Starting phenix.real_space_refine on Sat Oct 24 08:07:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wj0_66012/10_2026/9wj0_66012.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wj0_66012/10_2026/9wj0_66012.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wj0_66012/10_2026/9wj0_66012.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wj0_66012/10_2026/9wj0_66012.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wj0_66012/10_2026/9wj0_66012.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wj0_66012/10_2026/9wj0_66012.map" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.036 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 3 5.49 5 S 33 5.16 5 C 8041 2.51 5 N 2102 2.21 5 O 2326 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12505 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 100 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 6311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 839, 6311 Classifications: {'peptide': 839} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'PTRANS': 20, 'TRANS': 818} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 444 Unresolved non-hydrogen angles: 548 Unresolved non-hydrogen dihedrals: 354 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 26, 'ASP:plan': 17, 'ASN:plan1': 11, 'PHE:plan': 3, 'TRP:plan': 1, 'GLN:plan1': 6} Unresolved non-hydrogen planarities: 259 Chain: "B" Number of atoms: 6063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 838, 6063 Classifications: {'peptide': 838} Incomplete info: {'truncation_to_alanine': 197} Link IDs: {'PTRANS': 20, 'TRANS': 817} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 688 Unresolved non-hydrogen angles: 849 Unresolved non-hydrogen dihedrals: 557 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'ASP:plan': 33, 'HIS:plan': 2, 'ARG:plan': 7, 'GLU:plan': 32, 'PHE:plan': 6, 'ASN:plan1': 15, 'TYR:plan': 2, 'TRP:plan': 1, 'GLN:plan1': 9} Unresolved non-hydrogen planarities: 412 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.72, per 1000 atoms: 0.22 Number of scatterers: 12505 At special positions: 0 Unit cell: (92.22, 110.24, 139.92, 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 33 16.00 P 3 15.00 O 2326 8.00 N 2102 7.00 C 8041 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 567.7 milliseconds 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3154 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 10 sheets defined 48.1% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'C' and resid 2 through 13 Processing helix chain 'A' and resid 3 through 10 removed outlier: 3.899A pdb=" N LEU A 6 " --> pdb=" O GLY A 3 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N HIS A 8 " --> pdb=" O MET A 5 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR A 10 " --> pdb=" O TYR A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 88 removed outlier: 4.202A pdb=" N LYS A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 106 removed outlier: 3.528A pdb=" N GLU A 104 " --> pdb=" O GLU A 100 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET A 105 " --> pdb=" O THR A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 141 removed outlier: 3.841A pdb=" N ILE A 140 " --> pdb=" O LEU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 200 No H-bonds generated for 'chain 'A' and resid 198 through 200' Processing helix chain 'A' and resid 201 through 212 Processing helix chain 'A' and resid 270 through 285 Processing helix chain 'A' and resid 316 through 324 Processing helix chain 'A' and resid 332 through 356 Processing helix chain 'A' and resid 364 through 366 No H-bonds generated for 'chain 'A' and resid 364 through 366' Processing helix chain 'A' and resid 407 through 425 Processing helix chain 'A' and resid 437 through 450 removed outlier: 3.734A pdb=" N GLY A 450 " --> pdb=" O ARG A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 471 removed outlier: 3.748A pdb=" N PHE A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 505 Processing helix chain 'A' and resid 517 through 522 Processing helix chain 'A' and resid 532 through 543 removed outlier: 4.203A pdb=" N ALA A 536 " --> pdb=" O GLY A 532 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 558 removed outlier: 3.800A pdb=" N HIS A 551 " --> pdb=" O ASN A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 584 removed outlier: 4.055A pdb=" N ILE A 577 " --> pdb=" O GLY A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 596 removed outlier: 4.010A pdb=" N LYS A 596 " --> pdb=" O ASP A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 626 removed outlier: 4.031A pdb=" N ILE A 615 " --> pdb=" O GLY A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 648 removed outlier: 3.968A pdb=" N LEU A 632 " --> pdb=" O ASP A 628 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU A 648 " --> pdb=" O ASN A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 683 Processing helix chain 'A' and resid 684 through 700 removed outlier: 3.747A pdb=" N TYR A 688 " --> pdb=" O ASN A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 743 removed outlier: 3.846A pdb=" N ILE A 731 " --> pdb=" O GLY A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 756 Processing helix chain 'A' and resid 757 through 760 removed outlier: 3.625A pdb=" N ILE A 760 " --> pdb=" O LEU A 757 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 757 through 760' Processing helix chain 'A' and resid 773 through 776 Processing helix chain 'A' and resid 777 through 783 Processing helix chain 'A' and resid 788 through 801 Processing helix chain 'A' and resid 815 through 819 removed outlier: 3.972A pdb=" N PHE A 819 " --> pdb=" O GLN A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 842 removed outlier: 3.609A pdb=" N ILE A 832 " --> pdb=" O GLY A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 860 removed outlier: 3.529A pdb=" N THR A 860 " --> pdb=" O PHE A 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 10 removed outlier: 3.831A pdb=" N LEU B 6 " --> pdb=" O GLY B 3 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N TYR B 7 " --> pdb=" O ASP B 4 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N HIS B 8 " --> pdb=" O MET B 5 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER B 9 " --> pdb=" O LEU B 6 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR B 10 " --> pdb=" O TYR B 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3 through 10' Processing helix chain 'B' and resid 74 through 88 removed outlier: 4.180A pdb=" N LYS B 88 " --> pdb=" O LYS B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 106 removed outlier: 3.636A pdb=" N GLU B 104 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N MET B 105 " --> pdb=" O THR B 101 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN B 106 " --> pdb=" O LEU B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 140 removed outlier: 3.517A pdb=" N ILE B 140 " --> pdb=" O LEU B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 200 No H-bonds generated for 'chain 'B' and resid 198 through 200' Processing helix chain 'B' and resid 201 through 211 Processing helix chain 'B' and resid 270 through 285 Processing helix chain 'B' and resid 316 through 323 Processing helix chain 'B' and resid 333 through 356 Processing helix chain 'B' and resid 380 through 384 removed outlier: 4.560A pdb=" N THR B 383 " --> pdb=" O ASP B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 425 Processing helix chain 'B' and resid 438 through 471 removed outlier: 3.634A pdb=" N GLY B 450 " --> pdb=" O ARG B 446 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ASP B 451 " --> pdb=" O VAL B 447 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N ASP B 452 " --> pdb=" O ASN B 448 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE B 453 " --> pdb=" O TYR B 449 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE B 456 " --> pdb=" O ASP B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 504 Processing helix chain 'B' and resid 517 through 522 Processing helix chain 'B' and resid 524 through 528 removed outlier: 4.135A pdb=" N ASN B 528 " --> pdb=" O GLY B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 543 removed outlier: 4.349A pdb=" N ALA B 536 " --> pdb=" O GLY B 532 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 562 removed outlier: 3.627A pdb=" N HIS B 551 " --> pdb=" O ASN B 547 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR B 555 " --> pdb=" O HIS B 551 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN B 556 " --> pdb=" O GLN B 552 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LEU B 559 " --> pdb=" O THR B 555 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N LYS B 560 " --> pdb=" O GLN B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 565 No H-bonds generated for 'chain 'B' and resid 563 through 565' Processing helix chain 'B' and resid 573 through 584 removed outlier: 4.056A pdb=" N ILE B 577 " --> pdb=" O GLY B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 597 removed outlier: 3.760A pdb=" N SER B 590 " --> pdb=" O TYR B 586 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU B 591 " --> pdb=" O ARG B 587 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ASP B 592 " --> pdb=" O GLU B 588 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE B 593 " --> pdb=" O GLU B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 600 No H-bonds generated for 'chain 'B' and resid 598 through 600' Processing helix chain 'B' and resid 611 through 626 removed outlier: 3.529A pdb=" N ILE B 615 " --> pdb=" O GLY B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 647 removed outlier: 3.668A pdb=" N LEU B 632 " --> pdb=" O ASP B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 683 removed outlier: 4.251A pdb=" N VAL B 671 " --> pdb=" O GLY B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 700 removed outlier: 3.757A pdb=" N TYR B 688 " --> pdb=" O ASN B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 727 through 743 removed outlier: 3.588A pdb=" N ILE B 731 " --> pdb=" O GLY B 727 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA B 734 " --> pdb=" O GLY B 730 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER B 742 " --> pdb=" O LEU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 756 Processing helix chain 'B' and resid 757 through 760 removed outlier: 3.592A pdb=" N ILE B 760 " --> pdb=" O LEU B 757 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 757 through 760' Processing helix chain 'B' and resid 771 through 776 removed outlier: 3.672A pdb=" N PHE B 775 " --> pdb=" O ALA B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 777 through 783 Processing helix chain 'B' and resid 789 through 801 Processing helix chain 'B' and resid 816 through 819 removed outlier: 3.700A pdb=" N PHE B 819 " --> pdb=" O GLN B 816 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 816 through 819' Processing helix chain 'B' and resid 828 through 842 removed outlier: 3.874A pdb=" N ILE B 832 " --> pdb=" O GLY B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 860 removed outlier: 3.937A pdb=" N GLU B 858 " --> pdb=" O ASP B 854 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR B 860 " --> pdb=" O PHE B 856 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 43 removed outlier: 3.542A pdb=" N PHE A 93 " --> pdb=" O TYR A 52 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR A 162 " --> pdb=" O LYS A 153 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 227 through 236 removed outlier: 6.775A pdb=" N LEU A 243 " --> pdb=" O GLU A 230 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N SER A 232 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE A 241 " --> pdb=" O SER A 232 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ARG A 234 " --> pdb=" O GLY A 239 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N GLY A 239 " --> pdb=" O ARG A 234 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLY A 240 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE A 255 " --> pdb=" O TYR A 242 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS A 251 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N HIS A 303 " --> pdb=" O LYS A 299 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N LYS A 299 " --> pdb=" O HIS A 303 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N PHE A 305 " --> pdb=" O HIS A 297 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N HIS A 297 " --> pdb=" O PHE A 305 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL A 307 " --> pdb=" O LEU A 295 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 314 through 315 Processing sheet with id=AA4, first strand: chain 'A' and resid 702 through 705 removed outlier: 3.760A pdb=" N ASN A 712 " --> pdb=" O VAL A 703 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR A 713 " --> pdb=" O LEU A 721 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 805 through 807 removed outlier: 3.607A pdb=" N TYR A 810 " --> pdb=" O LYS A 807 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 39 through 43 removed outlier: 3.568A pdb=" N ILE B 66 " --> pdb=" O VAL B 121 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 227 through 231 removed outlier: 7.176A pdb=" N LEU B 243 " --> pdb=" O GLU B 230 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS B 251 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE B 298 " --> pdb=" O PHE B 305 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ASP B 296 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLU B 309 " --> pdb=" O VAL B 294 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N VAL B 294 " --> pdb=" O GLU B 309 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 313 through 315 removed outlier: 3.732A pdb=" N MET B 314 " --> pdb=" O ILE B 370 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AB1, first strand: chain 'B' and resid 805 through 806 removed outlier: 4.486A pdb=" N PHE B 813 " --> pdb=" O SER B 822 " (cutoff:3.500A) 587 hydrogen bonds defined for protein. 1704 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: 2.33 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 4171 1.37 - 1.51: 3854 1.51 - 1.66: 4676 1.66 - 1.80: 52 1.80 - 1.95: 8 Bond restraints: 12761 Sorted by residual: bond pdb=" O3B AGS A 901 " pdb=" PB AGS A 901 " ideal model delta sigma weight residual 1.673 1.589 0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" O3A AGS A 901 " pdb=" PA AGS A 901 " ideal model delta sigma weight residual 1.664 1.586 0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" N ILE A 437 " pdb=" CA ILE A 437 " ideal model delta sigma weight residual 1.456 1.486 -0.030 9.50e-03 1.11e+04 9.69e+00 bond pdb=" CA TRP A 301 " pdb=" C TRP A 301 " ideal model delta sigma weight residual 1.532 1.502 0.031 1.12e-02 7.97e+03 7.42e+00 bond pdb=" N LEU B 332 " pdb=" CA LEU B 332 " ideal model delta sigma weight residual 1.453 1.489 -0.037 1.36e-02 5.41e+03 7.30e+00 ... (remaining 12756 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.35: 17195 3.35 - 6.70: 154 6.70 - 10.05: 31 10.05 - 13.40: 4 13.40 - 16.75: 1 Bond angle restraints: 17385 Sorted by residual: angle pdb=" C TYR A 436 " pdb=" CA TYR A 436 " pdb=" CB TYR A 436 " ideal model delta sigma weight residual 109.75 93.00 16.75 1.72e+00 3.38e-01 9.48e+01 angle pdb=" N ASP B 434 " pdb=" CA ASP B 434 " pdb=" C ASP B 434 " ideal model delta sigma weight residual 111.71 104.77 6.94 1.15e+00 7.56e-01 3.65e+01 angle pdb=" N GLY B 771 " pdb=" CA GLY B 771 " pdb=" C GLY B 771 " ideal model delta sigma weight residual 111.21 117.14 -5.93 1.04e+00 9.25e-01 3.25e+01 angle pdb=" C SER B 331 " pdb=" N LEU B 332 " pdb=" CA LEU B 332 " ideal model delta sigma weight residual 121.64 115.18 6.46 1.20e+00 6.94e-01 2.90e+01 angle pdb=" N TRP A 301 " pdb=" CA TRP A 301 " pdb=" C TRP A 301 " ideal model delta sigma weight residual 108.00 100.39 7.61 1.48e+00 4.57e-01 2.64e+01 ... (remaining 17380 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.92: 7113 30.92 - 61.84: 352 61.84 - 92.76: 28 92.76 - 123.68: 2 123.68 - 154.60: 1 Dihedral angle restraints: 7496 sinusoidal: 2568 harmonic: 4928 Sorted by residual: dihedral pdb=" C TYR A 436 " pdb=" N TYR A 436 " pdb=" CA TYR A 436 " pdb=" CB TYR A 436 " ideal model delta harmonic sigma weight residual -122.60 -103.67 -18.93 0 2.50e+00 1.60e-01 5.73e+01 dihedral pdb=" CA LYS B 418 " pdb=" C LYS B 418 " pdb=" N ILE B 419 " pdb=" CA ILE B 419 " ideal model delta harmonic sigma weight residual 180.00 156.32 23.68 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" O3A AGS A 901 " pdb=" O3B AGS A 901 " pdb=" PB AGS A 901 " pdb=" PG AGS A 901 " ideal model delta sinusoidal sigma weight residual -107.39 47.21 -154.60 1 3.00e+01 1.11e-03 2.03e+01 ... (remaining 7493 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.139: 1973 0.139 - 0.279: 25 0.279 - 0.418: 1 0.418 - 0.557: 0 0.557 - 0.697: 1 Chirality restraints: 2000 Sorted by residual: chirality pdb=" CG LEU C 7 " pdb=" CB LEU C 7 " pdb=" CD1 LEU C 7 " pdb=" CD2 LEU C 7 " both_signs ideal model delta sigma weight residual False -2.59 -1.89 -0.70 2.00e-01 2.50e+01 1.21e+01 chirality pdb=" CA TYR A 436 " pdb=" N TYR A 436 " pdb=" C TYR A 436 " pdb=" CB TYR A 436 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" C3' AGS A 901 " pdb=" C2' AGS A 901 " pdb=" C4' AGS A 901 " pdb=" O3' AGS A 901 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 1997 not shown) Planarity restraints: 2224 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 433 " 0.017 2.00e-02 2.50e+03 3.60e-02 1.29e+01 pdb=" C LEU B 433 " -0.062 2.00e-02 2.50e+03 pdb=" O LEU B 433 " 0.024 2.00e-02 2.50e+03 pdb=" N ASP B 434 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 414 " 0.012 2.00e-02 2.50e+03 2.02e-02 7.13e+00 pdb=" CG PHE A 414 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE A 414 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE A 414 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE A 414 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 414 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 414 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 435 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.16e+00 pdb=" C LYS A 435 " -0.043 2.00e-02 2.50e+03 pdb=" O LYS A 435 " 0.016 2.00e-02 2.50e+03 pdb=" N TYR A 436 " 0.015 2.00e-02 2.50e+03 ... (remaining 2221 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3386 2.80 - 3.33: 10993 3.33 - 3.85: 21255 3.85 - 4.38: 23476 4.38 - 4.90: 40268 Nonbonded interactions: 99378 Sorted by model distance: nonbonded pdb=" O ASN A 438 " pdb=" N TYR A 441 " model vdw 2.280 3.120 nonbonded pdb=" O MET C 1 " pdb=" ND2 ASN A 217 " model vdw 2.321 3.120 nonbonded pdb=" O LEU C 7 " pdb=" OG SER C 11 " model vdw 2.424 3.040 nonbonded pdb=" N GLY B 399 " pdb=" N PHE B 400 " model vdw 2.495 2.560 nonbonded pdb=" N TRP A 301 " pdb=" O TRP A 301 " model vdw 2.496 2.496 ... (remaining 99373 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 or (resid 4 through 6 and (name N or name CA or name C o \ r name O or name CB )) or resid 7 or (resid 8 and (name N or name CA or name C o \ r name O or name CB )) or resid 9 through 11 or (resid 12 through 13 and (name N \ or name CA or name C or name O or name CB )) or resid 14 through 25 or (resid 2 \ 6 through 34 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 5 through 210 or (resid 211 and (name N or name CA or name C or name O or name C \ B )) or resid 212 through 232 or (resid 233 and (name N or name CA or name C or \ name O or name CB )) or resid 234 or (resid 235 through 237 and (name N or name \ CA or name C or name O or name CB )) or resid 238 through 242 or (resid 243 thro \ ugh 245 and (name N or name CA or name C or name O or name CB )) or resid 246 th \ rough 255 or (resid 256 through 258 and (name N or name CA or name C or name O o \ r name CB )) or resid 259 through 277 or (resid 278 and (name N or name CA or na \ me C or name O or name CB )) or resid 279 through 282 or (resid 283 through 287 \ and (name N or name CA or name C or name O or name CB )) or resid 288 through 30 \ 2 or (resid 303 through 305 and (name N or name CA or name C or name O or name C \ B )) or resid 306 through 308 or (resid 309 through 310 and (name N or name CA o \ r name C or name O or name CB )) or resid 311 through 363 or (resid 364 and (nam \ e N or name CA or name C or name O or name CB )) or resid 365 through 379 or (re \ sid 380 and (name N or name CA or name C or name O or name CB )) or resid 381 or \ (resid 382 through 385 and (name N or name CA or name C or name O or name CB )) \ or resid 386 through 400 or (resid 401 and (name N or name CA or name C or name \ O or name CB )) or resid 402 through 403 or (resid 404 and (name N or name CA o \ r name C or name O or name CB )) or resid 405 through 434 or (resid 435 and (nam \ e N or name CA or name C or name O or name CB )) or resid 436 through 475 or (re \ sid 476 through 477 and (name N or name CA or name C or name O or name CB )) or \ resid 478 or (resid 479 through 483 and (name N or name CA or name C or name O o \ r name CB )) or resid 484 or (resid 485 through 489 and (name N or name CA or na \ me C or name O or name CB )) or resid 490 through 491 or (resid 492 and (name N \ or name CA or name C or name O or name CB )) or resid 493 through 495 or (resid \ 496 and (name N or name CA or name C or name O or name CB )) or resid 497 throug \ h 498 or (resid 499 through 500 and (name N or name CA or name C or name O or na \ me CB )) or resid 501 through 525 or (resid 526 and (name N or name CA or name C \ or name O or name CB )) or resid 527 through 544 or (resid 545 through 546 and \ (name N or name CA or name C or name O or name CB )) or resid 547 or (resid 548 \ through 549 and (name N or name CA or name C or name O or name CB )) or resid 55 \ 0 through 551 or (resid 552 and (name N or name CA or name C or name O or name C \ B )) or resid 553 through 559 or (resid 560 through 561 and (name N or name CA o \ r name C or name O or name CB )) or resid 562 or (resid 563 and (name N or name \ CA or name C or name O or name CB )) or resid 564 through 580 or (resid 581 and \ (name N or name CA or name C or name O or name CB )) or resid 582 through 591 or \ (resid 592 and (name N or name CA or name C or name O or name CB )) or resid 59 \ 3 through 595 or (resid 596 and (name N or name CA or name C or name O or name C \ B )) or resid 597 or (resid 598 through 601 and (name N or name CA or name C or \ name O or name CB )) or resid 602 or (resid 603 and (name N or name CA or name C \ or name O or name CB )) or resid 604 or (resid 605 and (name N or name CA or na \ me C or name O or name CB )) or resid 606 through 622 or (resid 623 and (name N \ or name CA or name C or name O or name CB )) or resid 624 through 629 or (resid \ 630 and (name N or name CA or name C or name O or name CB )) or resid 631 throug \ h 632 or (resid 633 and (name N or name CA or name C or name O or name CB )) or \ resid 634 through 643 or (resid 644 and (name N or name CA or name C or name O o \ r name CB )) or resid 645 through 648 or (resid 649 and (name N or name CA or na \ me C or name O or name CB )) or resid 650 through 657 or (resid 658 and (name N \ or name CA or name C or name O or name CB )) or resid 659 through 689 or (resid \ 690 through 691 and (name N or name CA or name C or name O or name CB )) or resi \ d 692 through 704 or (resid 705 and (name N or name CA or name C or name O or na \ me CB )) or resid 706 or (resid 707 and (name N or name CA or name C or name O o \ r name CB )) or resid 708 through 717 or (resid 718 through 719 and (name N or n \ ame CA or name C or name O or name CB )) or resid 720 through 752 or (resid 753 \ and (name N or name CA or name C or name O or name CB )) or resid 754 through 75 \ 8 or (resid 759 and (name N or name CA or name C or name O or name CB )) or resi \ d 760 through 764 or (resid 765 and (name N or name CA or name C or name O or na \ me CB )) or resid 766 through 784 or (resid 785 through 787 and (name N or name \ CA or name C or name O or name CB )) or resid 788 through 793 or (resid 794 thro \ ugh 795 and (name N or name CA or name C or name O or name CB )) or resid 796 th \ rough 797 or (resid 798 and (name N or name CA or name C or name O or name CB )) \ or resid 799 through 805 or (resid 806 and (name N or name CA or name C or name \ O or name CB )) or resid 807 or (resid 808 through 809 and (name N or name CA o \ r name C or name O or name CB )) or resid 810 through 839 or (resid 840 and (nam \ e N or name CA or name C or name O or name CB )) or resid 841 or (resid 842 thro \ ugh 843 and (name N or name CA or name C or name O or name CB )) or resid 844 th \ rough 853 or (resid 854 and (name N or name CA or name C or name O or name CB )) \ or resid 855 through 857 or (resid 858 through 859 and (name N or name CA or na \ me C or name O or name CB )) or resid 860 through 862 or (resid 863 and (name N \ or name CA or name C or name O or name CB )))) selection = (chain 'B' and (resid 3 through 256 or (resid 257 through 258 and (name N or nam \ e CA or name C or name O or name CB )) or resid 259 through 276 or (resid 277 th \ rough 278 and (name N or name CA or name C or name O or name CB )) or resid 279 \ through 494 or (resid 495 through 496 and (name N or name CA or name C or name O \ or name CB )) or resid 497 through 523 or (resid 524 and (name N or name CA or \ name C or name O or name CB )) or resid 525 through 528 or (resid 529 and (name \ N or name CA or name C or name O or name CB )) or resid 530 through 566 or (resi \ d 567 through 568 and (name N or name CA or name C or name O or name CB )) or re \ sid 569 through 573 or (resid 574 through 575 and (name N or name CA or name C o \ r name O or name CB )) or resid 576 through 588 or (resid 589 and (name N or nam \ e CA or name C or name O or name CB )) or resid 590 through 631 or (resid 632 th \ rough 633 and (name N or name CA or name C or name O or name CB )) or resid 634 \ through 635 or (resid 636 and (name N or name CA or name C or name O or name CB \ )) or resid 637 or (resid 638 through 639 and (name N or name CA or name C or na \ me O or name CB )) or resid 640 through 646 or (resid 647 through 649 and (name \ N or name CA or name C or name O or name CB )) or resid 650 through 676 or (resi \ d 677 and (name N or name CA or name C or name O or name CB )) or resid 678 thro \ ugh 697 or (resid 698 and (name N or name CA or name C or name O or name CB )) o \ r resid 699 or (resid 700 and (name N or name CA or name C or name O or name CB \ )) or resid 701 through 715 or (resid 716 through 719 and (name N or name CA or \ name C or name O or name CB )) or resid 720 through 744 or (resid 745 and (name \ N or name CA or name C or name O or name CB )) or resid 746 through 749 or (resi \ d 750 and (name N or name CA or name C or name O or name CB )) or resid 751 thro \ ugh 775 or (resid 776 and (name N or name CA or name C or name O or name CB )) o \ r resid 777 through 790 or (resid 791 and (name N or name CA or name C or name O \ or name CB )) or resid 792 through 816 or (resid 817 through 818 and (name N or \ name CA or name C or name O or name CB )) or resid 819 through 821 or (resid 82 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 823 through \ 828 or (resid 829 and (name N or name CA or name C or name O or name CB )) or re \ sid 830 through 863)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.100 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 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 : 0.004 0.084 12761 Z= 0.220 Angle : 0.870 16.746 17385 Z= 0.476 Chirality : 0.054 0.697 2000 Planarity : 0.005 0.059 2224 Dihedral : 17.696 154.604 4342 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.65 % Favored : 94.17 % Rotamer: Outliers : 3.30 % Allowed : 26.63 % Favored : 70.08 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.17), residues: 1681 helix: -1.60 (0.15), residues: 738 sheet: -0.79 (0.41), residues: 137 loop : -2.08 (0.19), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 542 TYR 0.022 0.001 TYR A 436 PHE 0.045 0.002 PHE A 414 TRP 0.038 0.002 TRP B 444 HIS 0.010 0.001 HIS B 467 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.22 (12761) covalent geometry : angle 0.87010 / 0.48 (17385) hydrogen bonds : bond 0.15656 / 9.87 ( 587) hydrogen bonds : angle 7.44513 / 5.16 ( 1704) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 148 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: C 4 VAL cc_start: 0.7026 (t) cc_final: 0.6686 (p) REVERT: A 27 ILE cc_start: 0.5438 (OUTLIER) cc_final: 0.4602 (tp) REVERT: A 49 TRP cc_start: 0.7090 (m100) cc_final: 0.6660 (m100) REVERT: A 234 ARG cc_start: 0.7465 (ptp-110) cc_final: 0.6774 (mpp80) REVERT: A 242 TYR cc_start: 0.7078 (OUTLIER) cc_final: 0.5719 (p90) REVERT: A 360 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.7809 (tpt) REVERT: A 487 MET cc_start: 0.7779 (mmm) cc_final: 0.7508 (mmt) REVERT: A 666 ASP cc_start: 0.7291 (OUTLIER) cc_final: 0.6577 (t0) REVERT: A 827 SER cc_start: 0.8167 (p) cc_final: 0.7961 (p) REVERT: B 105 MET cc_start: 0.2133 (pmm) cc_final: 0.0661 (mmt) REVERT: B 288 VAL cc_start: -0.0650 (OUTLIER) cc_final: -0.1052 (p) REVERT: B 698 ASP cc_start: 0.7420 (t70) cc_final: 0.6914 (t0) outliers start: 38 outliers final: 23 residues processed: 176 average time/residue: 0.0818 time to fit residues: 23.2732 Evaluate side-chains 170 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 242 TYR Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 436 TYR Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 797 ILE Chi-restraints excluded: chain B residue 803 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 30.0000 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.0670 chunk 103 optimal weight: 0.0980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 HIS B 317 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.199416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.144748 restraints weight = 23103.594| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 4.67 r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 12761 Z= 0.094 Angle : 0.479 8.706 17385 Z= 0.255 Chirality : 0.040 0.143 2000 Planarity : 0.003 0.044 2224 Dihedral : 9.425 173.298 1904 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.46 % Favored : 95.42 % Rotamer: Outliers : 3.82 % Allowed : 25.24 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.19), residues: 1681 helix: -0.07 (0.18), residues: 741 sheet: -0.47 (0.40), residues: 141 loop : -1.77 (0.20), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 137 TYR 0.011 0.001 TYR A 586 PHE 0.011 0.001 PHE A 31 TRP 0.021 0.001 TRP B 413 HIS 0.005 0.001 HIS A 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.09 (12761) covalent geometry : angle 0.47898 / 0.25 (17385) hydrogen bonds : bond 0.03376 / 2.16 ( 587) hydrogen bonds : angle 5.11917 / 3.50 ( 1704) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 148 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 TRP cc_start: 0.7008 (m100) cc_final: 0.5939 (m100) REVERT: A 98 ASN cc_start: 0.7520 (m-40) cc_final: 0.7000 (t0) REVERT: A 105 MET cc_start: 0.7592 (pmm) cc_final: 0.6422 (ppp) REVERT: A 127 ASN cc_start: 0.7436 (OUTLIER) cc_final: 0.6836 (p0) REVERT: A 242 TYR cc_start: 0.7777 (OUTLIER) cc_final: 0.6284 (p90) REVERT: A 623 TYR cc_start: 0.7979 (t80) cc_final: 0.7730 (t80) REVERT: A 666 ASP cc_start: 0.7740 (OUTLIER) cc_final: 0.7096 (t0) REVERT: A 827 SER cc_start: 0.8361 (p) cc_final: 0.8107 (p) REVERT: B 105 MET cc_start: 0.2298 (pmm) cc_final: 0.1783 (ptt) REVERT: B 698 ASP cc_start: 0.8390 (t70) cc_final: 0.8072 (t0) REVERT: B 823 ASP cc_start: 0.6856 (m-30) cc_final: 0.6036 (p0) outliers start: 44 outliers final: 23 residues processed: 182 average time/residue: 0.0725 time to fit residues: 21.5115 Evaluate side-chains 162 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 242 TYR Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 436 TYR Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 206 HIS Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 803 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: [99, 38, 49, 41, 124, 95, 145, 159, 26, 4, 98] chunk 99 optimal weight: 30.0000 chunk 38 optimal weight: 9.9990 chunk 49 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 124 optimal weight: 0.1980 chunk 95 optimal weight: 9.9990 chunk 145 optimal weight: 2.9990 chunk 159 optimal weight: 0.6980 chunk 26 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 8 GLN A 89 HIS A 206 HIS B 77 GLN B 317 HIS ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.195062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.131434 restraints weight = 23481.034| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 3.87 r_work: 0.3648 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12761 Z= 0.153 Angle : 0.517 7.578 17385 Z= 0.274 Chirality : 0.042 0.148 2000 Planarity : 0.003 0.040 2224 Dihedral : 9.059 175.139 1885 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.18 % Favored : 94.71 % Rotamer: Outliers : 5.20 % Allowed : 24.63 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.20), residues: 1681 helix: 0.40 (0.19), residues: 755 sheet: -0.19 (0.41), residues: 141 loop : -1.73 (0.20), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 518 TYR 0.014 0.001 TYR B 688 PHE 0.016 0.001 PHE A 456 TRP 0.016 0.001 TRP B 413 HIS 0.024 0.001 HIS B 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (12761) covalent geometry : angle 0.51671 / 0.27 (17385) hydrogen bonds : bond 0.03394 / 2.20 ( 587) hydrogen bonds : angle 4.85416 / 3.33 ( 1704) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 131 time to evaluate : 0.480 Fit side-chains REVERT: A 49 TRP cc_start: 0.6990 (m100) cc_final: 0.6137 (m100) REVERT: A 77 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8632 (pm20) REVERT: A 105 MET cc_start: 0.7655 (pmm) cc_final: 0.6651 (ppp) REVERT: A 127 ASN cc_start: 0.7620 (OUTLIER) cc_final: 0.6940 (p0) REVERT: A 242 TYR cc_start: 0.7862 (OUTLIER) cc_final: 0.6264 (p90) REVERT: A 411 MET cc_start: 0.7688 (tpp) cc_final: 0.7436 (tmm) REVERT: A 591 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8835 (mm) REVERT: A 623 TYR cc_start: 0.8413 (t80) cc_final: 0.8040 (t80) REVERT: A 666 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7233 (t70) REVERT: A 733 VAL cc_start: 0.9078 (OUTLIER) cc_final: 0.8807 (p) REVERT: A 781 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8556 (mtt) REVERT: A 827 SER cc_start: 0.8820 (p) cc_final: 0.8613 (p) REVERT: B 288 VAL cc_start: 0.0309 (OUTLIER) cc_final: -0.0104 (p) REVERT: B 669 SER cc_start: 0.8532 (m) cc_final: 0.8109 (m) REVERT: B 698 ASP cc_start: 0.8417 (t70) cc_final: 0.8028 (t0) REVERT: B 750 GLU cc_start: 0.7521 (mp0) cc_final: 0.6881 (mp0) REVERT: B 823 ASP cc_start: 0.7464 (m-30) cc_final: 0.6099 (p0) outliers start: 60 outliers final: 28 residues processed: 179 average time/residue: 0.0786 time to fit residues: 23.1043 Evaluate side-chains 158 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 122 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 242 TYR Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 436 TYR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 728 SER Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 803 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: [76, 15, 23, 90, 40, 49, 25, 78, 134, 132, 37] chunk 76 optimal weight: 0.6980 chunk 15 optimal weight: 6.9990 chunk 23 optimal weight: 0.0370 chunk 90 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 25 optimal weight: 20.0000 chunk 78 optimal weight: 0.9980 chunk 134 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 overall best weight: 1.3260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 HIS A 206 HIS B 317 HIS ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.195074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.126499 restraints weight = 23079.339| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 4.09 r_work: 0.3666 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12761 Z= 0.131 Angle : 0.502 7.867 17385 Z= 0.263 Chirality : 0.041 0.149 2000 Planarity : 0.003 0.039 2224 Dihedral : 8.998 178.199 1885 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.53 % Favored : 94.35 % Rotamer: Outliers : 4.86 % Allowed : 24.89 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.20), residues: 1681 helix: 0.66 (0.19), residues: 748 sheet: -0.11 (0.41), residues: 141 loop : -1.67 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 518 TYR 0.017 0.001 TYR B 688 PHE 0.014 0.001 PHE B 204 TRP 0.018 0.001 TRP B 413 HIS 0.020 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (12761) covalent geometry : angle 0.50160 / 0.26 (17385) hydrogen bonds : bond 0.03190 / 2.07 ( 587) hydrogen bonds : angle 4.71500 / 3.22 ( 1704) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 128 time to evaluate : 0.491 Fit side-chains REVERT: A 49 TRP cc_start: 0.6931 (m100) cc_final: 0.6251 (m100) REVERT: A 77 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8552 (pm20) REVERT: A 105 MET cc_start: 0.7621 (pmm) cc_final: 0.6642 (ppp) REVERT: A 127 ASN cc_start: 0.7598 (OUTLIER) cc_final: 0.6907 (p0) REVERT: A 242 TYR cc_start: 0.7818 (OUTLIER) cc_final: 0.6255 (p90) REVERT: A 411 MET cc_start: 0.7724 (tpp) cc_final: 0.7474 (tmm) REVERT: A 587 ARG cc_start: 0.8690 (mtp85) cc_final: 0.8309 (mtp85) REVERT: A 591 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8749 (mm) REVERT: A 623 TYR cc_start: 0.8352 (t80) cc_final: 0.7948 (t80) REVERT: B 288 VAL cc_start: 0.0075 (OUTLIER) cc_final: -0.0351 (p) REVERT: B 411 MET cc_start: 0.5734 (tmm) cc_final: 0.4693 (ppp) REVERT: B 669 SER cc_start: 0.8487 (m) cc_final: 0.8070 (m) REVERT: B 698 ASP cc_start: 0.8387 (t70) cc_final: 0.8009 (t0) REVERT: B 750 GLU cc_start: 0.7559 (mp0) cc_final: 0.6949 (mp0) REVERT: B 823 ASP cc_start: 0.7349 (m-30) cc_final: 0.6045 (p0) outliers start: 56 outliers final: 33 residues processed: 169 average time/residue: 0.0815 time to fit residues: 22.2148 Evaluate side-chains 162 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 124 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 242 TYR Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 436 TYR Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain B residue 108 LYS Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 594 PHE Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 728 SER Chi-restraints excluded: chain B residue 803 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: [122, 88, 50, 51, 58, 33, 90, 0, 95, 8, 146] chunk 122 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 95 optimal weight: 20.0000 chunk 8 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 HIS A 206 HIS ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 HIS B 716 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.194273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.128060 restraints weight = 23218.141| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 3.50 r_work: 0.3640 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12761 Z= 0.142 Angle : 0.513 8.136 17385 Z= 0.267 Chirality : 0.042 0.167 2000 Planarity : 0.003 0.040 2224 Dihedral : 8.806 179.977 1878 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.47 % Favored : 94.41 % Rotamer: Outliers : 4.77 % Allowed : 25.24 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.20), residues: 1681 helix: 0.77 (0.19), residues: 743 sheet: -0.06 (0.41), residues: 143 loop : -1.60 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 518 TYR 0.018 0.001 TYR B 688 PHE 0.015 0.001 PHE B 622 TRP 0.020 0.001 TRP B 413 HIS 0.020 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (12761) covalent geometry : angle 0.51343 / 0.27 (17385) hydrogen bonds : bond 0.03174 / 2.06 ( 587) hydrogen bonds : angle 4.65001 / 3.16 ( 1704) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 122 time to evaluate : 0.459 Fit side-chains REVERT: A 49 TRP cc_start: 0.6820 (m100) cc_final: 0.6225 (m100) REVERT: A 77 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.8459 (pm20) REVERT: A 105 MET cc_start: 0.7618 (pmm) cc_final: 0.6764 (ppp) REVERT: A 127 ASN cc_start: 0.7648 (OUTLIER) cc_final: 0.6974 (p0) REVERT: A 242 TYR cc_start: 0.7724 (OUTLIER) cc_final: 0.6137 (p90) REVERT: A 411 MET cc_start: 0.7754 (tpp) cc_final: 0.7421 (tmm) REVERT: A 587 ARG cc_start: 0.8724 (mtp85) cc_final: 0.8312 (mtp85) REVERT: A 591 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8773 (mm) REVERT: B 288 VAL cc_start: 0.0204 (OUTLIER) cc_final: -0.0189 (p) REVERT: B 669 SER cc_start: 0.8486 (m) cc_final: 0.8095 (m) REVERT: B 698 ASP cc_start: 0.8418 (t70) cc_final: 0.7974 (t0) outliers start: 55 outliers final: 36 residues processed: 162 average time/residue: 0.0798 time to fit residues: 21.0981 Evaluate side-chains 159 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 118 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 242 TYR Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 436 TYR Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain B residue 108 LYS Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 728 SER Chi-restraints excluded: chain B residue 763 THR Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 803 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: [56, 118, 65, 146, 15, 104, 138, 134, 21, 90, 141] chunk 56 optimal weight: 0.9980 chunk 118 optimal weight: 30.0000 chunk 65 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 104 optimal weight: 6.9990 chunk 138 optimal weight: 0.8980 chunk 134 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 141 optimal weight: 10.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 HIS A 206 HIS ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.194756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.126708 restraints weight = 23104.742| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 3.87 r_work: 0.3667 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12761 Z= 0.121 Angle : 0.509 8.314 17385 Z= 0.265 Chirality : 0.041 0.151 2000 Planarity : 0.003 0.040 2224 Dihedral : 8.748 179.360 1877 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.41 % Favored : 94.47 % Rotamer: Outliers : 4.08 % Allowed : 26.54 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.20), residues: 1681 helix: 0.86 (0.19), residues: 748 sheet: 0.14 (0.42), residues: 143 loop : -1.57 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 690 TYR 0.021 0.001 TYR B 688 PHE 0.014 0.001 PHE B 622 TRP 0.022 0.001 TRP B 413 HIS 0.005 0.001 HIS A 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (12761) covalent geometry : angle 0.50883 / 0.27 (17385) hydrogen bonds : bond 0.03023 / 1.95 ( 587) hydrogen bonds : angle 4.57115 / 3.10 ( 1704) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 125 time to evaluate : 0.447 Fit side-chains REVERT: A 49 TRP cc_start: 0.6802 (m100) cc_final: 0.6339 (m100) REVERT: A 77 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8426 (pm20) REVERT: A 105 MET cc_start: 0.7684 (pmm) cc_final: 0.6806 (ppp) REVERT: A 127 ASN cc_start: 0.7646 (OUTLIER) cc_final: 0.6984 (p0) REVERT: A 242 TYR cc_start: 0.7668 (OUTLIER) cc_final: 0.6201 (p90) REVERT: A 411 MET cc_start: 0.7731 (tpp) cc_final: 0.7455 (tmm) REVERT: A 516 ASP cc_start: 0.8295 (t0) cc_final: 0.8059 (t70) REVERT: A 591 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8779 (mm) REVERT: B 288 VAL cc_start: -0.0005 (OUTLIER) cc_final: -0.0411 (p) REVERT: B 411 MET cc_start: 0.5641 (tmm) cc_final: 0.4653 (ppp) REVERT: B 669 SER cc_start: 0.8424 (m) cc_final: 0.8017 (m) REVERT: B 698 ASP cc_start: 0.8405 (t70) cc_final: 0.7974 (t0) outliers start: 47 outliers final: 34 residues processed: 160 average time/residue: 0.0766 time to fit residues: 20.1956 Evaluate side-chains 158 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 119 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 242 TYR Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 436 TYR Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain B residue 108 LYS Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 594 PHE Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 728 SER Chi-restraints excluded: chain B residue 763 THR Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 803 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: [19, 46, 7, 29, 30, 137, 0, 36, 119, 58, 116] chunk 19 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 29 optimal weight: 20.0000 chunk 30 optimal weight: 0.9990 chunk 137 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 36 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 116 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 HIS A 206 HIS ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 HIS B 740 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.188918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.120744 restraints weight = 22992.234| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 3.78 r_work: 0.3555 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 12761 Z= 0.285 Angle : 0.650 8.472 17385 Z= 0.342 Chirality : 0.046 0.192 2000 Planarity : 0.004 0.040 2224 Dihedral : 9.066 179.823 1877 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.78 % Favored : 93.10 % Rotamer: Outliers : 5.03 % Allowed : 25.50 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.20), residues: 1681 helix: 0.61 (0.19), residues: 739 sheet: -0.09 (0.45), residues: 130 loop : -1.60 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 518 TYR 0.026 0.002 TYR B 688 PHE 0.028 0.002 PHE B 622 TRP 0.025 0.002 TRP B 413 HIS 0.026 0.002 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00663 / 0.29 (12761) covalent geometry : angle 0.64983 / 0.34 (17385) hydrogen bonds : bond 0.04009 / 2.59 ( 587) hydrogen bonds : angle 5.02780 / 3.40 ( 1704) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 114 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 95 HIS cc_start: 0.2605 (OUTLIER) cc_final: 0.1352 (p90) REVERT: A 105 MET cc_start: 0.8073 (pmm) cc_final: 0.7239 (ppp) REVERT: A 127 ASN cc_start: 0.7585 (OUTLIER) cc_final: 0.6892 (p0) REVERT: A 242 TYR cc_start: 0.7738 (OUTLIER) cc_final: 0.6276 (p90) REVERT: A 411 MET cc_start: 0.7986 (tpp) cc_final: 0.7501 (tmm) REVERT: A 516 ASP cc_start: 0.8235 (t0) cc_final: 0.7928 (t70) REVERT: A 591 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8943 (mm) REVERT: A 826 PHE cc_start: 0.8396 (t80) cc_final: 0.8098 (t80) REVERT: B 288 VAL cc_start: -0.0343 (OUTLIER) cc_final: -0.0775 (p) REVERT: B 698 ASP cc_start: 0.8356 (t70) cc_final: 0.7990 (t70) outliers start: 58 outliers final: 41 residues processed: 159 average time/residue: 0.0791 time to fit residues: 20.6933 Evaluate side-chains 156 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 110 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 242 TYR Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 436 TYR Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain B residue 108 LYS Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 728 SER Chi-restraints excluded: chain B residue 763 THR Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 803 TYR Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 830 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: [162, 152, 115, 8, 54, 56, 120, 165, 100, 102, 35] chunk 162 optimal weight: 2.9990 chunk 152 optimal weight: 0.6980 chunk 115 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 120 optimal weight: 0.0670 chunk 165 optimal weight: 3.9990 chunk 100 optimal weight: 20.0000 chunk 102 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 HIS A 206 HIS ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.193925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.131190 restraints weight = 22938.704| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 3.77 r_work: 0.3638 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12761 Z= 0.106 Angle : 0.521 9.149 17385 Z= 0.271 Chirality : 0.042 0.187 2000 Planarity : 0.003 0.042 2224 Dihedral : 8.749 174.815 1877 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.29 % Favored : 94.65 % Rotamer: Outliers : 4.08 % Allowed : 26.71 % Favored : 69.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.20), residues: 1681 helix: 0.90 (0.19), residues: 748 sheet: 0.08 (0.45), residues: 132 loop : -1.54 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 542 TYR 0.017 0.001 TYR B 688 PHE 0.013 0.001 PHE B 622 TRP 0.024 0.002 TRP A 49 HIS 0.004 0.001 HIS B 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (12761) covalent geometry : angle 0.52058 / 0.27 (17385) hydrogen bonds : bond 0.03019 / 1.94 ( 587) hydrogen bonds : angle 4.60536 / 3.09 ( 1704) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 128 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: A 49 TRP cc_start: 0.7179 (m100) cc_final: 0.6595 (m100) REVERT: A 77 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.8236 (pm20) REVERT: A 105 MET cc_start: 0.7824 (pmm) cc_final: 0.6944 (ppp) REVERT: A 242 TYR cc_start: 0.7722 (OUTLIER) cc_final: 0.6185 (p90) REVERT: A 411 MET cc_start: 0.7773 (tpp) cc_final: 0.7407 (tmm) REVERT: A 487 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.8148 (mmp) REVERT: A 516 ASP cc_start: 0.8217 (t0) cc_final: 0.7993 (t70) REVERT: A 695 VAL cc_start: 0.8602 (OUTLIER) cc_final: 0.8286 (t) REVERT: B 288 VAL cc_start: 0.0014 (OUTLIER) cc_final: -0.0411 (p) REVERT: B 523 HIS cc_start: 0.7195 (OUTLIER) cc_final: 0.6872 (p90) REVERT: B 698 ASP cc_start: 0.8468 (t70) cc_final: 0.8028 (t70) outliers start: 47 outliers final: 32 residues processed: 161 average time/residue: 0.0766 time to fit residues: 20.3659 Evaluate side-chains 160 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 122 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 242 TYR Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 436 TYR Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain B residue 108 LYS Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 523 HIS Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 669 SER Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 728 SER Chi-restraints excluded: chain B residue 803 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: [65, 52, 120, 56, 78, 139, 132, 79, 47, 123, 97] chunk 65 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 120 optimal weight: 0.0170 chunk 56 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 123 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 overall best weight: 1.1622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 HIS A 206 HIS B 317 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.193432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.130340 restraints weight = 22979.234| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 3.69 r_work: 0.3625 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12761 Z= 0.127 Angle : 0.533 8.415 17385 Z= 0.275 Chirality : 0.042 0.248 2000 Planarity : 0.003 0.041 2224 Dihedral : 8.695 176.046 1877 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.25 % Favored : 93.69 % Rotamer: Outliers : 3.73 % Allowed : 26.54 % Favored : 69.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.20), residues: 1681 helix: 0.94 (0.19), residues: 748 sheet: 0.15 (0.46), residues: 132 loop : -1.50 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 690 TYR 0.026 0.001 TYR B 688 PHE 0.014 0.001 PHE B 622 TRP 0.023 0.001 TRP B 413 HIS 0.008 0.001 HIS B 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (12761) covalent geometry : angle 0.53305 / 0.28 (17385) hydrogen bonds : bond 0.03060 / 1.97 ( 587) hydrogen bonds : angle 4.58982 / 3.08 ( 1704) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 119 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 49 TRP cc_start: 0.7173 (m100) cc_final: 0.6566 (m100) REVERT: A 77 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.8221 (pm20) REVERT: A 105 MET cc_start: 0.7953 (pmm) cc_final: 0.7085 (ppp) REVERT: A 242 TYR cc_start: 0.7681 (OUTLIER) cc_final: 0.6171 (p90) REVERT: A 411 MET cc_start: 0.7801 (tpp) cc_final: 0.7414 (tmm) REVERT: A 487 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.8121 (mmp) REVERT: A 695 VAL cc_start: 0.8737 (OUTLIER) cc_final: 0.8435 (t) REVERT: B 288 VAL cc_start: 0.0039 (OUTLIER) cc_final: -0.0393 (p) REVERT: B 523 HIS cc_start: 0.7166 (OUTLIER) cc_final: 0.6848 (p90) REVERT: B 698 ASP cc_start: 0.8431 (t70) cc_final: 0.8029 (t70) REVERT: B 777 ILE cc_start: 0.8413 (mm) cc_final: 0.8165 (mp) outliers start: 43 outliers final: 31 residues processed: 152 average time/residue: 0.0756 time to fit residues: 18.9441 Evaluate side-chains 154 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 117 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 242 TYR Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain B residue 108 LYS Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 523 HIS Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 728 SER Chi-restraints excluded: chain B residue 803 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: [77, 107, 142, 28, 78, 42, 91, 33, 68, 141, 45] chunk 77 optimal weight: 0.9990 chunk 107 optimal weight: 0.0470 chunk 142 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 141 optimal weight: 6.9990 chunk 45 optimal weight: 8.9990 overall best weight: 1.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 HIS A 206 HIS B 317 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.193402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.129957 restraints weight = 23192.059| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 3.88 r_work: 0.3618 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12761 Z= 0.129 Angle : 0.539 8.378 17385 Z= 0.278 Chirality : 0.042 0.261 2000 Planarity : 0.003 0.041 2224 Dihedral : 8.628 176.015 1875 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.83 % Favored : 94.11 % Rotamer: Outliers : 3.56 % Allowed : 26.80 % Favored : 69.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.20), residues: 1681 helix: 0.96 (0.19), residues: 749 sheet: 0.15 (0.46), residues: 130 loop : -1.49 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 518 TYR 0.048 0.001 TYR B 688 PHE 0.014 0.001 PHE B 456 TRP 0.025 0.001 TRP B 413 HIS 0.004 0.001 HIS B 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (12761) covalent geometry : angle 0.53894 / 0.28 (17385) hydrogen bonds : bond 0.03038 / 1.95 ( 587) hydrogen bonds : angle 4.54538 / 3.06 ( 1704) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 118 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 TYR cc_start: 0.7148 (m-80) cc_final: 0.6782 (m-80) REVERT: A 77 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.8210 (pm20) REVERT: A 105 MET cc_start: 0.7935 (pmm) cc_final: 0.7077 (ppp) REVERT: A 242 TYR cc_start: 0.7719 (OUTLIER) cc_final: 0.6174 (p90) REVERT: A 411 MET cc_start: 0.7824 (tpp) cc_final: 0.7421 (tmm) REVERT: A 487 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.8246 (mmp) REVERT: A 695 VAL cc_start: 0.8751 (OUTLIER) cc_final: 0.8441 (t) REVERT: B 288 VAL cc_start: -0.0048 (OUTLIER) cc_final: -0.0490 (p) REVERT: B 523 HIS cc_start: 0.7252 (OUTLIER) cc_final: 0.6877 (p90) REVERT: B 698 ASP cc_start: 0.8463 (t70) cc_final: 0.8052 (t70) REVERT: B 777 ILE cc_start: 0.8431 (mm) cc_final: 0.8178 (mp) outliers start: 41 outliers final: 31 residues processed: 149 average time/residue: 0.0842 time to fit residues: 20.3900 Evaluate side-chains 153 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 116 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 242 TYR Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain B residue 108 LYS Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 523 HIS Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 728 SER Chi-restraints excluded: chain B residue 797 ILE Chi-restraints excluded: chain B residue 803 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: [99, 120, 27, 115, 52, 47, 60, 97, 119, 16, 85] chunk 99 optimal weight: 10.0000 chunk 120 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 115 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 97 optimal weight: 10.0000 chunk 119 optimal weight: 8.9990 chunk 16 optimal weight: 20.0000 chunk 85 optimal weight: 10.0000 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 HIS A 206 HIS ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.189412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.121237 restraints weight = 23137.750| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 3.74 r_work: 0.3559 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 12761 Z= 0.278 Angle : 0.655 8.839 17385 Z= 0.341 Chirality : 0.046 0.246 2000 Planarity : 0.004 0.041 2224 Dihedral : 8.853 177.212 1871 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.14 % Favored : 92.80 % Rotamer: Outliers : 3.90 % Allowed : 26.37 % Favored : 69.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.20), residues: 1681 helix: 0.73 (0.19), residues: 739 sheet: 0.09 (0.46), residues: 132 loop : -1.52 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 518 TYR 0.051 0.002 TYR B 688 PHE 0.030 0.002 PHE B 622 TRP 0.039 0.002 TRP B 413 HIS 0.005 0.001 HIS B 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00654 / 0.28 (12761) covalent geometry : angle 0.65488 / 0.34 (17385) hydrogen bonds : bond 0.03849 / 2.48 ( 587) hydrogen bonds : angle 4.94579 / 3.34 ( 1704) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3493.32 seconds wall clock time: 60 minutes 24.80 seconds (3624.80 seconds total)