Starting phenix.real_space_refine on Thu Feb 15 13:28:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lvf_0992/02_2024/6lvf_0992_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lvf_0992/02_2024/6lvf_0992.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lvf_0992/02_2024/6lvf_0992_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lvf_0992/02_2024/6lvf_0992_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lvf_0992/02_2024/6lvf_0992_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lvf_0992/02_2024/6lvf_0992.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lvf_0992/02_2024/6lvf_0992.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lvf_0992/02_2024/6lvf_0992_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lvf_0992/02_2024/6lvf_0992_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 40 5.16 5 C 8120 2.51 5 N 2036 2.21 5 O 2178 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 451": "NH1" <-> "NH2" Residue "B PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 619": "NH1" <-> "NH2" Residue "B ARG 670": "NH1" <-> "NH2" Residue "B ARG 756": "NH1" <-> "NH2" Residue "B ARG 806": "NH1" <-> "NH2" Residue "A TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 451": "NH1" <-> "NH2" Residue "A PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 619": "NH1" <-> "NH2" Residue "A ARG 670": "NH1" <-> "NH2" Residue "A ARG 756": "NH1" <-> "NH2" Residue "A ARG 806": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12380 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 6037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 793, 6037 Classifications: {'peptide': 793} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 31, 'TRANS': 761} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 6037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 793, 6037 Classifications: {'peptide': 793} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 31, 'TRANS': 761} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 153 Unusual residues: {'EV9': 1, 'LHG': 1, 'PGT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "A" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 153 Unusual residues: {'EV9': 1, 'LHG': 1, 'PGT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Residues with excluded nonbonded symmetry interactions: 16 residue: pdb=" N GLY B 659 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY B 659 " occ=0.00 residue: pdb=" N ALA B 706 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA B 706 " occ=0.00 residue: pdb=" N LYS B 707 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS B 707 " occ=0.00 residue: pdb=" N LYS B 731 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS B 731 " occ=0.00 residue: pdb=" N ASP B 732 " occ=0.00 ... (6 atoms not shown) pdb=" OD2 ASP B 732 " occ=0.00 residue: pdb=" N GLY B 733 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY B 733 " occ=0.00 residue: pdb=" N LYS B 734 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS B 734 " occ=0.00 residue: pdb=" N ARG B 806 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG B 806 " occ=0.00 residue: pdb=" N GLY A 659 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY A 659 " occ=0.00 residue: pdb=" N ALA A 706 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA A 706 " occ=0.00 residue: pdb=" N LYS A 707 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS A 707 " occ=0.00 residue: pdb=" N LYS A 731 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS A 731 " occ=0.00 ... (remaining 4 not shown) Time building chain proxies: 7.28, per 1000 atoms: 0.59 Number of scatterers: 12380 At special positions: 0 Unit cell: (109, 129, 111, 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 40 16.00 P 6 15.00 O 2178 8.00 N 2036 7.00 C 8120 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.16 Conformation dependent library (CDL) restraints added in 2.4 seconds 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2932 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 64 helices and 6 sheets defined 57.0% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.06 Creating SS restraints... Processing helix chain 'B' and resid 31 through 50 removed outlier: 3.615A pdb=" N VAL B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 64 Processing helix chain 'B' and resid 68 through 95 Processing helix chain 'B' and resid 102 through 110 removed outlier: 4.389A pdb=" N ALA B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LEU B 107 " --> pdb=" O HIS B 104 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER B 109 " --> pdb=" O ALA B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 116 No H-bonds generated for 'chain 'B' and resid 113 through 116' Processing helix chain 'B' and resid 127 through 134 removed outlier: 4.100A pdb=" N ARG B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 166 removed outlier: 3.931A pdb=" N THR B 145 " --> pdb=" O PRO B 141 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ARG B 146 " --> pdb=" O ASP B 142 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA B 149 " --> pdb=" O THR B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 202 removed outlier: 3.523A pdb=" N ALA B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 245 removed outlier: 3.512A pdb=" N SER B 225 " --> pdb=" O SER B 221 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARG B 226 " --> pdb=" O ARG B 222 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU B 242 " --> pdb=" O SER B 238 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU B 245 " --> pdb=" O VAL B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 267 removed outlier: 3.561A pdb=" N ILE B 262 " --> pdb=" O ALA B 258 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY B 265 " --> pdb=" O ALA B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 275 No H-bonds generated for 'chain 'B' and resid 273 through 275' Processing helix chain 'B' and resid 277 through 287 Processing helix chain 'B' and resid 293 through 308 removed outlier: 3.542A pdb=" N LEU B 302 " --> pdb=" O SER B 298 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE B 306 " --> pdb=" O LEU B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 324 removed outlier: 3.634A pdb=" N ILE B 319 " --> pdb=" O ALA B 315 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA B 322 " --> pdb=" O ALA B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 364 Proline residue: B 345 - end of helix removed outlier: 3.881A pdb=" N LEU B 353 " --> pdb=" O SER B 349 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 407 removed outlier: 3.549A pdb=" N GLN B 407 " --> pdb=" O ARG B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 427 Processing helix chain 'B' and resid 434 through 451 removed outlier: 3.748A pdb=" N ARG B 451 " --> pdb=" O LEU B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 489 removed outlier: 4.089A pdb=" N THR B 471 " --> pdb=" O ALA B 467 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG B 489 " --> pdb=" O PHE B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 529 Processing helix chain 'B' and resid 542 through 553 Processing helix chain 'B' and resid 558 through 562 removed outlier: 3.509A pdb=" N ASN B 561 " --> pdb=" O ALA B 558 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU B 562 " --> pdb=" O ASP B 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 558 through 562' Processing helix chain 'B' and resid 602 through 615 removed outlier: 3.704A pdb=" N TRP B 607 " --> pdb=" O PRO B 603 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG B 608 " --> pdb=" O ASP B 604 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL B 610 " --> pdb=" O ILE B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 removed outlier: 4.322A pdb=" N SER B 631 " --> pdb=" O ALA B 628 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ALA B 634 " --> pdb=" O SER B 631 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP B 635 " --> pdb=" O TYR B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 672 removed outlier: 3.625A pdb=" N ALA B 671 " --> pdb=" O THR B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 703 Processing helix chain 'B' and resid 763 through 765 No H-bonds generated for 'chain 'B' and resid 763 through 765' Processing helix chain 'B' and resid 768 through 780 removed outlier: 4.308A pdb=" N ILE B 773 " --> pdb=" O LEU B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 798 Processing helix chain 'B' and resid 806 through 818 Processing helix chain 'B' and resid 825 through 831 removed outlier: 4.388A pdb=" N PHE B 831 " --> pdb=" O PHE B 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 859 removed outlier: 3.596A pdb=" N LEU B 858 " --> pdb=" O ASP B 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 50 removed outlier: 3.615A pdb=" N VAL A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 64 Processing helix chain 'A' and resid 68 through 95 Processing helix chain 'A' and resid 102 through 110 removed outlier: 4.389A pdb=" N ALA A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LEU A 107 " --> pdb=" O HIS A 104 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER A 109 " --> pdb=" O ALA A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 116 No H-bonds generated for 'chain 'A' and resid 113 through 116' Processing helix chain 'A' and resid 127 through 134 removed outlier: 4.100A pdb=" N ARG A 132 " --> pdb=" O ALA A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 166 removed outlier: 3.931A pdb=" N THR A 145 " --> pdb=" O PRO A 141 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ARG A 146 " --> pdb=" O ASP A 142 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA A 149 " --> pdb=" O THR A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 202 removed outlier: 3.522A pdb=" N ALA A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 245 removed outlier: 3.511A pdb=" N SER A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ARG A 226 " --> pdb=" O ARG A 222 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 245 " --> pdb=" O VAL A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 267 removed outlier: 3.561A pdb=" N ILE A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY A 265 " --> pdb=" O ALA A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 275 No H-bonds generated for 'chain 'A' and resid 273 through 275' Processing helix chain 'A' and resid 277 through 287 Processing helix chain 'A' and resid 293 through 308 removed outlier: 3.543A pdb=" N LEU A 302 " --> pdb=" O SER A 298 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 306 " --> pdb=" O LEU A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 324 removed outlier: 3.634A pdb=" N ILE A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 364 Proline residue: A 345 - end of helix removed outlier: 3.881A pdb=" N LEU A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 407 removed outlier: 3.549A pdb=" N GLN A 407 " --> pdb=" O ARG A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 Processing helix chain 'A' and resid 434 through 451 removed outlier: 3.748A pdb=" N ARG A 451 " --> pdb=" O LEU A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 489 removed outlier: 4.088A pdb=" N THR A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG A 489 " --> pdb=" O PHE A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 529 Processing helix chain 'A' and resid 542 through 553 Processing helix chain 'A' and resid 558 through 562 removed outlier: 3.510A pdb=" N ASN A 561 " --> pdb=" O ALA A 558 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU A 562 " --> pdb=" O ASP A 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 558 through 562' Processing helix chain 'A' and resid 602 through 615 removed outlier: 3.705A pdb=" N TRP A 607 " --> pdb=" O PRO A 603 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG A 608 " --> pdb=" O ASP A 604 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL A 610 " --> pdb=" O ILE A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 636 removed outlier: 4.322A pdb=" N SER A 631 " --> pdb=" O ALA A 628 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ALA A 634 " --> pdb=" O SER A 631 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP A 635 " --> pdb=" O TYR A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 672 removed outlier: 3.625A pdb=" N ALA A 671 " --> pdb=" O THR A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 703 Processing helix chain 'A' and resid 763 through 765 No H-bonds generated for 'chain 'A' and resid 763 through 765' Processing helix chain 'A' and resid 768 through 780 removed outlier: 4.309A pdb=" N ILE A 773 " --> pdb=" O LEU A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 798 Processing helix chain 'A' and resid 806 through 818 Processing helix chain 'A' and resid 825 through 831 removed outlier: 4.388A pdb=" N PHE A 831 " --> pdb=" O PHE A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 859 removed outlier: 3.596A pdb=" N LEU A 858 " --> pdb=" O ASP A 854 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 570 through 572 Processing sheet with id= B, first strand: chain 'B' and resid 638 through 645 removed outlier: 7.082A pdb=" N ARG B 838 " --> pdb=" O LEU B 643 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 726 through 730 Processing sheet with id= D, first strand: chain 'A' and resid 570 through 572 Processing sheet with id= E, first strand: chain 'A' and resid 638 through 645 removed outlier: 7.081A pdb=" N ARG A 838 " --> pdb=" O LEU A 643 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 726 through 730 598 hydrogen bonds defined for protein. 1752 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: 3.67 Time building geometry restraints manager: 5.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1918 1.30 - 1.43: 3336 1.43 - 1.55: 7304 1.55 - 1.68: 12 1.68 - 1.81: 70 Bond restraints: 12640 Sorted by residual: bond pdb=" C7 LHG A1002 " pdb=" O7 LHG A1002 " ideal model delta sigma weight residual 1.329 1.456 -0.127 2.00e-02 2.50e+03 4.04e+01 bond pdb=" C7 LHG B1002 " pdb=" O7 LHG B1002 " ideal model delta sigma weight residual 1.329 1.456 -0.127 2.00e-02 2.50e+03 4.04e+01 bond pdb=" C31 PGT A1003 " pdb=" O2 PGT A1003 " ideal model delta sigma weight residual 1.331 1.455 -0.124 2.00e-02 2.50e+03 3.86e+01 bond pdb=" C31 PGT B1003 " pdb=" O2 PGT B1003 " ideal model delta sigma weight residual 1.331 1.455 -0.124 2.00e-02 2.50e+03 3.86e+01 bond pdb=" C11 PGT B1003 " pdb=" O3 PGT B1003 " ideal model delta sigma weight residual 1.327 1.449 -0.122 2.00e-02 2.50e+03 3.72e+01 ... (remaining 12635 not shown) Histogram of bond angle deviations from ideal: 96.85 - 104.33: 186 104.33 - 111.81: 5873 111.81 - 119.29: 4575 119.29 - 126.77: 6328 126.77 - 134.25: 156 Bond angle restraints: 17118 Sorted by residual: angle pdb=" C06 EV9 B1001 " pdb=" C07 EV9 B1001 " pdb=" C08 EV9 B1001 " ideal model delta sigma weight residual 80.36 112.05 -31.69 3.00e+00 1.11e-01 1.12e+02 angle pdb=" C06 EV9 A1001 " pdb=" C07 EV9 A1001 " pdb=" C08 EV9 A1001 " ideal model delta sigma weight residual 80.36 112.04 -31.68 3.00e+00 1.11e-01 1.12e+02 angle pdb=" N LEU A 592 " pdb=" CA LEU A 592 " pdb=" C LEU A 592 " ideal model delta sigma weight residual 112.68 122.48 -9.80 1.33e+00 5.65e-01 5.43e+01 angle pdb=" N LEU B 592 " pdb=" CA LEU B 592 " pdb=" C LEU B 592 " ideal model delta sigma weight residual 112.68 122.43 -9.75 1.33e+00 5.65e-01 5.38e+01 angle pdb=" N PRO B 512 " pdb=" CA PRO B 512 " pdb=" CB PRO B 512 " ideal model delta sigma weight residual 103.44 110.14 -6.70 1.12e+00 7.97e-01 3.58e+01 ... (remaining 17113 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.59: 7288 30.59 - 61.18: 168 61.18 - 91.78: 16 91.78 - 122.37: 2 122.37 - 152.96: 6 Dihedral angle restraints: 7480 sinusoidal: 2928 harmonic: 4552 Sorted by residual: dihedral pdb=" CA GLN A 555 " pdb=" C GLN A 555 " pdb=" N GLY A 556 " pdb=" CA GLY A 556 " ideal model delta harmonic sigma weight residual 180.00 -151.85 -28.15 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" CA GLN B 555 " pdb=" C GLN B 555 " pdb=" N GLY B 556 " pdb=" CA GLY B 556 " ideal model delta harmonic sigma weight residual -180.00 -151.87 -28.13 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" CA SER B 109 " pdb=" C SER B 109 " pdb=" N PHE B 110 " pdb=" CA PHE B 110 " ideal model delta harmonic sigma weight residual 180.00 154.81 25.19 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 7477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1562 0.070 - 0.140: 364 0.140 - 0.210: 42 0.210 - 0.280: 14 0.280 - 0.350: 2 Chirality restraints: 1984 Sorted by residual: chirality pdb=" CA LEU B 592 " pdb=" N LEU B 592 " pdb=" C LEU B 592 " pdb=" CB LEU B 592 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CA LEU A 592 " pdb=" N LEU A 592 " pdb=" C LEU A 592 " pdb=" CB LEU A 592 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" C5 PGT A1003 " pdb=" C4 PGT A1003 " pdb=" C6 PGT A1003 " pdb=" O5 PGT A1003 " both_signs ideal model delta sigma weight residual False -2.30 -2.57 0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 1981 not shown) Planarity restraints: 2120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 589 " -0.033 2.00e-02 2.50e+03 2.33e-02 1.36e+01 pdb=" CG TRP B 589 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP B 589 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP B 589 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 589 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 589 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 589 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 589 " -0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 589 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 589 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 589 " -0.033 2.00e-02 2.50e+03 2.33e-02 1.36e+01 pdb=" CG TRP A 589 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP A 589 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP A 589 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 589 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 589 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 589 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 589 " -0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 589 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 589 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 801 " 0.051 5.00e-02 4.00e+02 7.66e-02 9.38e+00 pdb=" N PRO B 802 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO B 802 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 802 " 0.043 5.00e-02 4.00e+02 ... (remaining 2117 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1818 2.75 - 3.29: 12178 3.29 - 3.83: 21010 3.83 - 4.36: 24172 4.36 - 4.90: 41097 Nonbonded interactions: 100275 Sorted by model distance: nonbonded pdb=" OD1 ASP B 594 " pdb=" CD PRO B 595 " model vdw 2.216 3.440 nonbonded pdb=" OD1 ASP A 594 " pdb=" CD PRO A 595 " model vdw 2.216 3.440 nonbonded pdb=" OD2 ASP B 89 " pdb=" OH TYR B 134 " model vdw 2.226 2.440 nonbonded pdb=" OD2 ASP A 89 " pdb=" OH TYR A 134 " model vdw 2.227 2.440 nonbonded pdb=" OH TYR A 623 " pdb=" OH TYR A 819 " model vdw 2.254 2.440 ... (remaining 100270 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.450 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 37.750 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 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 : 0.010 0.127 12640 Z= 0.665 Angle : 1.226 31.690 17118 Z= 0.618 Chirality : 0.062 0.350 1984 Planarity : 0.008 0.077 2120 Dihedral : 14.199 152.962 4548 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 0.16 % Allowed : 3.25 % Favored : 96.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.32 (0.16), residues: 1566 helix: -2.58 (0.12), residues: 950 sheet: -2.39 (0.61), residues: 80 loop : -3.18 (0.22), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.005 TRP A 589 HIS 0.007 0.002 HIS A 814 PHE 0.036 0.004 PHE A 422 TYR 0.037 0.004 TYR B 88 ARG 0.015 0.001 ARG A 614 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 297 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 136 ARG cc_start: 0.7852 (tpp-160) cc_final: 0.7646 (tpt-90) REVERT: B 342 ARG cc_start: 0.8416 (mmm-85) cc_final: 0.7791 (mpt180) REVERT: B 436 GLU cc_start: 0.8052 (tp30) cc_final: 0.7776 (tt0) REVERT: B 602 LEU cc_start: 0.8841 (mt) cc_final: 0.8414 (mt) REVERT: B 648 VAL cc_start: 0.8752 (t) cc_final: 0.8024 (t) REVERT: B 786 ASN cc_start: 0.8284 (m-40) cc_final: 0.7834 (m-40) REVERT: A 51 THR cc_start: 0.8647 (p) cc_final: 0.8417 (p) REVERT: A 136 ARG cc_start: 0.7844 (tpp-160) cc_final: 0.7641 (tpt-90) REVERT: A 342 ARG cc_start: 0.8411 (mmm-85) cc_final: 0.7794 (mpt180) REVERT: A 436 GLU cc_start: 0.8054 (tp30) cc_final: 0.7769 (tt0) REVERT: A 602 LEU cc_start: 0.8841 (mt) cc_final: 0.8407 (mt) REVERT: A 648 VAL cc_start: 0.8770 (t) cc_final: 0.8071 (t) REVERT: A 786 ASN cc_start: 0.8227 (m-40) cc_final: 0.7760 (m-40) outliers start: 2 outliers final: 2 residues processed: 299 average time/residue: 0.3000 time to fit residues: 121.3771 Evaluate side-chains 191 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 189 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain A residue 209 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 66 optimal weight: 0.4980 chunk 40 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 123 optimal weight: 0.9980 chunk 47 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 chunk 92 optimal weight: 0.7980 chunk 143 optimal weight: 7.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN B 90 GLN B 292 ASN B 462 ASN B 653 ASN B 814 HIS A 25 ASN A 90 GLN A 292 ASN A 462 ASN A 653 ASN A 814 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12640 Z= 0.243 Angle : 0.673 7.789 17118 Z= 0.344 Chirality : 0.042 0.200 1984 Planarity : 0.006 0.062 2120 Dihedral : 13.878 151.645 1968 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 2.11 % Allowed : 10.55 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.19), residues: 1566 helix: -1.06 (0.15), residues: 944 sheet: -1.47 (0.72), residues: 58 loop : -2.77 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 589 HIS 0.002 0.001 HIS B 814 PHE 0.016 0.002 PHE B 279 TYR 0.032 0.002 TYR B 88 ARG 0.010 0.001 ARG A 665 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 199 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 PHE cc_start: 0.8783 (t80) cc_final: 0.8494 (t80) REVERT: B 280 GLU cc_start: 0.7464 (mm-30) cc_final: 0.7254 (mt-10) REVERT: B 342 ARG cc_start: 0.8477 (mmm-85) cc_final: 0.7707 (mpt180) REVERT: B 553 ARG cc_start: 0.7869 (mtt90) cc_final: 0.7606 (mtm-85) REVERT: B 602 LEU cc_start: 0.8798 (mt) cc_final: 0.8274 (mt) REVERT: B 648 VAL cc_start: 0.8650 (t) cc_final: 0.8407 (t) REVERT: B 786 ASN cc_start: 0.7995 (m-40) cc_final: 0.7653 (m110) REVERT: A 51 THR cc_start: 0.8648 (p) cc_final: 0.8279 (p) REVERT: A 148 ILE cc_start: 0.8920 (mt) cc_final: 0.8517 (mp) REVERT: A 280 GLU cc_start: 0.7453 (mm-30) cc_final: 0.7239 (mt-10) REVERT: A 436 GLU cc_start: 0.7915 (tp30) cc_final: 0.7709 (tt0) REVERT: A 553 ARG cc_start: 0.7897 (mtt90) cc_final: 0.7625 (mtm-85) REVERT: A 602 LEU cc_start: 0.8793 (mt) cc_final: 0.8269 (mt) REVERT: A 648 VAL cc_start: 0.8669 (t) cc_final: 0.8388 (t) REVERT: A 786 ASN cc_start: 0.8004 (m-40) cc_final: 0.7662 (m-40) outliers start: 26 outliers final: 17 residues processed: 213 average time/residue: 0.2803 time to fit residues: 85.5986 Evaluate side-chains 181 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 164 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 286 TRP Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 559 ASP Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 286 TRP Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 559 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 20.0000 chunk 44 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 97 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 143 optimal weight: 10.0000 chunk 155 optimal weight: 6.9990 chunk 128 optimal weight: 0.9990 chunk 142 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 820 ASN A 820 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12640 Z= 0.280 Angle : 0.659 7.434 17118 Z= 0.336 Chirality : 0.042 0.198 1984 Planarity : 0.005 0.056 2120 Dihedral : 13.148 150.876 1968 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 2.84 % Allowed : 12.82 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.20), residues: 1566 helix: -0.24 (0.17), residues: 936 sheet: -1.37 (0.68), residues: 58 loop : -2.63 (0.24), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 589 HIS 0.002 0.001 HIS A 271 PHE 0.019 0.002 PHE A 82 TYR 0.032 0.002 TYR B 88 ARG 0.007 0.001 ARG B 665 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 193 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 148 ILE cc_start: 0.8957 (mt) cc_final: 0.8591 (mp) REVERT: B 162 VAL cc_start: 0.8479 (OUTLIER) cc_final: 0.8160 (t) REVERT: B 602 LEU cc_start: 0.8786 (mt) cc_final: 0.8294 (mt) REVERT: B 648 VAL cc_start: 0.8773 (t) cc_final: 0.8462 (t) REVERT: B 786 ASN cc_start: 0.7952 (m-40) cc_final: 0.7588 (m110) REVERT: A 51 THR cc_start: 0.8799 (p) cc_final: 0.8557 (p) REVERT: A 110 PHE cc_start: 0.8623 (t80) cc_final: 0.8400 (t80) REVERT: A 148 ILE cc_start: 0.8957 (mt) cc_final: 0.8598 (mp) REVERT: A 162 VAL cc_start: 0.8468 (OUTLIER) cc_final: 0.8154 (t) REVERT: A 436 GLU cc_start: 0.7875 (tp30) cc_final: 0.7669 (tt0) REVERT: A 553 ARG cc_start: 0.7945 (mtt90) cc_final: 0.7564 (mtm-85) REVERT: A 602 LEU cc_start: 0.8765 (mt) cc_final: 0.8293 (mt) REVERT: A 786 ASN cc_start: 0.7942 (m-40) cc_final: 0.7483 (m110) outliers start: 35 outliers final: 16 residues processed: 209 average time/residue: 0.2262 time to fit residues: 70.4817 Evaluate side-chains 184 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 166 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 286 TRP Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 559 ASP Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 286 TRP Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 559 ASP Chi-restraints excluded: chain A residue 849 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 20.0000 chunk 108 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 chunk 152 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 136 optimal weight: 9.9990 chunk 41 optimal weight: 0.0060 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 820 ASN A 820 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12640 Z= 0.236 Angle : 0.631 7.790 17118 Z= 0.318 Chirality : 0.041 0.151 1984 Planarity : 0.005 0.053 2120 Dihedral : 12.665 149.302 1968 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 1.95 % Allowed : 15.67 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.21), residues: 1566 helix: 0.09 (0.17), residues: 936 sheet: -1.15 (0.64), residues: 68 loop : -2.32 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 589 HIS 0.002 0.000 HIS B 814 PHE 0.016 0.001 PHE B 256 TYR 0.029 0.001 TYR A 88 ARG 0.004 0.000 ARG B 599 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 179 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 PHE cc_start: 0.8665 (t80) cc_final: 0.8402 (t80) REVERT: B 148 ILE cc_start: 0.9012 (mt) cc_final: 0.8683 (mp) REVERT: B 581 MET cc_start: 0.8108 (ptm) cc_final: 0.7649 (ptt) REVERT: B 593 PHE cc_start: 0.7499 (m-80) cc_final: 0.7243 (m-10) REVERT: B 602 LEU cc_start: 0.8727 (mt) cc_final: 0.8475 (mt) REVERT: B 648 VAL cc_start: 0.8735 (t) cc_final: 0.8473 (t) REVERT: A 51 THR cc_start: 0.8789 (p) cc_final: 0.8561 (p) REVERT: A 110 PHE cc_start: 0.8568 (t80) cc_final: 0.8286 (t80) REVERT: A 148 ILE cc_start: 0.9002 (mt) cc_final: 0.8697 (mp) REVERT: A 336 MET cc_start: 0.6521 (mmt) cc_final: 0.6197 (mmt) REVERT: A 436 GLU cc_start: 0.7871 (tp30) cc_final: 0.7631 (tt0) REVERT: A 553 ARG cc_start: 0.7931 (mtt90) cc_final: 0.7615 (mtm-85) REVERT: A 581 MET cc_start: 0.8099 (ptm) cc_final: 0.7666 (ptt) REVERT: A 593 PHE cc_start: 0.7551 (m-80) cc_final: 0.7272 (m-10) REVERT: A 602 LEU cc_start: 0.8712 (mt) cc_final: 0.8460 (mt) outliers start: 24 outliers final: 19 residues processed: 188 average time/residue: 0.2077 time to fit residues: 59.4342 Evaluate side-chains 184 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 165 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 88 TYR Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 286 TRP Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain B residue 559 ASP Chi-restraints excluded: chain B residue 653 ASN Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 88 TYR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 286 TRP Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 559 ASP Chi-restraints excluded: chain A residue 653 ASN Chi-restraints excluded: chain A residue 849 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 5.9990 chunk 86 optimal weight: 0.3980 chunk 2 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 63 optimal weight: 20.0000 chunk 130 optimal weight: 10.0000 chunk 105 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 77 optimal weight: 0.9980 chunk 137 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 HIS B 704 HIS A 704 HIS A 786 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 12640 Z= 0.369 Angle : 0.675 7.246 17118 Z= 0.340 Chirality : 0.043 0.163 1984 Planarity : 0.005 0.055 2120 Dihedral : 12.629 151.784 1968 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 3.25 % Allowed : 16.07 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.21), residues: 1566 helix: 0.20 (0.17), residues: 940 sheet: -1.04 (0.65), residues: 68 loop : -2.14 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 589 HIS 0.003 0.001 HIS A 104 PHE 0.020 0.002 PHE B 256 TYR 0.027 0.002 TYR A 88 ARG 0.004 0.000 ARG A 784 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 166 time to evaluate : 1.295 Fit side-chains REVERT: B 148 ILE cc_start: 0.9030 (mt) cc_final: 0.8670 (mp) REVERT: B 162 VAL cc_start: 0.8565 (OUTLIER) cc_final: 0.8269 (t) REVERT: B 413 TRP cc_start: 0.8160 (t60) cc_final: 0.7849 (t60) REVERT: B 439 LEU cc_start: 0.8243 (tt) cc_final: 0.7991 (tp) REVERT: B 648 VAL cc_start: 0.8797 (t) cc_final: 0.8520 (t) REVERT: A 51 THR cc_start: 0.8763 (p) cc_final: 0.8541 (p) REVERT: A 110 PHE cc_start: 0.8598 (t80) cc_final: 0.8336 (t80) REVERT: A 148 ILE cc_start: 0.9016 (mt) cc_final: 0.8687 (mp) REVERT: A 162 VAL cc_start: 0.8561 (OUTLIER) cc_final: 0.8266 (t) REVERT: A 336 MET cc_start: 0.6590 (mmt) cc_final: 0.6270 (mmt) REVERT: A 553 ARG cc_start: 0.7978 (mtt90) cc_final: 0.7696 (mtm-85) REVERT: A 581 MET cc_start: 0.8267 (ptm) cc_final: 0.7820 (ptt) REVERT: A 786 ASN cc_start: 0.7988 (m-40) cc_final: 0.7183 (m-40) outliers start: 40 outliers final: 26 residues processed: 190 average time/residue: 0.2058 time to fit residues: 59.4516 Evaluate side-chains 186 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 158 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 88 TYR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 286 TRP Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 559 ASP Chi-restraints excluded: chain B residue 653 ASN Chi-restraints excluded: chain B residue 786 ASN Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 88 TYR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 286 TRP Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 559 ASP Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 653 ASN Chi-restraints excluded: chain A residue 849 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 9.9990 chunk 137 optimal weight: 8.9990 chunk 30 optimal weight: 0.5980 chunk 89 optimal weight: 0.0470 chunk 37 optimal weight: 5.9990 chunk 152 optimal weight: 9.9990 chunk 126 optimal weight: 0.2980 chunk 70 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12640 Z= 0.180 Angle : 0.605 7.663 17118 Z= 0.302 Chirality : 0.040 0.148 1984 Planarity : 0.004 0.055 2120 Dihedral : 12.204 147.994 1968 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 3.00 % Allowed : 16.88 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.21), residues: 1566 helix: 0.53 (0.17), residues: 944 sheet: -0.57 (0.66), residues: 68 loop : -2.13 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 224 HIS 0.002 0.001 HIS A 814 PHE 0.020 0.001 PHE A 641 TYR 0.027 0.002 TYR A 776 ARG 0.008 0.000 ARG A 665 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 174 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 110 PHE cc_start: 0.8527 (t80) cc_final: 0.8271 (t80) REVERT: B 148 ILE cc_start: 0.8986 (mt) cc_final: 0.8711 (mt) REVERT: B 439 LEU cc_start: 0.8203 (tt) cc_final: 0.7942 (tp) REVERT: B 648 VAL cc_start: 0.8814 (t) cc_final: 0.8578 (t) REVERT: A 148 ILE cc_start: 0.8979 (mt) cc_final: 0.8699 (mt) REVERT: A 336 MET cc_start: 0.6463 (mmt) cc_final: 0.6219 (mmt) REVERT: A 439 LEU cc_start: 0.8187 (tt) cc_final: 0.7935 (tp) REVERT: A 786 ASN cc_start: 0.7844 (m-40) cc_final: 0.7373 (m110) outliers start: 37 outliers final: 25 residues processed: 194 average time/residue: 0.1990 time to fit residues: 59.3000 Evaluate side-chains 181 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 156 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 88 TYR Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 286 TRP Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 786 ASN Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 88 TYR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 286 TRP Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 849 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 8.9990 chunk 17 optimal weight: 0.6980 chunk 87 optimal weight: 0.4980 chunk 111 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 chunk 128 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 92 optimal weight: 0.5980 chunk 70 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12640 Z= 0.177 Angle : 0.594 8.879 17118 Z= 0.298 Chirality : 0.040 0.147 1984 Planarity : 0.004 0.054 2120 Dihedral : 11.916 147.177 1968 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 2.60 % Allowed : 16.96 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.22), residues: 1566 helix: 0.84 (0.17), residues: 938 sheet: -0.20 (0.67), residues: 68 loop : -1.98 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 224 HIS 0.002 0.001 HIS A 104 PHE 0.018 0.001 PHE A 641 TYR 0.024 0.001 TYR A 88 ARG 0.006 0.000 ARG A 665 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 165 time to evaluate : 1.392 Fit side-chains REVERT: B 148 ILE cc_start: 0.8993 (mt) cc_final: 0.8716 (mt) REVERT: B 439 LEU cc_start: 0.8154 (tt) cc_final: 0.7892 (tp) REVERT: B 648 VAL cc_start: 0.8847 (t) cc_final: 0.8418 (t) REVERT: A 148 ILE cc_start: 0.8982 (mt) cc_final: 0.8710 (mt) REVERT: A 162 VAL cc_start: 0.8335 (OUTLIER) cc_final: 0.8035 (t) REVERT: A 336 MET cc_start: 0.6430 (mmt) cc_final: 0.6165 (mmt) REVERT: A 439 LEU cc_start: 0.8145 (tt) cc_final: 0.7903 (tp) REVERT: A 749 GLU cc_start: 0.6882 (mm-30) cc_final: 0.5763 (mm-30) REVERT: A 784 ARG cc_start: 0.7952 (ptt-90) cc_final: 0.7708 (ptp90) REVERT: A 786 ASN cc_start: 0.7970 (m-40) cc_final: 0.7047 (m-40) outliers start: 32 outliers final: 23 residues processed: 184 average time/residue: 0.2184 time to fit residues: 60.7092 Evaluate side-chains 181 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 157 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 88 TYR Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 286 TRP Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 653 ASN Chi-restraints excluded: chain B residue 786 ASN Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 88 TYR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 286 TRP Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 849 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 94 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 103 optimal weight: 0.5980 chunk 75 optimal weight: 6.9990 chunk 14 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 chunk 138 optimal weight: 9.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 653 ASN ** A 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12640 Z= 0.200 Angle : 0.588 8.147 17118 Z= 0.296 Chirality : 0.040 0.144 1984 Planarity : 0.004 0.054 2120 Dihedral : 11.900 146.828 1968 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 2.84 % Allowed : 16.48 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.22), residues: 1566 helix: 0.97 (0.17), residues: 946 sheet: -0.11 (0.67), residues: 68 loop : -1.91 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 224 HIS 0.002 0.001 HIS B 704 PHE 0.017 0.001 PHE B 593 TYR 0.023 0.001 TYR A 88 ARG 0.005 0.000 ARG B 806 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 160 time to evaluate : 1.456 Fit side-chains REVERT: B 148 ILE cc_start: 0.9006 (mt) cc_final: 0.8714 (mt) REVERT: B 162 VAL cc_start: 0.8397 (OUTLIER) cc_final: 0.8130 (t) REVERT: B 439 LEU cc_start: 0.8149 (tt) cc_final: 0.7896 (tp) REVERT: A 148 ILE cc_start: 0.8985 (mt) cc_final: 0.8704 (mt) REVERT: A 162 VAL cc_start: 0.8390 (OUTLIER) cc_final: 0.8120 (t) REVERT: A 336 MET cc_start: 0.6419 (mmt) cc_final: 0.6166 (mmt) REVERT: A 439 LEU cc_start: 0.8153 (tt) cc_final: 0.7894 (tp) REVERT: A 749 GLU cc_start: 0.6915 (mm-30) cc_final: 0.6430 (mm-30) REVERT: A 755 MET cc_start: 0.6181 (mmm) cc_final: 0.5972 (ttt) REVERT: A 786 ASN cc_start: 0.7888 (m-40) cc_final: 0.6995 (m-40) outliers start: 35 outliers final: 24 residues processed: 178 average time/residue: 0.1996 time to fit residues: 55.3040 Evaluate side-chains 176 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 150 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 88 TYR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 286 TRP Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 559 ASP Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 786 ASN Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 88 TYR Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 286 TRP Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 849 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 0.0370 chunk 133 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 85 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 111 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 150 optimal weight: 7.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 555 GLN B 653 ASN ** A 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12640 Z= 0.173 Angle : 0.589 9.064 17118 Z= 0.293 Chirality : 0.040 0.158 1984 Planarity : 0.004 0.054 2120 Dihedral : 11.685 145.767 1968 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.27 % Allowed : 17.78 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.22), residues: 1566 helix: 1.10 (0.18), residues: 948 sheet: 0.13 (0.57), residues: 98 loop : -1.80 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 224 HIS 0.002 0.001 HIS B 704 PHE 0.013 0.001 PHE B 641 TYR 0.022 0.001 TYR B 88 ARG 0.005 0.000 ARG A 784 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 162 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 148 ILE cc_start: 0.9026 (mt) cc_final: 0.8748 (mt) REVERT: B 162 VAL cc_start: 0.8392 (OUTLIER) cc_final: 0.8134 (t) REVERT: B 439 LEU cc_start: 0.8083 (tt) cc_final: 0.7835 (tp) REVERT: A 148 ILE cc_start: 0.9000 (mt) cc_final: 0.8754 (mt) REVERT: A 162 VAL cc_start: 0.8382 (OUTLIER) cc_final: 0.8120 (t) REVERT: A 336 MET cc_start: 0.6325 (mmt) cc_final: 0.6111 (mmt) REVERT: A 439 LEU cc_start: 0.8080 (tt) cc_final: 0.7836 (tp) outliers start: 28 outliers final: 22 residues processed: 178 average time/residue: 0.2121 time to fit residues: 57.1142 Evaluate side-chains 178 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 154 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 88 TYR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 286 TRP Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 555 GLN Chi-restraints excluded: chain B residue 786 ASN Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 88 TYR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 286 TRP Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 849 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 91 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 157 optimal weight: 0.9990 chunk 144 optimal weight: 7.9990 chunk 125 optimal weight: 20.0000 chunk 13 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 76 optimal weight: 7.9990 chunk 99 optimal weight: 0.9980 chunk 133 optimal weight: 0.9980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 555 GLN A 555 GLN A 786 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12640 Z= 0.199 Angle : 0.602 9.172 17118 Z= 0.299 Chirality : 0.040 0.141 1984 Planarity : 0.004 0.055 2120 Dihedral : 11.663 145.891 1968 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 2.84 % Allowed : 17.37 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.22), residues: 1566 helix: 1.17 (0.18), residues: 940 sheet: 0.12 (0.56), residues: 98 loop : -1.78 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 224 HIS 0.003 0.001 HIS A 704 PHE 0.021 0.001 PHE A 593 TYR 0.022 0.001 TYR A 88 ARG 0.006 0.000 ARG B 553 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 153 time to evaluate : 1.359 Fit side-chains REVERT: B 148 ILE cc_start: 0.9028 (mt) cc_final: 0.8748 (mt) REVERT: B 162 VAL cc_start: 0.8425 (OUTLIER) cc_final: 0.8172 (t) REVERT: B 439 LEU cc_start: 0.8078 (tt) cc_final: 0.7830 (tp) REVERT: B 853 MET cc_start: 0.7178 (mmt) cc_final: 0.6705 (mmt) REVERT: A 148 ILE cc_start: 0.8987 (mt) cc_final: 0.8733 (mt) REVERT: A 162 VAL cc_start: 0.8410 (OUTLIER) cc_final: 0.8149 (t) REVERT: A 447 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7811 (mp) REVERT: A 853 MET cc_start: 0.7156 (mmt) cc_final: 0.6671 (mmt) outliers start: 35 outliers final: 27 residues processed: 176 average time/residue: 0.2060 time to fit residues: 56.4556 Evaluate side-chains 181 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 151 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 88 TYR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 286 TRP Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 555 GLN Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 786 ASN Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 88 TYR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 286 TRP Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 559 ASP Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 849 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 8.9990 chunk 115 optimal weight: 0.6980 chunk 18 optimal weight: 0.2980 chunk 34 optimal weight: 8.9990 chunk 125 optimal weight: 9.9990 chunk 52 optimal weight: 0.6980 chunk 128 optimal weight: 0.0470 chunk 15 optimal weight: 0.4980 chunk 23 optimal weight: 0.7980 chunk 110 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 555 GLN B 653 ASN ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 653 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.186435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.141022 restraints weight = 15195.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.137266 restraints weight = 17656.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.139448 restraints weight = 16493.543| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12640 Z= 0.160 Angle : 0.591 9.513 17118 Z= 0.292 Chirality : 0.040 0.147 1984 Planarity : 0.004 0.054 2120 Dihedral : 11.528 144.914 1968 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.35 % Allowed : 18.10 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.22), residues: 1566 helix: 1.28 (0.18), residues: 932 sheet: 0.17 (0.56), residues: 98 loop : -1.68 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 224 HIS 0.003 0.001 HIS A 104 PHE 0.018 0.001 PHE A 593 TYR 0.030 0.001 TYR B 776 ARG 0.004 0.000 ARG A 784 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2362.13 seconds wall clock time: 44 minutes 17.59 seconds (2657.59 seconds total)