Starting phenix.real_space_refine on Sun Apr 7 02:46:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ekl_31169/04_2024/7ekl_31169_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ekl_31169/04_2024/7ekl_31169.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ekl_31169/04_2024/7ekl_31169.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ekl_31169/04_2024/7ekl_31169.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ekl_31169/04_2024/7ekl_31169_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ekl_31169/04_2024/7ekl_31169_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 34 5.16 5 C 6022 2.51 5 N 1624 2.21 5 O 1706 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 247": "NH1" <-> "NH2" Residue "A ARG 276": "NH1" <-> "NH2" Residue "A ARG 330": "NH1" <-> "NH2" Residue "A ARG 344": "NH1" <-> "NH2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "A ARG 439": "NH1" <-> "NH2" Residue "A ARG 475": "NH1" <-> "NH2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "A ARG 603": "NH1" <-> "NH2" Residue "A ARG 723": "NH1" <-> "NH2" Residue "A ARG 734": "NH1" <-> "NH2" Residue "A ARG 807": "NH1" <-> "NH2" Residue "B ARG 247": "NH1" <-> "NH2" Residue "B ARG 276": "NH1" <-> "NH2" Residue "B ARG 330": "NH1" <-> "NH2" Residue "B ARG 344": "NH1" <-> "NH2" Residue "B ARG 365": "NH1" <-> "NH2" Residue "B ARG 439": "NH1" <-> "NH2" Residue "B ARG 475": "NH1" <-> "NH2" Residue "B ARG 584": "NH1" <-> "NH2" Residue "B ARG 603": "NH1" <-> "NH2" Residue "B ARG 723": "NH1" <-> "NH2" Residue "B ARG 734": "NH1" <-> "NH2" Residue "B ARG 807": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 9394 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4665 Classifications: {'peptide': 590} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 576} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 4665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4665 Classifications: {'peptide': 590} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 576} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.39, per 1000 atoms: 0.57 Number of scatterers: 9394 At special positions: 0 Unit cell: (88.27, 74.69, 138.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 34 16.00 P 6 15.00 Mg 2 11.99 O 1706 8.00 N 1624 7.00 C 6022 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: 3.25 Conformation dependent library (CDL) restraints added in 1.9 seconds 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2168 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 62 helices and 6 sheets defined 50.7% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.18 Creating SS restraints... Processing helix chain 'A' and resid 242 through 252 removed outlier: 3.516A pdb=" N ARG A 247 " --> pdb=" O GLY A 243 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY A 251 " --> pdb=" O ARG A 247 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N TYR A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 262 No H-bonds generated for 'chain 'A' and resid 259 through 262' Processing helix chain 'A' and resid 265 through 294 removed outlier: 3.560A pdb=" N GLY A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG A 276 " --> pdb=" O MET A 272 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA A 277 " --> pdb=" O GLY A 273 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL A 280 " --> pdb=" O ARG A 276 " (cutoff:3.500A) Proline residue: A 283 - end of helix removed outlier: 3.716A pdb=" N ILE A 289 " --> pdb=" O PHE A 285 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU A 293 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 316 removed outlier: 4.578A pdb=" N TRP A 304 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N THR A 305 " --> pdb=" O SER A 301 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER A 308 " --> pdb=" O TRP A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 338 through 344 removed outlier: 3.888A pdb=" N ARG A 343 " --> pdb=" O GLN A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 363 removed outlier: 3.556A pdb=" N LEU A 362 " --> pdb=" O LEU A 358 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 358 through 363' Processing helix chain 'A' and resid 366 through 372 removed outlier: 3.537A pdb=" N ARG A 371 " --> pdb=" O GLY A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 384 removed outlier: 3.678A pdb=" N THR A 381 " --> pdb=" O THR A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 403 Processing helix chain 'A' and resid 413 through 426 removed outlier: 3.662A pdb=" N VAL A 417 " --> pdb=" O PHE A 413 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE A 418 " --> pdb=" O GLY A 414 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET A 421 " --> pdb=" O VAL A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 446 removed outlier: 5.053A pdb=" N LYS A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N PHE A 438 " --> pdb=" O TRP A 434 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG A 439 " --> pdb=" O ARG A 435 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG A 440 " --> pdb=" O THR A 436 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA A 441 " --> pdb=" O LYS A 437 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N MET A 442 " --> pdb=" O PHE A 438 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN A 443 " --> pdb=" O ARG A 439 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N THR A 444 " --> pdb=" O ARG A 440 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLN A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 465 Processing helix chain 'A' and resid 471 through 477 removed outlier: 3.879A pdb=" N TYR A 476 " --> pdb=" O GLU A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 491 removed outlier: 3.876A pdb=" N LEU A 486 " --> pdb=" O LYS A 482 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TRP A 488 " --> pdb=" O GLN A 484 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LYS A 489 " --> pdb=" O GLY A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 500 Processing helix chain 'A' and resid 502 through 521 removed outlier: 3.564A pdb=" N LEU A 510 " --> pdb=" O GLY A 506 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU A 515 " --> pdb=" O ALA A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 534 Processing helix chain 'A' and resid 537 through 549 Proline residue: A 543 - end of helix removed outlier: 3.982A pdb=" N GLY A 548 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N THR A 549 " --> pdb=" O ASN A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 568 removed outlier: 3.969A pdb=" N THR A 556 " --> pdb=" O ARG A 552 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN A 557 " --> pdb=" O MET A 553 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET A 561 " --> pdb=" O ASN A 557 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N MET A 564 " --> pdb=" O ASP A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 635 removed outlier: 3.863A pdb=" N LEU A 633 " --> pdb=" O LYS A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 662 No H-bonds generated for 'chain 'A' and resid 659 through 662' Processing helix chain 'A' and resid 680 through 684 Processing helix chain 'A' and resid 693 through 699 removed outlier: 3.515A pdb=" N ALA A 698 " --> pdb=" O ASP A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 709 No H-bonds generated for 'chain 'A' and resid 706 through 709' Processing helix chain 'A' and resid 715 through 717 No H-bonds generated for 'chain 'A' and resid 715 through 717' Processing helix chain 'A' and resid 722 through 724 No H-bonds generated for 'chain 'A' and resid 722 through 724' Processing helix chain 'A' and resid 731 through 743 removed outlier: 3.708A pdb=" N VAL A 735 " --> pdb=" O GLU A 731 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA A 736 " --> pdb=" O LYS A 732 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR A 740 " --> pdb=" O ALA A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 769 removed outlier: 4.578A pdb=" N ARG A 763 " --> pdb=" O THR A 759 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ALA A 764 " --> pdb=" O SER A 760 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A 765 " --> pdb=" O ASN A 761 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER A 768 " --> pdb=" O ALA A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 812 No H-bonds generated for 'chain 'A' and resid 809 through 812' Processing helix chain 'A' and resid 817 through 826 removed outlier: 3.761A pdb=" N GLN A 825 " --> pdb=" O MET A 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 252 removed outlier: 3.516A pdb=" N ARG B 247 " --> pdb=" O GLY B 243 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 249 " --> pdb=" O LYS B 245 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY B 251 " --> pdb=" O ARG B 247 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N TYR B 252 " --> pdb=" O LEU B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 262 No H-bonds generated for 'chain 'B' and resid 259 through 262' Processing helix chain 'B' and resid 265 through 294 removed outlier: 3.560A pdb=" N GLY B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG B 276 " --> pdb=" O MET B 272 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA B 277 " --> pdb=" O GLY B 273 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL B 280 " --> pdb=" O ARG B 276 " (cutoff:3.500A) Proline residue: B 283 - end of helix removed outlier: 3.716A pdb=" N ILE B 289 " --> pdb=" O PHE B 285 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU B 293 " --> pdb=" O ILE B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 316 removed outlier: 4.578A pdb=" N TRP B 304 " --> pdb=" O ASN B 300 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N THR B 305 " --> pdb=" O SER B 301 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER B 308 " --> pdb=" O TRP B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 338 through 344 removed outlier: 3.888A pdb=" N ARG B 343 " --> pdb=" O GLN B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 363 removed outlier: 3.556A pdb=" N LEU B 362 " --> pdb=" O LEU B 358 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY B 363 " --> pdb=" O ARG B 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 358 through 363' Processing helix chain 'B' and resid 366 through 372 removed outlier: 3.537A pdb=" N ARG B 371 " --> pdb=" O GLY B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 384 removed outlier: 3.678A pdb=" N THR B 381 " --> pdb=" O THR B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 403 Processing helix chain 'B' and resid 413 through 426 removed outlier: 3.662A pdb=" N VAL B 417 " --> pdb=" O PHE B 413 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE B 418 " --> pdb=" O GLY B 414 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET B 421 " --> pdb=" O VAL B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 446 removed outlier: 5.053A pdb=" N LYS B 437 " --> pdb=" O GLU B 433 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N PHE B 438 " --> pdb=" O TRP B 434 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG B 439 " --> pdb=" O ARG B 435 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG B 440 " --> pdb=" O THR B 436 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA B 441 " --> pdb=" O LYS B 437 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N MET B 442 " --> pdb=" O PHE B 438 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN B 443 " --> pdb=" O ARG B 439 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N THR B 444 " --> pdb=" O ARG B 440 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLN B 445 " --> pdb=" O ALA B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 465 Processing helix chain 'B' and resid 471 through 477 removed outlier: 3.879A pdb=" N TYR B 476 " --> pdb=" O GLU B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 491 removed outlier: 3.876A pdb=" N LEU B 486 " --> pdb=" O LYS B 482 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TRP B 488 " --> pdb=" O GLN B 484 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LYS B 489 " --> pdb=" O GLY B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 500 Processing helix chain 'B' and resid 502 through 521 removed outlier: 3.563A pdb=" N LEU B 510 " --> pdb=" O GLY B 506 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU B 515 " --> pdb=" O ALA B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 534 Processing helix chain 'B' and resid 537 through 549 Proline residue: B 543 - end of helix removed outlier: 3.982A pdb=" N GLY B 548 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N THR B 549 " --> pdb=" O ASN B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 568 removed outlier: 3.969A pdb=" N THR B 556 " --> pdb=" O ARG B 552 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN B 557 " --> pdb=" O MET B 553 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET B 561 " --> pdb=" O ASN B 557 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N MET B 564 " --> pdb=" O ASP B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 635 removed outlier: 3.863A pdb=" N LEU B 633 " --> pdb=" O LYS B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 662 No H-bonds generated for 'chain 'B' and resid 659 through 662' Processing helix chain 'B' and resid 680 through 684 Processing helix chain 'B' and resid 693 through 699 removed outlier: 3.514A pdb=" N ALA B 698 " --> pdb=" O ASP B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 709 No H-bonds generated for 'chain 'B' and resid 706 through 709' Processing helix chain 'B' and resid 715 through 717 No H-bonds generated for 'chain 'B' and resid 715 through 717' Processing helix chain 'B' and resid 722 through 724 No H-bonds generated for 'chain 'B' and resid 722 through 724' Processing helix chain 'B' and resid 731 through 743 removed outlier: 3.708A pdb=" N VAL B 735 " --> pdb=" O GLU B 731 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA B 736 " --> pdb=" O LYS B 732 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR B 740 " --> pdb=" O ALA B 736 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 769 removed outlier: 4.578A pdb=" N ARG B 763 " --> pdb=" O THR B 759 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA B 764 " --> pdb=" O SER B 760 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE B 765 " --> pdb=" O ASN B 761 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER B 768 " --> pdb=" O ALA B 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 812 No H-bonds generated for 'chain 'B' and resid 809 through 812' Processing helix chain 'B' and resid 817 through 826 removed outlier: 3.760A pdb=" N GLN B 825 " --> pdb=" O MET B 821 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 590 through 593 Processing sheet with id= B, first strand: chain 'A' and resid 802 through 806 removed outlier: 7.409A pdb=" N VAL A 796 " --> pdb=" O VAL A 803 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ARG A 805 " --> pdb=" O ILE A 794 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE A 794 " --> pdb=" O ARG A 805 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN A 793 " --> pdb=" O THR A 618 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N THR A 778 " --> pdb=" O LEU A 619 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N LEU A 621 " --> pdb=" O THR A 778 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL A 780 " --> pdb=" O LEU A 621 " (cutoff:3.500A) removed outlier: 9.027A pdb=" N GLY A 623 " --> pdb=" O VAL A 780 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 595 through 597 removed outlier: 7.876A pdb=" N PHE A 597 " --> pdb=" O GLN A 607 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N GLN A 607 " --> pdb=" O PHE A 597 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 590 through 593 Processing sheet with id= E, first strand: chain 'B' and resid 802 through 806 removed outlier: 7.409A pdb=" N VAL B 796 " --> pdb=" O VAL B 803 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ARG B 805 " --> pdb=" O ILE B 794 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE B 794 " --> pdb=" O ARG B 805 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN B 793 " --> pdb=" O THR B 618 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR B 778 " --> pdb=" O LEU B 619 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N LEU B 621 " --> pdb=" O THR B 778 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL B 780 " --> pdb=" O LEU B 621 " (cutoff:3.500A) removed outlier: 9.027A pdb=" N GLY B 623 " --> pdb=" O VAL B 780 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 595 through 597 removed outlier: 7.876A pdb=" N PHE B 597 " --> pdb=" O GLN B 607 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N GLN B 607 " --> pdb=" O PHE B 597 " (cutoff:3.500A) 272 hydrogen bonds defined for protein. 804 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: 2.39 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: 1985 1.33 - 1.45: 2196 1.45 - 1.57: 5335 1.57 - 1.69: 10 1.69 - 1.81: 56 Bond restraints: 9582 Sorted by residual: bond pdb=" C4 ATP B 901 " pdb=" C5 ATP B 901 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.42e+01 bond pdb=" C4 ATP A 901 " pdb=" C5 ATP A 901 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.30e+01 bond pdb=" C5 ATP B 901 " pdb=" C6 ATP B 901 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.77e+01 bond pdb=" C5 ATP A 901 " pdb=" C6 ATP A 901 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.77e+01 bond pdb=" C8 ATP B 901 " pdb=" N7 ATP B 901 " ideal model delta sigma weight residual 1.310 1.354 -0.044 1.00e-02 1.00e+04 1.98e+01 ... (remaining 9577 not shown) Histogram of bond angle deviations from ideal: 99.97 - 107.19: 218 107.19 - 114.41: 5537 114.41 - 121.63: 5371 121.63 - 128.85: 1812 128.85 - 136.07: 74 Bond angle restraints: 13012 Sorted by residual: angle pdb=" PA ATP B 901 " pdb=" O3A ATP B 901 " pdb=" PB ATP B 901 " ideal model delta sigma weight residual 136.83 118.95 17.88 1.00e+00 1.00e+00 3.20e+02 angle pdb=" PA ATP A 901 " pdb=" O3A ATP A 901 " pdb=" PB ATP A 901 " ideal model delta sigma weight residual 136.83 118.96 17.87 1.00e+00 1.00e+00 3.19e+02 angle pdb=" PB ATP A 901 " pdb=" O3B ATP A 901 " pdb=" PG ATP A 901 " ideal model delta sigma weight residual 139.87 123.78 16.09 1.00e+00 1.00e+00 2.59e+02 angle pdb=" PB ATP B 901 " pdb=" O3B ATP B 901 " pdb=" PG ATP B 901 " ideal model delta sigma weight residual 139.87 123.79 16.08 1.00e+00 1.00e+00 2.59e+02 angle pdb=" C5 ATP A 901 " pdb=" C4 ATP A 901 " pdb=" N3 ATP A 901 " ideal model delta sigma weight residual 126.80 118.75 8.05 1.00e+00 1.00e+00 6.49e+01 ... (remaining 13007 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.91: 5276 14.91 - 29.82: 280 29.82 - 44.73: 88 44.73 - 59.65: 10 59.65 - 74.56: 12 Dihedral angle restraints: 5666 sinusoidal: 2276 harmonic: 3390 Sorted by residual: dihedral pdb=" CA MET A 553 " pdb=" C MET A 553 " pdb=" N ILE A 554 " pdb=" CA ILE A 554 " ideal model delta harmonic sigma weight residual 180.00 155.99 24.01 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA MET B 553 " pdb=" C MET B 553 " pdb=" N ILE B 554 " pdb=" CA ILE B 554 " ideal model delta harmonic sigma weight residual 180.00 156.02 23.98 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA ILE A 267 " pdb=" C ILE A 267 " pdb=" N CYS A 268 " pdb=" CA CYS A 268 " ideal model delta harmonic sigma weight residual 180.00 157.02 22.98 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 5663 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1061 0.044 - 0.087: 311 0.087 - 0.131: 99 0.131 - 0.175: 20 0.175 - 0.219: 5 Chirality restraints: 1496 Sorted by residual: chirality pdb=" CA GLU A 469 " pdb=" N GLU A 469 " pdb=" C GLU A 469 " pdb=" CB GLU A 469 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA GLU B 469 " pdb=" N GLU B 469 " pdb=" C GLU B 469 " pdb=" CB GLU B 469 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA LYS B 464 " pdb=" N LYS B 464 " pdb=" C LYS B 464 " pdb=" CB LYS B 464 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 1493 not shown) Planarity restraints: 1632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 727 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.40e+00 pdb=" C LEU A 727 " 0.032 2.00e-02 2.50e+03 pdb=" O LEU A 727 " -0.012 2.00e-02 2.50e+03 pdb=" N SER A 728 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 727 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.38e+00 pdb=" C LEU B 727 " 0.032 2.00e-02 2.50e+03 pdb=" O LEU B 727 " -0.012 2.00e-02 2.50e+03 pdb=" N SER B 728 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 258 " -0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO A 259 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 259 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 259 " -0.026 5.00e-02 4.00e+02 ... (remaining 1629 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 347 2.69 - 3.24: 8638 3.24 - 3.80: 14183 3.80 - 4.35: 19909 4.35 - 4.90: 31706 Nonbonded interactions: 74783 Sorted by model distance: nonbonded pdb=" OE1 GLN A 671 " pdb="MG MG A 902 " model vdw 2.141 2.170 nonbonded pdb=" OE1 GLN B 671 " pdb="MG MG B 902 " model vdw 2.141 2.170 nonbonded pdb=" O1G ATP A 901 " pdb="MG MG A 902 " model vdw 2.160 2.170 nonbonded pdb=" O1G ATP B 901 " pdb="MG MG B 902 " model vdw 2.161 2.170 nonbonded pdb=" OG SER A 630 " pdb="MG MG A 902 " model vdw 2.216 2.170 ... (remaining 74778 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: 0.340 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: 2.150 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 27.800 Find NCS groups from input model: 0.470 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 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 : 0.005 0.080 9582 Z= 0.337 Angle : 1.133 17.881 13012 Z= 0.754 Chirality : 0.048 0.219 1496 Planarity : 0.005 0.046 1632 Dihedral : 11.151 74.557 3498 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.89 % Favored : 96.94 % Rotamer: Outliers : 0.81 % Allowed : 5.24 % Favored : 93.95 % 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: -5.70 (0.17), residues: 1176 helix: -4.63 (0.08), residues: 716 sheet: -0.16 (0.61), residues: 82 loop : -2.26 (0.25), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 488 HIS 0.007 0.002 HIS A 354 PHE 0.022 0.003 PHE B 639 TYR 0.031 0.002 TYR B 551 ARG 0.011 0.001 ARG A 365 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 213 time to evaluate : 1.106 Fit side-chains REVERT: A 455 ASP cc_start: 0.7905 (t70) cc_final: 0.7618 (t0) REVERT: A 491 SER cc_start: 0.9230 (t) cc_final: 0.8851 (m) REVERT: A 518 TYR cc_start: 0.8572 (t80) cc_final: 0.8133 (t80) REVERT: A 759 THR cc_start: 0.8355 (t) cc_final: 0.8118 (p) REVERT: B 455 ASP cc_start: 0.7960 (t70) cc_final: 0.7648 (t0) REVERT: B 491 SER cc_start: 0.9181 (t) cc_final: 0.8793 (m) REVERT: B 518 TYR cc_start: 0.8492 (t80) cc_final: 0.8064 (t80) REVERT: B 563 ASN cc_start: 0.8150 (m110) cc_final: 0.7897 (m110) REVERT: B 759 THR cc_start: 0.8406 (t) cc_final: 0.8079 (p) outliers start: 8 outliers final: 2 residues processed: 217 average time/residue: 0.2880 time to fit residues: 80.9390 Evaluate side-chains 99 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 97 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain B residue 781 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.0070 chunk 89 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 47 optimal weight: 0.3980 chunk 92 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 56 optimal weight: 0.0030 chunk 68 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 overall best weight: 0.4608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN A 316 GLN A 498 ASN A 563 ASN A 607 GLN A 752 GLN A 766 GLN B 279 ASN B 316 GLN B 498 ASN B 607 GLN B 752 GLN B 766 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 9582 Z= 0.131 Angle : 0.540 7.048 13012 Z= 0.290 Chirality : 0.039 0.148 1496 Planarity : 0.004 0.035 1632 Dihedral : 8.367 87.751 1374 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.72 % Allowed : 8.77 % Favored : 88.51 % 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: -3.90 (0.19), residues: 1176 helix: -3.23 (0.14), residues: 682 sheet: 0.20 (0.59), residues: 82 loop : -1.60 (0.25), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 822 HIS 0.001 0.000 HIS B 596 PHE 0.010 0.001 PHE B 409 TYR 0.014 0.001 TYR A 465 ARG 0.005 0.000 ARG A 648 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 118 time to evaluate : 1.025 Fit side-chains REVERT: A 346 GLU cc_start: 0.7737 (tp30) cc_final: 0.7425 (mm-30) REVERT: A 455 ASP cc_start: 0.7823 (t70) cc_final: 0.7553 (t0) REVERT: A 496 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8720 (tp) REVERT: A 759 THR cc_start: 0.8325 (t) cc_final: 0.8085 (p) REVERT: B 346 GLU cc_start: 0.7690 (tp30) cc_final: 0.7425 (mm-30) REVERT: B 455 ASP cc_start: 0.7849 (t70) cc_final: 0.7595 (t0) REVERT: B 496 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8671 (tp) REVERT: B 614 MET cc_start: 0.8353 (mmm) cc_final: 0.8004 (mmm) outliers start: 27 outliers final: 7 residues processed: 139 average time/residue: 0.2350 time to fit residues: 44.4029 Evaluate side-chains 98 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 89 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 781 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 107 optimal weight: 0.0770 chunk 115 optimal weight: 0.5980 chunk 95 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 overall best weight: 1.3344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 GLN ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN B 683 ASN B 766 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9582 Z= 0.207 Angle : 0.511 5.895 13012 Z= 0.271 Chirality : 0.039 0.132 1496 Planarity : 0.003 0.027 1632 Dihedral : 7.939 85.582 1374 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.72 % Allowed : 10.08 % Favored : 87.20 % 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: -2.78 (0.22), residues: 1176 helix: -2.18 (0.17), residues: 690 sheet: 0.26 (0.59), residues: 82 loop : -1.29 (0.27), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 488 HIS 0.002 0.001 HIS B 361 PHE 0.010 0.001 PHE B 409 TYR 0.018 0.002 TYR A 471 ARG 0.004 0.000 ARG B 648 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 100 time to evaluate : 1.041 Fit side-chains REVERT: A 346 GLU cc_start: 0.7791 (tp30) cc_final: 0.7550 (mm-30) REVERT: A 455 ASP cc_start: 0.7915 (t70) cc_final: 0.7563 (t0) REVERT: A 496 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8798 (tp) REVERT: A 553 MET cc_start: 0.7585 (ptm) cc_final: 0.7375 (ptp) REVERT: A 759 THR cc_start: 0.8449 (t) cc_final: 0.8218 (p) REVERT: B 455 ASP cc_start: 0.7885 (t70) cc_final: 0.7569 (t0) REVERT: B 496 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8778 (tp) REVERT: B 603 ARG cc_start: 0.6689 (ptm160) cc_final: 0.6467 (ttp-170) REVERT: B 614 MET cc_start: 0.8467 (mmm) cc_final: 0.8224 (mmm) outliers start: 27 outliers final: 16 residues processed: 127 average time/residue: 0.1864 time to fit residues: 35.0210 Evaluate side-chains 100 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 82 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 804 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 114 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 683 ASN ** A 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 752 GLN A 766 GLN B 596 HIS ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 752 GLN B 766 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 9582 Z= 0.378 Angle : 0.601 7.887 13012 Z= 0.313 Chirality : 0.044 0.142 1496 Planarity : 0.004 0.032 1632 Dihedral : 8.225 88.834 1374 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.73 % Allowed : 11.69 % Favored : 84.58 % 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: -2.32 (0.23), residues: 1176 helix: -1.78 (0.19), residues: 694 sheet: 1.12 (0.67), residues: 62 loop : -1.18 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 488 HIS 0.003 0.001 HIS A 706 PHE 0.017 0.002 PHE A 676 TYR 0.017 0.002 TYR B 471 ARG 0.006 0.001 ARG B 648 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 87 time to evaluate : 1.166 Fit side-chains REVERT: A 346 GLU cc_start: 0.7834 (tp30) cc_final: 0.7353 (tp30) REVERT: A 496 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8896 (tm) REVERT: A 759 THR cc_start: 0.8636 (t) cc_final: 0.8422 (p) REVERT: B 346 GLU cc_start: 0.7698 (tp30) cc_final: 0.7410 (mm-30) REVERT: B 496 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8912 (tm) REVERT: B 614 MET cc_start: 0.8428 (mmm) cc_final: 0.8124 (mmm) REVERT: B 804 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7607 (pm20) outliers start: 37 outliers final: 25 residues processed: 121 average time/residue: 0.2122 time to fit residues: 37.8462 Evaluate side-chains 98 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 70 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 804 GLU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 673 THR Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 804 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 102 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 766 GLN ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 766 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9582 Z= 0.264 Angle : 0.525 7.845 13012 Z= 0.274 Chirality : 0.041 0.133 1496 Planarity : 0.003 0.022 1632 Dihedral : 8.014 85.115 1374 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.53 % Allowed : 12.20 % Favored : 84.27 % 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: -1.89 (0.23), residues: 1176 helix: -1.43 (0.19), residues: 696 sheet: 1.20 (0.66), residues: 62 loop : -1.00 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 822 HIS 0.004 0.001 HIS B 596 PHE 0.011 0.001 PHE A 676 TYR 0.017 0.001 TYR B 471 ARG 0.005 0.000 ARG B 648 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 86 time to evaluate : 1.125 Fit side-chains REVERT: A 346 GLU cc_start: 0.7835 (tp30) cc_final: 0.7381 (tp30) REVERT: A 407 MET cc_start: 0.7111 (mtp) cc_final: 0.6857 (mtp) REVERT: A 523 GLN cc_start: 0.8971 (mp10) cc_final: 0.8570 (mp10) REVERT: A 542 MET cc_start: 0.7949 (ttm) cc_final: 0.7747 (ttm) REVERT: A 603 ARG cc_start: 0.6861 (ptm160) cc_final: 0.6591 (ttp-170) REVERT: A 672 ASP cc_start: 0.7599 (p0) cc_final: 0.7396 (p0) REVERT: A 759 THR cc_start: 0.8679 (t) cc_final: 0.8471 (p) REVERT: B 407 MET cc_start: 0.7216 (mtp) cc_final: 0.6937 (mtp) REVERT: B 522 GLU cc_start: 0.8225 (mp0) cc_final: 0.7843 (mp0) REVERT: B 603 ARG cc_start: 0.6808 (ptm160) cc_final: 0.6550 (ttp-170) REVERT: B 614 MET cc_start: 0.8472 (mmm) cc_final: 0.8178 (mmm) REVERT: B 804 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7586 (pm20) outliers start: 35 outliers final: 26 residues processed: 119 average time/residue: 0.1836 time to fit residues: 32.8386 Evaluate side-chains 109 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 82 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 804 GLU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 673 THR Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 804 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 59 optimal weight: 10.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9582 Z= 0.160 Angle : 0.483 7.675 13012 Z= 0.248 Chirality : 0.039 0.130 1496 Planarity : 0.002 0.022 1632 Dihedral : 7.766 86.823 1374 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.32 % Allowed : 13.10 % Favored : 84.58 % 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: -1.59 (0.24), residues: 1176 helix: -1.11 (0.20), residues: 714 sheet: 0.51 (0.60), residues: 84 loop : -0.94 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 299 HIS 0.004 0.001 HIS B 596 PHE 0.008 0.001 PHE A 676 TYR 0.016 0.001 TYR B 471 ARG 0.004 0.000 ARG B 648 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 92 time to evaluate : 1.043 Fit side-chains REVERT: A 346 GLU cc_start: 0.7752 (tp30) cc_final: 0.7378 (tp30) REVERT: A 407 MET cc_start: 0.7050 (mtp) cc_final: 0.6830 (mtp) REVERT: A 455 ASP cc_start: 0.8115 (t70) cc_final: 0.7457 (t0) REVERT: A 523 GLN cc_start: 0.8975 (mp10) cc_final: 0.8282 (mp10) REVERT: A 603 ARG cc_start: 0.6838 (ptm160) cc_final: 0.6624 (ttp-170) REVERT: B 292 LEU cc_start: 0.8795 (mt) cc_final: 0.8451 (mp) REVERT: B 407 MET cc_start: 0.7099 (mtp) cc_final: 0.6862 (mtp) REVERT: B 523 GLN cc_start: 0.8953 (mp10) cc_final: 0.8546 (mp10) REVERT: B 603 ARG cc_start: 0.6760 (ptm160) cc_final: 0.6544 (ttp-170) REVERT: B 614 MET cc_start: 0.8497 (mmm) cc_final: 0.8219 (mmm) REVERT: B 804 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7594 (pm20) outliers start: 23 outliers final: 18 residues processed: 112 average time/residue: 0.1966 time to fit residues: 32.5324 Evaluate side-chains 99 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 80 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 804 GLU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 804 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 83 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 0.4980 chunk 63 optimal weight: 0.8980 chunk 113 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 752 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9582 Z= 0.141 Angle : 0.460 8.454 13012 Z= 0.240 Chirality : 0.039 0.135 1496 Planarity : 0.002 0.022 1632 Dihedral : 7.641 88.870 1374 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.12 % Allowed : 13.51 % Favored : 84.38 % 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: -1.16 (0.25), residues: 1176 helix: -0.78 (0.20), residues: 700 sheet: 0.60 (0.60), residues: 84 loop : -0.73 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP A 822 HIS 0.004 0.001 HIS B 596 PHE 0.006 0.001 PHE B 611 TYR 0.015 0.001 TYR B 471 ARG 0.004 0.000 ARG B 648 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 87 time to evaluate : 1.237 Fit side-chains REVERT: A 272 MET cc_start: 0.7803 (ttm) cc_final: 0.7581 (mtp) REVERT: A 346 GLU cc_start: 0.7751 (tp30) cc_final: 0.7393 (tp30) REVERT: A 455 ASP cc_start: 0.8136 (t70) cc_final: 0.7478 (t0) REVERT: A 523 GLN cc_start: 0.8971 (mp10) cc_final: 0.8273 (mp10) REVERT: B 272 MET cc_start: 0.7816 (ttm) cc_final: 0.7592 (mtp) REVERT: B 292 LEU cc_start: 0.8747 (mt) cc_final: 0.8396 (mp) REVERT: B 346 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7496 (mm-30) REVERT: B 407 MET cc_start: 0.7101 (mtp) cc_final: 0.6879 (mtp) REVERT: B 455 ASP cc_start: 0.8122 (t70) cc_final: 0.7456 (t0) REVERT: B 522 GLU cc_start: 0.8281 (mp0) cc_final: 0.8058 (mp0) REVERT: B 603 ARG cc_start: 0.6758 (ptm160) cc_final: 0.6554 (ttp-170) REVERT: B 614 MET cc_start: 0.8470 (mmm) cc_final: 0.8200 (mmm) REVERT: B 804 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7577 (pm20) outliers start: 21 outliers final: 16 residues processed: 105 average time/residue: 0.1894 time to fit residues: 29.9065 Evaluate side-chains 99 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 82 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 804 GLU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 409 PHE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 804 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9582 Z= 0.236 Angle : 0.503 8.784 13012 Z= 0.261 Chirality : 0.041 0.163 1496 Planarity : 0.003 0.022 1632 Dihedral : 7.671 84.772 1374 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.72 % Allowed : 13.61 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.25), residues: 1176 helix: -0.71 (0.20), residues: 702 sheet: 0.53 (0.60), residues: 80 loop : -0.60 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 822 HIS 0.004 0.001 HIS B 596 PHE 0.010 0.001 PHE B 676 TYR 0.015 0.001 TYR B 471 ARG 0.003 0.000 ARG B 648 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 83 time to evaluate : 1.076 Fit side-chains REVERT: A 272 MET cc_start: 0.7811 (ttm) cc_final: 0.7576 (mtp) REVERT: A 346 GLU cc_start: 0.7829 (tp30) cc_final: 0.7461 (tp30) REVERT: A 523 GLN cc_start: 0.9002 (mp10) cc_final: 0.8323 (mp10) REVERT: B 272 MET cc_start: 0.7818 (ttm) cc_final: 0.7593 (mtp) REVERT: B 292 LEU cc_start: 0.8759 (mt) cc_final: 0.8385 (mp) REVERT: B 455 ASP cc_start: 0.8079 (t70) cc_final: 0.7421 (t0) REVERT: B 496 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8809 (tp) REVERT: B 522 GLU cc_start: 0.8219 (mp0) cc_final: 0.7818 (mp0) REVERT: B 603 ARG cc_start: 0.6870 (ptm160) cc_final: 0.6630 (ttp-170) REVERT: B 614 MET cc_start: 0.8468 (mmm) cc_final: 0.8162 (mmm) REVERT: B 804 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7568 (pm20) outliers start: 27 outliers final: 23 residues processed: 107 average time/residue: 0.1826 time to fit residues: 29.6773 Evaluate side-chains 105 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 80 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 804 GLU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 804 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.7980 chunk 99 optimal weight: 0.4980 chunk 105 optimal weight: 0.3980 chunk 63 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 766 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9582 Z= 0.127 Angle : 0.451 8.820 13012 Z= 0.236 Chirality : 0.039 0.149 1496 Planarity : 0.002 0.022 1632 Dihedral : 7.523 86.383 1374 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.52 % Allowed : 13.91 % Favored : 83.57 % 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: -0.71 (0.25), residues: 1176 helix: -0.40 (0.21), residues: 704 sheet: 0.66 (0.61), residues: 84 loop : -0.55 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 822 HIS 0.004 0.000 HIS B 596 PHE 0.006 0.001 PHE B 676 TYR 0.015 0.001 TYR B 471 ARG 0.003 0.000 ARG B 648 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 89 time to evaluate : 1.027 Fit side-chains REVERT: A 346 GLU cc_start: 0.7755 (tp30) cc_final: 0.7427 (tp30) REVERT: A 407 MET cc_start: 0.7021 (mtp) cc_final: 0.6784 (mtp) REVERT: A 455 ASP cc_start: 0.8138 (t70) cc_final: 0.7466 (t0) REVERT: B 292 LEU cc_start: 0.8716 (mt) cc_final: 0.8345 (mp) REVERT: B 407 MET cc_start: 0.7068 (mtp) cc_final: 0.6818 (mtp) REVERT: B 455 ASP cc_start: 0.8115 (t70) cc_final: 0.7470 (t0) REVERT: B 496 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8808 (tp) REVERT: B 522 GLU cc_start: 0.8229 (mp0) cc_final: 0.7971 (mp0) REVERT: B 603 ARG cc_start: 0.6829 (ptm160) cc_final: 0.6605 (ttp-170) REVERT: B 614 MET cc_start: 0.8487 (mmm) cc_final: 0.8199 (mmm) REVERT: B 804 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7550 (pm20) outliers start: 25 outliers final: 18 residues processed: 111 average time/residue: 0.1641 time to fit residues: 28.2872 Evaluate side-chains 105 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 85 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 409 PHE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 804 GLU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 409 PHE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 804 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 74 optimal weight: 0.0040 chunk 99 optimal weight: 4.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 766 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9582 Z= 0.200 Angle : 0.486 9.442 13012 Z= 0.252 Chirality : 0.040 0.173 1496 Planarity : 0.002 0.022 1632 Dihedral : 7.520 83.855 1374 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.52 % Allowed : 14.31 % Favored : 83.17 % 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: -0.64 (0.25), residues: 1176 helix: -0.36 (0.21), residues: 704 sheet: 0.74 (0.62), residues: 80 loop : -0.47 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 822 HIS 0.004 0.001 HIS B 596 PHE 0.008 0.001 PHE A 676 TYR 0.015 0.001 TYR A 471 ARG 0.003 0.000 ARG B 648 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 82 time to evaluate : 1.223 Fit side-chains REVERT: A 346 GLU cc_start: 0.7786 (tp30) cc_final: 0.7460 (tp30) REVERT: A 407 MET cc_start: 0.7055 (mtp) cc_final: 0.6822 (mtp) REVERT: A 455 ASP cc_start: 0.8157 (t70) cc_final: 0.7488 (t0) REVERT: B 292 LEU cc_start: 0.8735 (mt) cc_final: 0.8363 (mp) REVERT: B 455 ASP cc_start: 0.8170 (t70) cc_final: 0.7504 (t0) REVERT: B 496 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8822 (tp) REVERT: B 522 GLU cc_start: 0.8283 (mp0) cc_final: 0.7981 (mp0) REVERT: B 603 ARG cc_start: 0.6863 (ptm160) cc_final: 0.6634 (ttp-170) REVERT: B 614 MET cc_start: 0.8460 (mmm) cc_final: 0.8167 (mmm) REVERT: B 804 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7551 (pm20) outliers start: 25 outliers final: 23 residues processed: 103 average time/residue: 0.1698 time to fit residues: 27.4549 Evaluate side-chains 104 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 79 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 409 PHE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 804 GLU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 409 PHE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 804 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 chunk 13 optimal weight: 0.0870 chunk 26 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 39 optimal weight: 0.0050 chunk 96 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 82 optimal weight: 0.6980 chunk 5 optimal weight: 0.3980 overall best weight: 0.3772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 GLN ** 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 = 0.3296 r_free = 0.3296 target = 0.119088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.098498 restraints weight = 12617.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.101205 restraints weight = 7480.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.102869 restraints weight = 5315.435| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9582 Z= 0.108 Angle : 0.447 9.569 13012 Z= 0.233 Chirality : 0.038 0.135 1496 Planarity : 0.002 0.022 1632 Dihedral : 7.410 88.484 1374 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.51 % Allowed : 15.32 % Favored : 83.17 % 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: -0.49 (0.26), residues: 1176 helix: -0.18 (0.21), residues: 718 sheet: 0.76 (0.59), residues: 88 loop : -0.60 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP A 822 HIS 0.004 0.000 HIS B 596 PHE 0.006 0.001 PHE B 311 TYR 0.015 0.001 TYR A 471 ARG 0.003 0.000 ARG B 648 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1813.91 seconds wall clock time: 33 minutes 55.94 seconds (2035.94 seconds total)