Processing helix chain 'A' and resid 361 through 385 removed outlier: 3.657A pdb=" N ARG A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) Proline residue: A 376 - end of helix removed outlier: 3.796A pdb=" N THR A 384 " --> pdb=" O ALA A 380 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL A 385 " --> pdb=" O GLN A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 398 removed outlier: 3.506A pdb=" N GLN A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 411 Processing helix chain 'A' and resid 430 through 442 removed outlier: 3.899A pdb=" N LEU A 439 " --> pdb=" O GLU A 435 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA A 440 " --> pdb=" O TRP A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 459 removed outlier: 3.901A pdb=" N TYR A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU A 447 " --> pdb=" O ALA A 443 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLU A 448 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG A 455 " --> pdb=" O GLU A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 536 removed outlier: 3.848A pdb=" N PHE A 532 " --> pdb=" O TYR A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 565 removed outlier: 4.215A pdb=" N GLU A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU A 555 " --> pdb=" O GLU A 551 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A 559 " --> pdb=" O LEU A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 591 Processing helix chain 'A' and resid 621 through 635 removed outlier: 3.848A pdb=" N THR A 627 " --> pdb=" O TYR A 623 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR A 635 " --> pdb=" O ALA A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 684 removed outlier: 3.730A pdb=" N THR A 675 " --> pdb=" O MET A 671 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU A 676 " --> pdb=" O VAL A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 716 removed outlier: 3.943A pdb=" N SER A 706 " --> pdb=" O TYR A 702 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ALA A 710 " --> pdb=" O SER A 706 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU A 713 " --> pdb=" O TRP A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 739 removed outlier: 3.563A pdb=" N LYS A 738 " --> pdb=" O GLN A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 776 removed outlier: 4.078A pdb=" N ALA A 774 " --> pdb=" O SER A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 800 Processing helix chain 'B' and resid 11 through 24 removed outlier: 3.698A pdb=" N HIS B 24 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 51 Processing helix chain 'B' and resid 72 through 74 No H-bonds generated for 'chain 'B' and resid 72 through 74' Processing helix chain 'B' and resid 75 through 86 removed outlier: 3.816A pdb=" N TYR B 79 " --> pdb=" O ALA B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 125 Processing helix chain 'B' and resid 162 through 174 Processing helix chain 'B' and resid 186 through 191 removed outlier: 4.323A pdb=" N ILE B 190 " --> pdb=" O GLU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 204 Processing helix chain 'B' and resid 205 through 218 removed outlier: 3.638A pdb=" N ALA B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 226 Processing helix chain 'B' and resid 230 through 249 removed outlier: 3.598A pdb=" N LEU B 234 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA B 236 " --> pdb=" O ARG B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 266 Processing helix chain 'B' and resid 270 through 277 removed outlier: 3.590A pdb=" N ASN B 276 " --> pdb=" O ALA B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 296 Processing helix chain 'B' and resid 300 through 313 Processing helix chain 'B' and resid 317 through 332 removed outlier: 3.883A pdb=" N LEU B 321 " --> pdb=" O ASP B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 344 Proline residue: B 340 - end of helix removed outlier: 3.948A pdb=" N GLN B 344 " --> pdb=" O PRO B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 357 Processing helix chain 'B' and resid 361 through 385 removed outlier: 3.664A pdb=" N ARG B 367 " --> pdb=" O ARG B 363 " (cutoff:3.500A) Proline residue: B 376 - end of helix removed outlier: 3.806A pdb=" N THR B 384 " --> pdb=" O ALA B 380 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL B 385 " --> pdb=" O GLN B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 398 removed outlier: 3.532A pdb=" N GLN B 391 " --> pdb=" O SER B 387 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY B 398 " --> pdb=" O ARG B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 411 Processing helix chain 'B' and resid 430 through 442 removed outlier: 3.955A pdb=" N LEU B 439 " --> pdb=" O GLU B 435 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA B 440 " --> pdb=" O TRP B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 459 removed outlier: 3.887A pdb=" N TYR B 446 " --> pdb=" O GLY B 442 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU B 447 " --> pdb=" O ALA B 443 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU B 448 " --> pdb=" O THR B 444 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG B 455 " --> pdb=" O GLU B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 536 removed outlier: 3.847A pdb=" N PHE B 532 " --> pdb=" O TYR B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 566 removed outlier: 4.299A pdb=" N GLU B 551 " --> pdb=" O SER B 547 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU B 555 " --> pdb=" O GLU B 551 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA B 559 " --> pdb=" O LEU B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 591 Processing helix chain 'B' and resid 621 through 635 removed outlier: 3.659A pdb=" N THR B 627 " --> pdb=" O TYR B 623 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR B 635 " --> pdb=" O ALA B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 684 removed outlier: 3.725A pdb=" N THR B 675 " --> pdb=" O MET B 671 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU B 676 " --> pdb=" O VAL B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 716 removed outlier: 3.850A pdb=" N ALA B 710 " --> pdb=" O SER B 706 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU B 713 " --> pdb=" O TRP B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 733 No H-bonds generated for 'chain 'B' and resid 731 through 733' Processing helix chain 'B' and resid 734 through 739 removed outlier: 3.577A pdb=" N LYS B 738 " --> pdb=" O GLN B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 776 removed outlier: 4.045A pdb=" N ALA B 774 " --> pdb=" O SER B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 800 removed outlier: 3.613A pdb=" N SER B 800 " --> pdb=" O LEU B 796 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 58 removed outlier: 4.310A pdb=" N ILE A 66 " --> pdb=" O ARG A 58 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A 71 " --> pdb=" O TYR A 37 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR A 31 " --> pdb=" O GLU A 38 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N PHE A 40 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N LEU A 29 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU A 28 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N CYS A 93 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N PHE A 30 " --> pdb=" O CYS A 93 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N GLN A 95 " --> pdb=" O PHE A 30 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N ARG A 32 " --> pdb=" O GLN A 95 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLU A 94 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N VAL A 110 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 196 through 199 removed outlier: 6.630A pdb=" N LEU A 178 " --> pdb=" O ARG A 197 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ARG A 199 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TYR A 180 " --> pdb=" O ARG A 199 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ALA A 134 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 9.173A pdb=" N ALA A 181 " --> pdb=" O ALA A 134 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N ILE A 136 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 135 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N PHE A 155 " --> pdb=" O THR A 259 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 268 through 269 removed outlier: 6.952A pdb=" N ILE A 268 " --> pdb=" O ILE A 653 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N THR A 655 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ARG A 652 " --> pdb=" O LEU A 689 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N LEU A 691 " --> pdb=" O ARG A 652 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N PHE A 654 " --> pdb=" O LEU A 691 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 464 through 468 removed outlier: 3.641A pdb=" N GLY A 466 " --> pdb=" O TYR A 474 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ALA A 498 " --> pdb=" O THR A 494 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N THR A 494 " --> pdb=" O ALA A 498 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ARG A 500 " --> pdb=" O ARG A 492 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 571 through 572 removed outlier: 6.886A pdb=" N THR A 571 " --> pdb=" O ILE A 647 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS A 644 " --> pdb=" O THR A 581 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLU A 582 " --> pdb=" O ASN A 599 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ASN A 599 " --> pdb=" O GLU A 582 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 609 through 613 removed outlier: 6.790A pdb=" N MET A 609 " --> pdb=" O ALA A 743 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N VAL A 745 " --> pdb=" O MET A 609 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ILE A 611 " --> pdb=" O VAL A 745 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N LEU A 747 " --> pdb=" O ILE A 611 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N THR A 613 " --> pdb=" O LEU A 747 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ALA A 749 " --> pdb=" O THR A 613 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ASN A 744 " --> pdb=" O GLN A 763 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N GLN A 763 " --> pdb=" O ASN A 744 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N HIS A 746 " --> pdb=" O SER A 761 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N SER A 761 " --> pdb=" O HIS A 746 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ASP A 748 " --> pdb=" O MET A 759 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N MET A 759 " --> pdb=" O ASP A 748 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS A 752 " --> pdb=" O THR A 755 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR A 755 " --> pdb=" O HIS A 752 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 28 through 31 removed outlier: 6.273A pdb=" N GLU B 94 " --> pdb=" O VAL B 110 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N VAL B 110 " --> pdb=" O GLU B 94 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 39 through 40 removed outlier: 3.909A pdb=" N ILE B 66 " --> pdb=" O ARG B 58 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 196 through 199 removed outlier: 6.619A pdb=" N LEU B 178 " --> pdb=" O ARG B 197 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ARG B 199 " --> pdb=" O LEU B 178 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N TYR B 180 " --> pdb=" O ARG B 199 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA B 134 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 9.212A pdb=" N ALA B 181 " --> pdb=" O ALA B 134 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N ILE B 136 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA B 135 " --> pdb=" O ALA B 146 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TRP B 137 " --> pdb=" O GLY B 144 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N PHE B 155 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 464 through 468 removed outlier: 3.649A pdb=" N GLY B 466 " --> pdb=" O TYR B 474 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ALA B 498 " --> pdb=" O THR B 494 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N THR B 494 " --> pdb=" O ALA B 498 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ARG B 500 " --> pdb=" O ARG B 492 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 571 through 572 removed outlier: 6.816A pdb=" N THR B 571 " --> pdb=" O ILE B 647 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS B 644 " --> pdb=" O THR B 581 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLU B 582 " --> pdb=" O ASN B 599 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ASN B 599 " --> pdb=" O GLU B 582 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 609 through 613 removed outlier: 6.792A pdb=" N MET B 609 " --> pdb=" O ALA B 743 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL B 745 " --> pdb=" O MET B 609 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ILE B 611 " --> pdb=" O VAL B 745 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU B 747 " --> pdb=" O ILE B 611 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N THR B 613 " --> pdb=" O LEU B 747 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 652 through 657 removed outlier: 6.313A pdb=" N ARG B 652 " --> pdb=" O LEU B 689 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N LEU B 691 " --> pdb=" O ARG B 652 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N PHE B 654 " --> pdb=" O LEU B 691 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ASP B 693 " --> pdb=" O PHE B 654 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ARG B 656 " --> pdb=" O ASP B 693 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 750 through 752 removed outlier: 3.546A pdb=" N HIS B 752 " --> pdb=" O THR B 755 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR B 755 " --> pdb=" O HIS B 752 " (cutoff:3.500A) 573 hydrogen bonds defined for protein. 1602 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 56 hydrogen bonds 112 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 4.78 Time building geometry restraints manager: 5.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2168 1.30 - 1.44: 3618 1.44 - 1.58: 7714 1.58 - 1.72: 96 1.72 - 1.86: 104 Bond restraints: 13700 Sorted by residual: bond pdb=" C ILE A 650 " pdb=" O ILE A 650 " ideal model delta sigma weight residual 1.236 1.317 -0.080 1.04e-02 9.25e+03 5.99e+01 bond pdb=" C ILE A 636 " pdb=" O ILE A 636 " ideal model delta sigma weight residual 1.242 1.309 -0.067 1.13e-02 7.83e+03 3.55e+01 bond pdb=" C THR A 685 " pdb=" O THR A 685 " ideal model delta sigma weight residual 1.238 1.177 0.061 1.06e-02 8.90e+03 3.26e+01 bond pdb=" C PRO A 175 " pdb=" O PRO A 175 " ideal model delta sigma weight residual 1.235 1.165 0.070 1.30e-02 5.92e+03 2.87e+01 bond pdb=" C GLY A 780 " pdb=" O GLY A 780 " ideal model delta sigma weight residual 1.232 1.283 -0.051 1.03e-02 9.43e+03 2.49e+01 ... (remaining 13695 not shown) Histogram of bond angle deviations from ideal: 96.62 - 104.25: 353 104.25 - 111.87: 5856 111.87 - 119.50: 7037 119.50 - 127.13: 5304 127.13 - 134.76: 196 Bond angle restraints: 18746 Sorted by residual: angle pdb=" PB ATP B 901 " pdb=" O3B ATP B 901 " pdb=" PG ATP B 901 " ideal model delta sigma weight residual 139.87 131.11 8.76 1.00e+00 1.00e+00 7.67e+01 angle pdb=" C PRO A 615 " pdb=" CA PRO A 615 " pdb=" CB PRO A 615 " ideal model delta sigma weight residual 110.98 99.55 11.43 1.31e+00 5.83e-01 7.61e+01 angle pdb=" PB ATP A 901 " pdb=" O3B ATP A 901 " pdb=" PG ATP A 901 " ideal model delta sigma weight residual 139.87 131.37 8.50 1.00e+00 1.00e+00 7.23e+01 angle pdb=" CA PHE A 155 " pdb=" CB PHE A 155 " pdb=" CG PHE A 155 " ideal model delta sigma weight residual 113.80 121.58 -7.78 1.00e+00 1.00e+00 6.05e+01 angle pdb=" N SER A 621 " pdb=" CA SER A 621 " pdb=" C SER A 621 " ideal model delta sigma weight residual 111.14 119.34 -8.20 1.08e+00 8.57e-01 5.76e+01 ... (remaining 18741 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 7149 17.99 - 35.97: 713 35.97 - 53.96: 336 53.96 - 71.95: 78 71.95 - 89.93: 22 Dihedral angle restraints: 8298 sinusoidal: 3722 harmonic: 4576 Sorted by residual: dihedral pdb=" C THR A 273 " pdb=" N THR A 273 " pdb=" CA THR A 273 " pdb=" CB THR A 273 " ideal model delta harmonic sigma weight residual -122.00 -109.90 -12.10 0 2.50e+00 1.60e-01 2.34e+01 dihedral pdb=" C PRO A 615 " pdb=" N PRO A 615 " pdb=" CA PRO A 615 " pdb=" CB PRO A 615 " ideal model delta harmonic sigma weight residual -120.70 -108.69 -12.01 0 2.50e+00 1.60e-01 2.31e+01 dihedral pdb=" C ASN B 593 " pdb=" N ASN B 593 " pdb=" CA ASN B 593 " pdb=" CB ASN B 593 " ideal model delta harmonic sigma weight residual -122.60 -111.92 -10.68 0 2.50e+00 1.60e-01 1.82e+01 ... (remaining 8295 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1228 0.088 - 0.177: 731 0.177 - 0.265: 139 0.265 - 0.353: 21 0.353 - 0.442: 3 Chirality restraints: 2122 Sorted by residual: chirality pdb=" CB VAL A 640 " pdb=" CA VAL A 640 " pdb=" CG1 VAL A 640 " pdb=" CG2 VAL A 640 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.44 2.00e-01 2.50e+01 4.87e+00 chirality pdb=" CA ALA A 766 " pdb=" N ALA A 766 " pdb=" C ALA A 766 " pdb=" CB ALA A 766 " both_signs ideal model delta sigma weight residual False 2.48 2.87 -0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CA VAL B 657 " pdb=" N VAL B 657 " pdb=" C VAL B 657 " pdb=" CB VAL B 657 " both_signs ideal model delta sigma weight residual False 2.44 2.81 -0.37 2.00e-01 2.50e+01 3.36e+00 ... (remaining 2119 not shown) Planarity restraints: 2288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 635 " 0.021 2.00e-02 2.50e+03 3.60e-02 2.59e+01 pdb=" CG TYR A 635 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 635 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR A 635 " -0.072 2.00e-02 2.50e+03 pdb=" CE1 TYR A 635 " -0.037 2.00e-02 2.50e+03 pdb=" CE2 TYR A 635 " 0.028 2.00e-02 2.50e+03 pdb=" CZ TYR A 635 " 0.041 2.00e-02 2.50e+03 pdb=" OH TYR A 635 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 132 " 0.022 2.00e-02 2.50e+03 4.59e-02 2.10e+01 pdb=" C LEU A 132 " -0.079 2.00e-02 2.50e+03 pdb=" O LEU A 132 " 0.029 2.00e-02 2.50e+03 pdb=" N LEU A 133 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 309 " -0.020 2.00e-02 2.50e+03 4.20e-02 1.76e+01 pdb=" C ARG A 309 " 0.073 2.00e-02 2.50e+03 pdb=" O ARG A 309 " -0.027 2.00e-02 2.50e+03 pdb=" N TRP A 310 " -0.025 2.00e-02 2.50e+03 ... (remaining 2285 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.96: 5547 2.96 - 3.44: 13307 3.44 - 3.93: 22952 3.93 - 4.41: 26036 4.41 - 4.90: 40766 Nonbonded interactions: 108608 Sorted by model distance: nonbonded pdb=" N ASN B 616 " pdb=" O ASN B 616 " model vdw 2.472 2.496 nonbonded pdb=" OD1 ASP B 296 " pdb=" OG1 THR B 298 " model vdw 2.479 2.440 nonbonded pdb=" O ASP B 98 " pdb=" OG1 THR B 101 " model vdw 2.484 2.440 nonbonded pdb=" N GLU A 731 " pdb=" OE1 GLU A 731 " model vdw 2.511 2.520 nonbonded pdb=" N TYR A 702 " pdb=" N ASP A 703 " model vdw 2.521 2.560 ... (remaining 108603 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 40.910 Find NCS groups from input model: 0.480 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: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 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 : 0.014 0.080 13700 Z= 0.918 Angle : 1.846 11.431 18746 Z= 1.375 Chirality : 0.104 0.442 2122 Planarity : 0.008 0.054 2288 Dihedral : 18.260 89.933 5346 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.14 % Allowed : 9.60 % Favored : 89.25 % Cbeta Deviations : 0.34 % 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: -2.02 (0.18), residues: 1568 helix: -0.83 (0.18), residues: 665 sheet: -1.88 (0.36), residues: 137 loop : -1.65 (0.19), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.005 TRP A 310 HIS 0.040 0.006 HIS A 728 PHE 0.070 0.006 PHE A 36 TYR 0.072 0.007 TYR A 635 ARG 0.032 0.002 ARG A 652 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 289 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 MET cc_start: 0.8196 (mmm) cc_final: 0.7995 (mmm) REVERT: A 187 MET cc_start: 0.8972 (mmm) cc_final: 0.8043 (mmt) REVERT: A 269 MET cc_start: 0.7066 (mtm) cc_final: 0.6796 (mmm) REVERT: A 365 LEU cc_start: 0.9282 (mt) cc_final: 0.8913 (mm) REVERT: A 574 ASP cc_start: 0.8482 (m-30) cc_final: 0.7958 (p0) REVERT: A 674 MET cc_start: 0.8911 (mmm) cc_final: 0.8247 (mmt) REVERT: A 686 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8191 (tp30) REVERT: A 730 PHE cc_start: 0.8007 (t80) cc_final: 0.7600 (t80) REVERT: B 88 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8122 (mm-30) REVERT: B 171 GLN cc_start: 0.9430 (tt0) cc_final: 0.9137 (tt0) REVERT: B 173 THR cc_start: 0.8876 (p) cc_final: 0.8181 (p) REVERT: B 258 ILE cc_start: 0.9151 (tt) cc_final: 0.8771 (tt) REVERT: B 441 ASP cc_start: 0.7806 (m-30) cc_final: 0.7556 (p0) REVERT: B 603 LEU cc_start: 0.8852 (mt) cc_final: 0.8558 (mm) REVERT: B 616 ASN cc_start: 0.8846 (OUTLIER) cc_final: 0.8520 (m-40) REVERT: B 633 MET cc_start: 0.8694 (mtm) cc_final: 0.8270 (mtm) REVERT: B 703 ASP cc_start: 0.8564 (t70) cc_final: 0.7946 (t70) REVERT: B 730 PHE cc_start: 0.7229 (t80) cc_final: 0.6938 (t80) REVERT: B 732 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8237 (mt) outliers start: 15 outliers final: 3 residues processed: 300 average time/residue: 0.3181 time to fit residues: 128.7833 Evaluate side-chains 160 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 155 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 8.9990 chunk 121 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 64 optimal weight: 0.8980 chunk 125 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 76 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 145 optimal weight: 0.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN A 276 ASN ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN A 606 GLN A 683 ASN ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 ASN B 683 ASN ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 13700 Z= 0.249 Angle : 0.665 6.705 18746 Z= 0.358 Chirality : 0.044 0.219 2122 Planarity : 0.005 0.072 2288 Dihedral : 18.323 88.881 2292 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.23 % Allowed : 2.52 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.20), residues: 1568 helix: 0.53 (0.19), residues: 724 sheet: -1.40 (0.32), residues: 193 loop : -1.29 (0.22), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 137 HIS 0.006 0.001 HIS B 370 PHE 0.026 0.002 PHE A 372 TYR 0.020 0.002 TYR A 528 ARG 0.009 0.001 ARG B 579 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 177 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 ASP cc_start: 0.8477 (m-30) cc_final: 0.7754 (p0) REVERT: A 674 MET cc_start: 0.9024 (mmm) cc_final: 0.8251 (mmt) REVERT: A 744 ASN cc_start: 0.8993 (t0) cc_final: 0.8764 (t0) REVERT: A 771 TYR cc_start: 0.8331 (p90) cc_final: 0.7877 (p90) REVERT: B 68 MET cc_start: 0.4503 (tmm) cc_final: 0.3599 (tmm) REVERT: B 128 ARG cc_start: 0.6431 (mtt180) cc_final: 0.5996 (ptp-110) REVERT: B 243 TYR cc_start: 0.8392 (t80) cc_final: 0.7975 (t80) REVERT: B 629 LEU cc_start: 0.8240 (mt) cc_final: 0.7897 (mt) REVERT: B 633 MET cc_start: 0.8784 (mtm) cc_final: 0.8392 (mtm) REVERT: B 759 MET cc_start: 0.7614 (mmt) cc_final: 0.7378 (mmp) REVERT: B 771 TYR cc_start: 0.7807 (p90) cc_final: 0.7515 (p90) outliers start: 3 outliers final: 1 residues processed: 179 average time/residue: 0.2616 time to fit residues: 66.5240 Evaluate side-chains 116 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 115 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 120 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 chunk 157 optimal weight: 10.0000 chunk 129 optimal weight: 0.9990 chunk 144 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 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 242 GLN ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN ** A 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 13700 Z= 0.289 Angle : 0.651 6.547 18746 Z= 0.347 Chirality : 0.042 0.247 2122 Planarity : 0.005 0.057 2288 Dihedral : 18.455 89.738 2292 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.20), residues: 1568 helix: 0.56 (0.19), residues: 729 sheet: -1.22 (0.31), residues: 199 loop : -1.25 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 436 HIS 0.005 0.001 HIS B 746 PHE 0.019 0.002 PHE A 372 TYR 0.020 0.002 TYR A 528 ARG 0.007 0.001 ARG B 788 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 HIS cc_start: 0.8069 (p-80) cc_final: 0.7581 (p90) REVERT: A 372 PHE cc_start: 0.8690 (m-80) cc_final: 0.8440 (m-80) REVERT: A 771 TYR cc_start: 0.8599 (p90) cc_final: 0.7898 (p90) REVERT: B 13 MET cc_start: 0.7768 (ppp) cc_final: 0.7465 (ppp) REVERT: B 68 MET cc_start: 0.5169 (tmm) cc_final: 0.4660 (tmm) REVERT: B 609 MET cc_start: 0.8443 (tpp) cc_final: 0.8153 (tpp) REVERT: B 633 MET cc_start: 0.8882 (mtm) cc_final: 0.8590 (mtm) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.2707 time to fit residues: 57.7752 Evaluate side-chains 102 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 154 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 138 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 GLN ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 746 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13700 Z= 0.212 Angle : 0.593 6.547 18746 Z= 0.317 Chirality : 0.041 0.179 2122 Planarity : 0.004 0.049 2288 Dihedral : 18.351 89.985 2292 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.20), residues: 1568 helix: 0.85 (0.19), residues: 726 sheet: -1.09 (0.31), residues: 192 loop : -1.15 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.004 0.001 HIS B 24 PHE 0.022 0.002 PHE B 155 TYR 0.020 0.002 TYR A 528 ARG 0.004 0.000 ARG B 656 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 PHE cc_start: 0.8699 (m-80) cc_final: 0.8445 (m-80) REVERT: A 671 MET cc_start: 0.8511 (mmm) cc_final: 0.8027 (tpp) REVERT: A 744 ASN cc_start: 0.8916 (t0) cc_final: 0.8707 (p0) REVERT: A 771 TYR cc_start: 0.8605 (p90) cc_final: 0.7947 (p90) REVERT: B 68 MET cc_start: 0.5453 (tmm) cc_final: 0.5215 (tmm) REVERT: B 441 ASP cc_start: 0.8074 (m-30) cc_final: 0.7689 (p0) REVERT: B 609 MET cc_start: 0.8328 (tpp) cc_final: 0.8035 (tpp) REVERT: B 671 MET cc_start: 0.8322 (ptt) cc_final: 0.7029 (tpp) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.2568 time to fit residues: 52.4531 Evaluate side-chains 102 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 115 optimal weight: 10.0000 chunk 63 optimal weight: 0.0060 chunk 131 optimal weight: 0.9980 chunk 106 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 chunk 138 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 overall best weight: 1.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13700 Z= 0.192 Angle : 0.584 8.034 18746 Z= 0.307 Chirality : 0.041 0.149 2122 Planarity : 0.004 0.051 2288 Dihedral : 18.211 88.872 2292 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.20), residues: 1568 helix: 1.11 (0.19), residues: 727 sheet: -1.02 (0.32), residues: 198 loop : -1.11 (0.23), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 709 HIS 0.004 0.001 HIS B 24 PHE 0.019 0.001 PHE B 36 TYR 0.019 0.002 TYR A 528 ARG 0.005 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8277 (tp) cc_final: 0.7975 (tp) REVERT: A 372 PHE cc_start: 0.8704 (m-10) cc_final: 0.8399 (m-80) REVERT: A 574 ASP cc_start: 0.8642 (m-30) cc_final: 0.8031 (p0) REVERT: A 671 MET cc_start: 0.8471 (tpt) cc_final: 0.8144 (tpp) REVERT: A 674 MET cc_start: 0.8437 (tpp) cc_final: 0.7817 (mmt) REVERT: A 691 LEU cc_start: 0.8429 (mm) cc_final: 0.7828 (tp) REVERT: A 771 TYR cc_start: 0.8696 (p90) cc_final: 0.8112 (p90) REVERT: B 13 MET cc_start: 0.7667 (ppp) cc_final: 0.7431 (ppp) REVERT: B 397 MET cc_start: 0.8666 (mtm) cc_final: 0.8091 (mmm) REVERT: B 441 ASP cc_start: 0.8063 (m-30) cc_final: 0.7729 (p0) REVERT: B 671 MET cc_start: 0.8211 (ptt) cc_final: 0.6925 (tpp) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.2592 time to fit residues: 51.7509 Evaluate side-chains 107 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 154 optimal weight: 7.9990 chunk 128 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 GLN ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.5139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13700 Z= 0.226 Angle : 0.603 10.316 18746 Z= 0.314 Chirality : 0.041 0.238 2122 Planarity : 0.005 0.047 2288 Dihedral : 18.162 88.203 2292 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.08 % Allowed : 1.75 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.21), residues: 1568 helix: 1.17 (0.19), residues: 727 sheet: -0.92 (0.33), residues: 195 loop : -1.16 (0.23), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 137 HIS 0.004 0.001 HIS B 24 PHE 0.015 0.002 PHE B 155 TYR 0.023 0.002 TYR A 446 ARG 0.006 0.000 ARG B 697 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8247 (tp) cc_final: 0.7793 (tp) REVERT: A 372 PHE cc_start: 0.8698 (m-10) cc_final: 0.8468 (m-80) REVERT: A 574 ASP cc_start: 0.8629 (m-30) cc_final: 0.7946 (p0) REVERT: A 671 MET cc_start: 0.8577 (tpt) cc_final: 0.8172 (tpp) REVERT: A 771 TYR cc_start: 0.8375 (p90) cc_final: 0.7846 (p90) REVERT: B 441 ASP cc_start: 0.8074 (m-30) cc_final: 0.7603 (p0) REVERT: B 671 MET cc_start: 0.8254 (ptt) cc_final: 0.6986 (tpp) outliers start: 1 outliers final: 1 residues processed: 137 average time/residue: 0.2579 time to fit residues: 51.9645 Evaluate side-chains 97 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 88 optimal weight: 0.5980 chunk 113 optimal weight: 9.9990 chunk 87 optimal weight: 8.9990 chunk 130 optimal weight: 0.9990 chunk 86 optimal weight: 7.9990 chunk 154 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 ASN ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.5305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13700 Z= 0.171 Angle : 0.586 8.632 18746 Z= 0.307 Chirality : 0.041 0.227 2122 Planarity : 0.004 0.046 2288 Dihedral : 18.093 89.384 2292 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.21), residues: 1568 helix: 1.33 (0.20), residues: 722 sheet: -0.90 (0.33), residues: 195 loop : -1.13 (0.23), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 709 HIS 0.004 0.001 HIS B 24 PHE 0.013 0.001 PHE B 155 TYR 0.020 0.001 TYR A 446 ARG 0.004 0.000 ARG B 697 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8309 (tp) cc_final: 0.7972 (tp) REVERT: A 306 MET cc_start: 0.9290 (tpt) cc_final: 0.9040 (tpt) REVERT: A 372 PHE cc_start: 0.8772 (m-10) cc_final: 0.8553 (m-80) REVERT: A 561 ARG cc_start: 0.9089 (mmm-85) cc_final: 0.8738 (mmm-85) REVERT: A 574 ASP cc_start: 0.8590 (m-30) cc_final: 0.7886 (p0) REVERT: A 671 MET cc_start: 0.8578 (tpt) cc_final: 0.8178 (tpp) REVERT: A 771 TYR cc_start: 0.8306 (p90) cc_final: 0.7773 (p90) REVERT: B 441 ASP cc_start: 0.8052 (m-30) cc_final: 0.7576 (p0) REVERT: B 671 MET cc_start: 0.8155 (ptt) cc_final: 0.7000 (tpp) REVERT: B 759 MET cc_start: 0.8156 (mmm) cc_final: 0.7870 (mmt) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.2604 time to fit residues: 51.7366 Evaluate side-chains 103 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 0.0070 chunk 61 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 105 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 overall best weight: 1.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.5518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13700 Z= 0.190 Angle : 0.588 7.693 18746 Z= 0.306 Chirality : 0.041 0.211 2122 Planarity : 0.004 0.048 2288 Dihedral : 18.039 89.649 2292 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.21), residues: 1568 helix: 1.33 (0.19), residues: 727 sheet: -0.71 (0.34), residues: 185 loop : -1.11 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 137 HIS 0.005 0.001 HIS B 24 PHE 0.013 0.001 PHE B 155 TYR 0.018 0.001 TYR A 446 ARG 0.004 0.000 ARG B 354 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8301 (tp) cc_final: 0.7969 (tp) REVERT: A 306 MET cc_start: 0.9301 (tpt) cc_final: 0.9015 (tpt) REVERT: A 372 PHE cc_start: 0.8791 (m-10) cc_final: 0.8577 (m-80) REVERT: A 561 ARG cc_start: 0.9110 (mmm-85) cc_final: 0.8717 (mmm-85) REVERT: A 574 ASP cc_start: 0.8636 (m-30) cc_final: 0.7867 (p0) REVERT: A 671 MET cc_start: 0.8584 (tpt) cc_final: 0.8197 (tpp) REVERT: A 692 MET cc_start: 0.6785 (tpp) cc_final: 0.6319 (mmm) REVERT: A 771 TYR cc_start: 0.8339 (p90) cc_final: 0.7793 (p90) REVERT: B 13 MET cc_start: 0.7773 (ppp) cc_final: 0.7444 (ppp) REVERT: B 441 ASP cc_start: 0.8094 (m-30) cc_final: 0.7602 (p0) REVERT: B 671 MET cc_start: 0.8203 (ptt) cc_final: 0.7039 (tpp) REVERT: B 759 MET cc_start: 0.8151 (mmm) cc_final: 0.7870 (mmt) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2893 time to fit residues: 56.4581 Evaluate side-chains 103 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 0.6980 chunk 147 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 129 optimal weight: 0.9990 chunk 135 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 744 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.5694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13700 Z= 0.167 Angle : 0.570 8.079 18746 Z= 0.295 Chirality : 0.040 0.198 2122 Planarity : 0.004 0.049 2288 Dihedral : 17.965 89.270 2292 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.21), residues: 1568 helix: 1.51 (0.19), residues: 725 sheet: -0.57 (0.36), residues: 183 loop : -1.07 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 709 HIS 0.006 0.001 HIS B 24 PHE 0.013 0.001 PHE A 143 TYR 0.016 0.001 TYR A 528 ARG 0.003 0.000 ARG B 697 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8377 (tp) cc_final: 0.8036 (tp) REVERT: A 269 MET cc_start: 0.7368 (tpp) cc_final: 0.7043 (mmt) REVERT: A 306 MET cc_start: 0.9269 (tpt) cc_final: 0.9020 (tpt) REVERT: A 372 PHE cc_start: 0.8797 (m-10) cc_final: 0.8574 (m-80) REVERT: A 561 ARG cc_start: 0.9074 (mmm-85) cc_final: 0.8742 (mmm-85) REVERT: A 574 ASP cc_start: 0.8635 (m-30) cc_final: 0.7818 (p0) REVERT: A 671 MET cc_start: 0.8477 (tpt) cc_final: 0.8163 (tpp) REVERT: A 692 MET cc_start: 0.6657 (tpp) cc_final: 0.6160 (mmm) REVERT: A 771 TYR cc_start: 0.8342 (p90) cc_final: 0.7791 (p90) REVERT: B 13 MET cc_start: 0.7657 (ppp) cc_final: 0.7406 (ppp) REVERT: B 441 ASP cc_start: 0.8119 (m-30) cc_final: 0.7611 (p0) REVERT: B 617 MET cc_start: 0.7954 (mmt) cc_final: 0.7598 (ttm) REVERT: B 671 MET cc_start: 0.8233 (ptt) cc_final: 0.7016 (tpp) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2504 time to fit residues: 48.7585 Evaluate side-chains 103 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 159 optimal weight: 10.0000 chunk 146 optimal weight: 0.2980 chunk 126 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 GLN ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.5839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13700 Z= 0.176 Angle : 0.572 7.874 18746 Z= 0.298 Chirality : 0.041 0.264 2122 Planarity : 0.004 0.048 2288 Dihedral : 17.934 89.659 2292 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.21), residues: 1568 helix: 1.50 (0.19), residues: 717 sheet: -0.71 (0.34), residues: 198 loop : -0.96 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 709 HIS 0.006 0.001 HIS B 24 PHE 0.022 0.001 PHE B 155 TYR 0.015 0.001 TYR A 528 ARG 0.004 0.000 ARG A 788 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8350 (tp) cc_final: 0.8012 (tp) REVERT: A 269 MET cc_start: 0.7517 (tpp) cc_final: 0.7308 (tpp) REVERT: A 306 MET cc_start: 0.9272 (tpt) cc_final: 0.9023 (tpt) REVERT: A 372 PHE cc_start: 0.8817 (m-10) cc_final: 0.8598 (m-80) REVERT: A 561 ARG cc_start: 0.9092 (mmm-85) cc_final: 0.8759 (mmm-85) REVERT: A 574 ASP cc_start: 0.8662 (m-30) cc_final: 0.7830 (p0) REVERT: A 671 MET cc_start: 0.8498 (tpt) cc_final: 0.8168 (tpp) REVERT: A 692 MET cc_start: 0.6721 (tpp) cc_final: 0.6418 (mmm) REVERT: A 759 MET cc_start: 0.8540 (mpp) cc_final: 0.8291 (mpp) REVERT: A 771 TYR cc_start: 0.8375 (p90) cc_final: 0.7902 (p90) REVERT: B 13 MET cc_start: 0.7716 (ppp) cc_final: 0.7355 (ppp) REVERT: B 302 MET cc_start: 0.8878 (mtm) cc_final: 0.8657 (mpp) REVERT: B 441 ASP cc_start: 0.8157 (m-30) cc_final: 0.7638 (p0) REVERT: B 543 GLN cc_start: 0.8619 (mt0) cc_final: 0.8080 (mt0) REVERT: B 617 MET cc_start: 0.7939 (mmt) cc_final: 0.7584 (ttm) REVERT: B 671 MET cc_start: 0.8235 (ptt) cc_final: 0.7014 (tpp) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.2625 time to fit residues: 49.1922 Evaluate side-chains 101 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 117 optimal weight: 0.9980 chunk 18 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 127 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 111 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.075049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.054873 restraints weight = 85382.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.056383 restraints weight = 53026.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.057341 restraints weight = 37473.323| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.5921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13700 Z= 0.153 Angle : 0.566 8.409 18746 Z= 0.292 Chirality : 0.040 0.189 2122 Planarity : 0.004 0.050 2288 Dihedral : 17.892 89.897 2292 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.21), residues: 1568 helix: 1.58 (0.19), residues: 713 sheet: -0.51 (0.34), residues: 214 loop : -0.89 (0.23), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 709 HIS 0.003 0.001 HIS A 752 PHE 0.020 0.001 PHE B 155 TYR 0.017 0.001 TYR A 528 ARG 0.003 0.000 ARG B 697 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2439.65 seconds wall clock time: 44 minutes 26.87 seconds (2666.87 seconds total)