Starting phenix.real_space_refine on Mon Aug 5 20:53:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tko_41355/08_2024/8tko_41355.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tko_41355/08_2024/8tko_41355.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tko_41355/08_2024/8tko_41355.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tko_41355/08_2024/8tko_41355.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tko_41355/08_2024/8tko_41355.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tko_41355/08_2024/8tko_41355.cif" } resolution = 3.05 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= 0.031 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 1 5.49 5 S 37 5.16 5 C 8851 2.51 5 N 2628 2.21 5 O 2765 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 336": "OE1" <-> "OE2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "A ASP 747": "OD1" <-> "OD2" Residue "A TYR 752": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 765": "OE1" <-> "OE2" Residue "B ASP 200": "OD1" <-> "OD2" Residue "B GLU 459": "OE1" <-> "OE2" Residue "C GLU 16": "OE1" <-> "OE2" Residue "C GLU 20": "OE1" <-> "OE2" Residue "C ASP 91": "OD1" <-> "OD2" Residue "C GLU 93": "OE1" <-> "OE2" Residue "C ASP 172": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 14282 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6747 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 900, 6697 Classifications: {'peptide': 900} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 46, 'TRANS': 853} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 900, 6697 Classifications: {'peptide': 900} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 46, 'TRANS': 853} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 6769 Chain: "B" Number of atoms: 6760 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 903, 6699 Classifications: {'peptide': 903} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 46, 'TRANS': 856} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 903, 6699 Classifications: {'peptide': 903} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 46, 'TRANS': 856} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 6760 Chain: "C" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 775 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'4HH:plan-3': 1} Unresolved non-hydrogen planarities: 1 Residues with excluded nonbonded symmetry interactions: 9 residue: pdb=" N AASN A 48 " occ=0.42 ... (14 atoms not shown) pdb=" ND2BASN A 48 " occ=0.58 residue: pdb=" N AARG A 58 " occ=0.52 ... (20 atoms not shown) pdb=" NH2BARG A 58 " occ=0.48 residue: pdb=" N AGLU A 161 " occ=0.39 ... (16 atoms not shown) pdb=" OE2BGLU A 161 " occ=0.61 residue: pdb=" N AARG A 486 " occ=0.49 ... (20 atoms not shown) pdb=" NH2BARG A 486 " occ=0.51 residue: pdb=" N AARG B 13 " occ=0.45 ... (20 atoms not shown) pdb=" NH2BARG B 13 " occ=0.55 residue: pdb=" N AARG B 27 " occ=0.65 ... (20 atoms not shown) pdb=" NH2BARG B 27 " occ=0.35 residue: pdb=" N AASN B 48 " occ=0.47 ... (14 atoms not shown) pdb=" ND2BASN B 48 " occ=0.53 residue: pdb=" N AARG B 58 " occ=0.24 ... (20 atoms not shown) pdb=" NH2BARG B 58 " occ=0.76 residue: pdb=" N AGLU B 161 " occ=0.40 ... (16 atoms not shown) pdb=" OE2BGLU B 161 " occ=0.60 Time building chain proxies: 15.62, per 1000 atoms: 1.09 Number of scatterers: 14282 At special positions: 0 Unit cell: (93.654, 113.52, 196.768, 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 37 16.00 P 1 15.00 O 2765 8.00 N 2628 7.00 C 8851 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: 6.49 Conformation dependent library (CDL) restraints added in 5.6 seconds 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3450 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 15 sheets defined 46.4% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.829A pdb=" N ASP A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 60 Processing helix chain 'A' and resid 74 through 79 removed outlier: 4.239A pdb=" N HIS A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 118 Processing helix chain 'A' and resid 119 through 136 removed outlier: 3.518A pdb=" N ARG A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 144 Processing helix chain 'A' and resid 171 through 176 removed outlier: 3.708A pdb=" N THR A 175 " --> pdb=" O GLY A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 191 removed outlier: 4.092A pdb=" N SER A 183 " --> pdb=" O PRO A 179 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ILE A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 220 Processing helix chain 'A' and resid 236 through 246 removed outlier: 3.613A pdb=" N GLN A 245 " --> pdb=" O ASP A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 285 Processing helix chain 'A' and resid 310 through 325 removed outlier: 3.521A pdb=" N GLN A 314 " --> pdb=" O SER A 310 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N CYS A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 358 Processing helix chain 'A' and resid 372 through 377 Processing helix chain 'A' and resid 379 through 381 No H-bonds generated for 'chain 'A' and resid 379 through 381' Processing helix chain 'A' and resid 382 through 398 Processing helix chain 'A' and resid 414 through 418 removed outlier: 4.284A pdb=" N SER A 417 " --> pdb=" O ASP A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 498 removed outlier: 3.759A pdb=" N ARG A 498 " --> pdb=" O GLU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 514 removed outlier: 4.001A pdb=" N ARG A 514 " --> pdb=" O LEU A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 541 removed outlier: 3.668A pdb=" N GLY A 541 " --> pdb=" O GLU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 580 Processing helix chain 'A' and resid 582 through 597 Processing helix chain 'A' and resid 603 through 609 Processing helix chain 'A' and resid 619 through 640 Proline residue: A 625 - end of helix Processing helix chain 'A' and resid 653 through 663 removed outlier: 4.067A pdb=" N ALA A 657 " --> pdb=" O GLN A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 684 removed outlier: 3.628A pdb=" N LEU A 684 " --> pdb=" O LEU A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 702 Processing helix chain 'A' and resid 727 through 738 removed outlier: 3.759A pdb=" N ALA A 733 " --> pdb=" O GLY A 729 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE A 734 " --> pdb=" O ALA A 730 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLU A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N CYS A 738 " --> pdb=" O PHE A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 762 removed outlier: 3.597A pdb=" N VAL A 762 " --> pdb=" O ILE A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 771 Processing helix chain 'A' and resid 792 through 796 Processing helix chain 'A' and resid 797 through 807 Processing helix chain 'A' and resid 811 through 822 Processing helix chain 'A' and resid 835 through 846 Processing helix chain 'A' and resid 864 through 877 Processing helix chain 'A' and resid 883 through 888 removed outlier: 3.641A pdb=" N VAL A 886 " --> pdb=" O ARG A 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 32 removed outlier: 3.669A pdb=" N ASP B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 60 Processing helix chain 'B' and resid 74 through 79 removed outlier: 3.751A pdb=" N HIS B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 118 Processing helix chain 'B' and resid 119 through 136 removed outlier: 3.519A pdb=" N ARG B 123 " --> pdb=" O ASP B 119 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 178 removed outlier: 3.714A pdb=" N THR B 175 " --> pdb=" O GLY B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 191 removed outlier: 3.902A pdb=" N SER B 183 " --> pdb=" O PRO B 179 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER B 187 " --> pdb=" O SER B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 203 No H-bonds generated for 'chain 'B' and resid 201 through 203' Processing helix chain 'B' and resid 204 through 220 removed outlier: 3.662A pdb=" N LYS B 219 " --> pdb=" O GLU B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 245 removed outlier: 3.883A pdb=" N VAL B 240 " --> pdb=" O PRO B 236 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN B 245 " --> pdb=" O ASP B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 285 Processing helix chain 'B' and resid 310 through 326 removed outlier: 3.553A pdb=" N GLN B 314 " --> pdb=" O SER B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 357 removed outlier: 3.573A pdb=" N ILE B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 377 Processing helix chain 'B' and resid 383 through 398 Processing helix chain 'B' and resid 481 through 498 removed outlier: 3.641A pdb=" N ARG B 498 " --> pdb=" O GLU B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 513 Processing helix chain 'B' and resid 527 through 541 Processing helix chain 'B' and resid 575 through 582 Processing helix chain 'B' and resid 582 through 592 removed outlier: 3.632A pdb=" N ALA B 586 " --> pdb=" O SER B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 600 Processing helix chain 'B' and resid 603 through 609 Processing helix chain 'B' and resid 619 through 640 Proline residue: B 625 - end of helix Processing helix chain 'B' and resid 653 through 662 removed outlier: 4.034A pdb=" N ALA B 657 " --> pdb=" O GLN B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 683 Processing helix chain 'B' and resid 696 through 704 Processing helix chain 'B' and resid 727 through 738 removed outlier: 3.966A pdb=" N GLU B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N CYS B 738 " --> pdb=" O PHE B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 760 Processing helix chain 'B' and resid 762 through 770 Processing helix chain 'B' and resid 792 through 796 removed outlier: 4.228A pdb=" N GLU B 795 " --> pdb=" O ASP B 792 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU B 796 " --> pdb=" O GLY B 793 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 792 through 796' Processing helix chain 'B' and resid 797 through 806 Processing helix chain 'B' and resid 812 through 822 Processing helix chain 'B' and resid 835 through 846 Processing helix chain 'B' and resid 864 through 877 Processing helix chain 'B' and resid 883 through 888 Processing helix chain 'C' and resid 13 through 34 removed outlier: 3.589A pdb=" N THR C 31 " --> pdb=" O THR C 27 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL C 32 " --> pdb=" O SER C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 69 removed outlier: 3.698A pdb=" N ALA C 57 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 80 Processing helix chain 'C' and resid 82 through 95 Processing helix chain 'C' and resid 163 through 168 Processing helix chain 'C' and resid 169 through 172 Processing sheet with id=AA1, first strand: chain 'A' and resid 196 through 199 removed outlier: 8.835A pdb=" N ILE A 197 " --> pdb=" O THR A 148 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL A 150 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N VAL A 199 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU A 152 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL A 270 " --> pdb=" O CYS A 41 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N CYS A 41 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU A 272 " --> pdb=" O MET A 39 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N MET A 39 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU A 274 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA A 290 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE A 453 " --> pdb=" O ARG A 293 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER A 295 " --> pdb=" O HIS A 451 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N HIS A 451 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU A 297 " --> pdb=" O ASN A 449 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ASN A 449 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA A 334 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY A 370 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N LEU A 367 " --> pdb=" O ALA A 421 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 65 through 66 Processing sheet with id=AA3, first strand: chain 'A' and resid 102 through 103 Processing sheet with id=AA4, first strand: chain 'A' and resid 399 through 400 Processing sheet with id=AA5, first strand: chain 'A' and resid 473 through 479 Processing sheet with id=AA6, first strand: chain 'A' and resid 647 through 650 removed outlier: 3.696A pdb=" N ALA A 647 " --> pdb=" O VAL A 560 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL A 561 " --> pdb=" O ILE A 827 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 691 through 692 removed outlier: 4.317A pdb=" N ALA A 691 " --> pdb=" O VAL A 724 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 782 through 783 removed outlier: 4.507A pdb=" N PHE A 782 " --> pdb=" O MET A 791 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N MET A 791 " --> pdb=" O PHE A 782 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 196 through 199 removed outlier: 8.999A pdb=" N ILE B 197 " --> pdb=" O THR B 148 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL B 150 " --> pdb=" O ILE B 197 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N VAL B 199 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU B 152 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL B 270 " --> pdb=" O CYS B 41 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N CYS B 41 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU B 272 " --> pdb=" O MET B 39 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N MET B 39 " --> pdb=" O LEU B 272 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU B 274 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA B 290 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE B 453 " --> pdb=" O ARG B 293 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N SER B 295 " --> pdb=" O HIS B 451 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N HIS B 451 " --> pdb=" O SER B 295 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU B 297 " --> pdb=" O ASN B 449 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ASN B 449 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA B 334 " --> pdb=" O ARG B 437 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 65 through 66 Processing sheet with id=AB2, first strand: chain 'B' and resid 102 through 103 Processing sheet with id=AB3, first strand: chain 'B' and resid 367 through 368 removed outlier: 6.009A pdb=" N LEU B 367 " --> pdb=" O ALA B 421 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 399 through 400 Processing sheet with id=AB5, first strand: chain 'B' and resid 473 through 479 Processing sheet with id=AB6, first strand: chain 'B' and resid 789 through 790 removed outlier: 3.584A pdb=" N ARG B 789 " --> pdb=" O SER B 784 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL B 648 " --> pdb=" O HIS B 783 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N VAL B 561 " --> pdb=" O ILE B 827 " (cutoff:3.500A) 666 hydrogen bonds defined for protein. 1900 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: 5.21 Time building geometry restraints manager: 6.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5094 1.34 - 1.46: 3022 1.46 - 1.58: 6376 1.58 - 1.70: 2 1.70 - 1.82: 63 Bond restraints: 14557 Sorted by residual: bond pdb=" N GLU A 577 " pdb=" CA GLU A 577 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.41e+00 bond pdb=" N MET A 574 " pdb=" CA MET A 574 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.30e+00 bond pdb=" N GLU B 577 " pdb=" CA GLU B 577 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.23e-02 6.61e+03 4.91e+00 bond pdb=" N GLN B 653 " pdb=" CA GLN B 653 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.29e-02 6.01e+03 4.62e+00 bond pdb=" N LEU B 578 " pdb=" CA LEU B 578 " ideal model delta sigma weight residual 1.459 1.485 -0.025 1.19e-02 7.06e+03 4.59e+00 ... (remaining 14552 not shown) Histogram of bond angle deviations from ideal: 96.34 - 103.87: 218 103.87 - 111.40: 6465 111.40 - 118.93: 5324 118.93 - 126.45: 7569 126.45 - 133.98: 237 Bond angle restraints: 19813 Sorted by residual: angle pdb=" C ALA A 576 " pdb=" CA ALA A 576 " pdb=" CB ALA A 576 " ideal model delta sigma weight residual 117.23 111.54 5.69 1.36e+00 5.41e-01 1.75e+01 angle pdb=" CA ALA A 576 " pdb=" C ALA A 576 " pdb=" N GLU A 577 " ideal model delta sigma weight residual 119.98 117.13 2.85 8.50e-01 1.38e+00 1.13e+01 angle pdb=" N GLY A 573 " pdb=" CA GLY A 573 " pdb=" C GLY A 573 " ideal model delta sigma weight residual 115.72 111.28 4.44 1.51e+00 4.39e-01 8.64e+00 angle pdb=" CB MET A 690 " pdb=" CG MET A 690 " pdb=" SD MET A 690 " ideal model delta sigma weight residual 112.70 121.31 -8.61 3.00e+00 1.11e-01 8.23e+00 angle pdb=" N GLY A 726 " pdb=" CA GLY A 726 " pdb=" C GLY A 726 " ideal model delta sigma weight residual 110.71 115.05 -4.34 1.53e+00 4.27e-01 8.06e+00 ... (remaining 19808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 7895 17.89 - 35.79: 638 35.79 - 53.68: 144 53.68 - 71.58: 30 71.58 - 89.47: 12 Dihedral angle restraints: 8719 sinusoidal: 3325 harmonic: 5394 Sorted by residual: dihedral pdb=" CB GLU B 459 " pdb=" CG GLU B 459 " pdb=" CD GLU B 459 " pdb=" OE1 GLU B 459 " ideal model delta sinusoidal sigma weight residual 0.00 89.47 -89.47 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CG ARG A 536 " pdb=" CD ARG A 536 " pdb=" NE ARG A 536 " pdb=" CZ ARG A 536 " ideal model delta sinusoidal sigma weight residual -180.00 -136.39 -43.61 2 1.50e+01 4.44e-03 1.01e+01 dihedral pdb=" CB GLU A 459 " pdb=" CG GLU A 459 " pdb=" CD GLU A 459 " pdb=" OE1 GLU A 459 " ideal model delta sinusoidal sigma weight residual 0.00 -86.81 86.81 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 8716 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1567 0.036 - 0.071: 464 0.071 - 0.107: 150 0.107 - 0.142: 45 0.142 - 0.178: 2 Chirality restraints: 2228 Sorted by residual: chirality pdb=" CG LEU B 704 " pdb=" CB LEU B 704 " pdb=" CD1 LEU B 704 " pdb=" CD2 LEU B 704 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.93e-01 chirality pdb=" CB ILE B 743 " pdb=" CA ILE B 743 " pdb=" CG1 ILE B 743 " pdb=" CG2 ILE B 743 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.46e-01 chirality pdb=" CA MET B 574 " pdb=" N MET B 574 " pdb=" C MET B 574 " pdb=" CB MET B 574 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.49e-01 ... (remaining 2225 not shown) Planarity restraints: 2669 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 756 " 0.033 5.00e-02 4.00e+02 4.97e-02 3.96e+00 pdb=" N PRO B 757 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 757 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 757 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 406 " -0.010 2.00e-02 2.50e+03 1.97e-02 3.86e+00 pdb=" C VAL A 406 " 0.034 2.00e-02 2.50e+03 pdb=" O VAL A 406 " -0.013 2.00e-02 2.50e+03 pdb=" N GLU A 407 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 49 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.71e+00 pdb=" N PRO A 50 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 50 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 50 " -0.023 5.00e-02 4.00e+02 ... (remaining 2666 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1422 2.74 - 3.28: 13990 3.28 - 3.82: 23349 3.82 - 4.36: 26131 4.36 - 4.90: 46892 Nonbonded interactions: 111784 Sorted by model distance: nonbonded pdb=" OE2 GLU B 828 " pdb=" OG SER B 830 " model vdw 2.204 3.040 nonbonded pdb=" OG SER B 254 " pdb=" O LYS B 373 " model vdw 2.260 3.040 nonbonded pdb=" OE1 GLU C 165 " pdb=" N ALA C 166 " model vdw 2.296 3.120 nonbonded pdb=" N GLU A 765 " pdb=" OE1 GLU A 765 " model vdw 2.314 3.120 nonbonded pdb=" O ARG B 732 " pdb=" OG SER B 735 " model vdw 2.316 3.040 ... (remaining 111779 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 5 through 12 or resid 14 through 26 or resid 28 through 47 \ or resid 49 through 57 or resid 59 through 160 or resid 162 through 462 or (res \ id 463 and (name N or name CA or name C or name O or name CB )) or resid 464 thr \ ough 470 or (resid 471 and (name N or name CA or name C or name O or name CB )) \ or resid 472 through 485 or resid 487 through 696 or (resid 697 through 699 and \ (name N or name CA or name C or name O or name CB )) or resid 700 through 745 or \ (resid 746 and (name N or name CA or name C or name O or name CB )) or resid 74 \ 7 through 910)) selection = (chain 'B' and (resid 5 through 12 or resid 14 through 26 or resid 28 through 47 \ or resid 49 through 57 or resid 59 through 160 or resid 162 through 485 or resi \ d 487 through 693 or resid 696 through 708 or resid 713 through 762 or (resid 76 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 764 through \ 910)) } 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=0.99 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: 5.000 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: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 53.640 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.100 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 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 : 0.002 0.031 14557 Z= 0.168 Angle : 0.485 8.609 19813 Z= 0.256 Chirality : 0.040 0.178 2228 Planarity : 0.004 0.050 2669 Dihedral : 14.068 89.470 5269 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.67 % Favored : 95.28 % Rotamer: Outliers : 1.25 % Allowed : 9.38 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.20), residues: 1919 helix: 2.28 (0.20), residues: 770 sheet: 0.68 (0.38), residues: 196 loop : -1.02 (0.21), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 54 HIS 0.002 0.000 HIS B 876 PHE 0.008 0.001 PHE B 264 TYR 0.009 0.001 TYR B 802 ARG 0.002 0.000 ARG A 806 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 63 time to evaluate : 1.672 Fit side-chains REVERT: B 18 ASP cc_start: 0.9039 (m-30) cc_final: 0.8767 (m-30) REVERT: B 574 MET cc_start: 0.7487 (OUTLIER) cc_final: 0.6553 (mpt) REVERT: B 681 MET cc_start: 0.9157 (tmm) cc_final: 0.8956 (tmm) outliers start: 13 outliers final: 9 residues processed: 71 average time/residue: 0.2919 time to fit residues: 31.4267 Evaluate side-chains 71 residues out of total 1426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 61 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 791 MET Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain C residue 165 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 7.9990 chunk 144 optimal weight: 3.9990 chunk 79 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.0980 chunk 76 optimal weight: 6.9990 chunk 148 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 chunk 172 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 708 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.0743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14557 Z= 0.181 Angle : 0.491 7.545 19813 Z= 0.252 Chirality : 0.041 0.152 2228 Planarity : 0.004 0.050 2669 Dihedral : 4.401 61.258 2135 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.09 % Favored : 94.86 % Rotamer: Outliers : 1.18 % Allowed : 9.24 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.20), residues: 1919 helix: 2.61 (0.19), residues: 781 sheet: 0.53 (0.37), residues: 196 loop : -1.00 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 571 HIS 0.003 0.001 HIS B 660 PHE 0.009 0.001 PHE A 242 TYR 0.009 0.001 TYR B 641 ARG 0.003 0.000 ARG C 14 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 59 time to evaluate : 1.762 Fit side-chains REVERT: A 791 MET cc_start: 0.8860 (mpp) cc_final: 0.8642 (mpp) REVERT: B 574 MET cc_start: 0.7873 (mpt) cc_final: 0.7122 (mmt) REVERT: B 681 MET cc_start: 0.9151 (tmm) cc_final: 0.8864 (tmm) REVERT: C 23 ARG cc_start: 0.8865 (ttm-80) cc_final: 0.8604 (tpp80) outliers start: 12 outliers final: 8 residues processed: 68 average time/residue: 0.2961 time to fit residues: 30.6137 Evaluate side-chains 64 residues out of total 1426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 56 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 592 CYS Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 858 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 95 optimal weight: 0.0010 chunk 53 optimal weight: 3.9990 chunk 143 optimal weight: 0.9980 chunk 117 optimal weight: 0.4980 chunk 47 optimal weight: 0.8980 chunk 172 optimal weight: 0.8980 chunk 186 optimal weight: 7.9990 chunk 153 optimal weight: 0.7980 chunk 171 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 138 optimal weight: 0.5980 overall best weight: 0.5586 ------------------------------------------------------------------------------- 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: 0.8440 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14557 Z= 0.165 Angle : 0.477 8.732 19813 Z= 0.242 Chirality : 0.040 0.189 2228 Planarity : 0.004 0.048 2669 Dihedral : 3.615 34.109 2120 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.51 % Favored : 95.44 % Rotamer: Outliers : 1.11 % Allowed : 9.86 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.20), residues: 1919 helix: 2.66 (0.19), residues: 782 sheet: 0.47 (0.37), residues: 195 loop : -1.07 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 571 HIS 0.002 0.000 HIS B 660 PHE 0.009 0.001 PHE A 585 TYR 0.009 0.001 TYR B 802 ARG 0.003 0.000 ARG C 23 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 1.730 Fit side-chains REVERT: A 791 MET cc_start: 0.8813 (mpp) cc_final: 0.8560 (mpp) REVERT: B 241 ASP cc_start: 0.8869 (m-30) cc_final: 0.8644 (m-30) REVERT: B 574 MET cc_start: 0.7955 (mpt) cc_final: 0.7212 (mmt) REVERT: C 23 ARG cc_start: 0.8854 (ttm-80) cc_final: 0.8621 (tpp80) outliers start: 11 outliers final: 8 residues processed: 66 average time/residue: 0.3194 time to fit residues: 32.2664 Evaluate side-chains 62 residues out of total 1426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 54 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 592 CYS Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 571 TRP Chi-restraints excluded: chain B residue 858 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 0.9990 chunk 129 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 116 optimal weight: 0.6980 chunk 173 optimal weight: 1.9990 chunk 183 optimal weight: 0.1980 chunk 90 optimal weight: 0.4980 chunk 164 optimal weight: 4.9990 chunk 49 optimal weight: 0.2980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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: 0.8435 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14557 Z= 0.151 Angle : 0.466 7.973 19813 Z= 0.235 Chirality : 0.040 0.150 2228 Planarity : 0.004 0.048 2669 Dihedral : 3.559 33.507 2120 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.72 % Favored : 95.23 % Rotamer: Outliers : 1.25 % Allowed : 9.86 % Favored : 88.89 % 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: 1.07 (0.20), residues: 1919 helix: 2.74 (0.19), residues: 783 sheet: 0.40 (0.37), residues: 196 loop : -1.06 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 571 HIS 0.002 0.000 HIS A 338 PHE 0.009 0.001 PHE A 585 TYR 0.009 0.001 TYR A 752 ARG 0.002 0.000 ARG C 23 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 58 time to evaluate : 1.652 Fit side-chains REVERT: A 791 MET cc_start: 0.8804 (mpp) cc_final: 0.8568 (mpp) REVERT: B 574 MET cc_start: 0.8091 (mpt) cc_final: 0.7269 (mmt) outliers start: 13 outliers final: 10 residues processed: 68 average time/residue: 0.2912 time to fit residues: 30.3111 Evaluate side-chains 64 residues out of total 1426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 592 CYS Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 858 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 75 optimal weight: 0.0060 chunk 156 optimal weight: 4.9990 chunk 126 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.2800 ------------------------------------------------------------------------------- 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: 0.8482 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14557 Z= 0.295 Angle : 0.526 8.224 19813 Z= 0.268 Chirality : 0.042 0.154 2228 Planarity : 0.004 0.047 2669 Dihedral : 3.931 39.161 2120 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.51 % Favored : 94.43 % Rotamer: Outliers : 1.53 % Allowed : 9.79 % Favored : 88.68 % 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: 0.90 (0.20), residues: 1919 helix: 2.60 (0.19), residues: 787 sheet: 0.14 (0.36), residues: 202 loop : -1.15 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 571 HIS 0.004 0.001 HIS B 660 PHE 0.013 0.001 PHE A 242 TYR 0.010 0.001 TYR B 802 ARG 0.002 0.000 ARG A 806 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 53 time to evaluate : 1.706 Fit side-chains REVERT: A 791 MET cc_start: 0.8753 (mpp) cc_final: 0.8448 (mpp) REVERT: B 342 THR cc_start: 0.6030 (OUTLIER) cc_final: 0.5785 (t) REVERT: B 574 MET cc_start: 0.8260 (mpt) cc_final: 0.7941 (mmt) outliers start: 17 outliers final: 13 residues processed: 67 average time/residue: 0.3026 time to fit residues: 30.6413 Evaluate side-chains 67 residues out of total 1426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 53 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 255 LYS Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 592 CYS Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 571 TRP Chi-restraints excluded: chain B residue 858 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 61 optimal weight: 3.9990 chunk 165 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 183 optimal weight: 8.9990 chunk 152 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.8462 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14557 Z= 0.195 Angle : 0.486 8.059 19813 Z= 0.246 Chirality : 0.041 0.160 2228 Planarity : 0.004 0.048 2669 Dihedral : 3.829 47.243 2120 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.04 % Favored : 94.91 % Rotamer: Outliers : 1.60 % Allowed : 10.00 % Favored : 88.40 % 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: 0.95 (0.20), residues: 1919 helix: 2.66 (0.19), residues: 783 sheet: 0.22 (0.37), residues: 197 loop : -1.13 (0.21), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 571 HIS 0.002 0.001 HIS A 660 PHE 0.009 0.001 PHE A 585 TYR 0.011 0.001 TYR B 802 ARG 0.003 0.000 ARG C 71 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 55 time to evaluate : 1.617 Fit side-chains REVERT: A 791 MET cc_start: 0.8740 (mpp) cc_final: 0.8444 (mpp) REVERT: B 574 MET cc_start: 0.8228 (mpt) cc_final: 0.7894 (mmt) outliers start: 18 outliers final: 16 residues processed: 71 average time/residue: 0.3068 time to fit residues: 32.4883 Evaluate side-chains 70 residues out of total 1426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 54 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 255 LYS Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 592 CYS Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 571 TRP Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain C residue 167 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 177 optimal weight: 0.0870 chunk 20 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 183 optimal weight: 0.1980 chunk 114 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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: 0.8452 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14557 Z= 0.171 Angle : 0.482 8.421 19813 Z= 0.243 Chirality : 0.041 0.182 2228 Planarity : 0.004 0.048 2669 Dihedral : 3.797 59.137 2120 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.25 % Favored : 94.70 % Rotamer: Outliers : 1.53 % Allowed : 10.14 % Favored : 88.33 % 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: 0.98 (0.20), residues: 1919 helix: 2.67 (0.19), residues: 787 sheet: 0.25 (0.37), residues: 197 loop : -1.11 (0.21), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 571 HIS 0.002 0.000 HIS A 660 PHE 0.009 0.001 PHE A 585 TYR 0.010 0.001 TYR B 802 ARG 0.007 0.000 ARG B 77 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 54 time to evaluate : 1.601 Fit side-chains REVERT: A 791 MET cc_start: 0.8751 (mpp) cc_final: 0.8449 (mpp) REVERT: B 574 MET cc_start: 0.8229 (mpt) cc_final: 0.7896 (mmt) REVERT: B 681 MET cc_start: 0.9164 (tmm) cc_final: 0.8742 (tmm) REVERT: C 16 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8098 (mm-30) outliers start: 17 outliers final: 15 residues processed: 68 average time/residue: 0.2886 time to fit residues: 29.7782 Evaluate side-chains 69 residues out of total 1426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 54 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 LYS Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 592 CYS Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 571 TRP Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain C residue 167 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 73 optimal weight: 0.0040 chunk 109 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 143 optimal weight: 0.2980 chunk 166 optimal weight: 0.9980 chunk 175 optimal weight: 3.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- 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: 0.8450 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14557 Z= 0.168 Angle : 0.477 8.247 19813 Z= 0.240 Chirality : 0.041 0.178 2228 Planarity : 0.004 0.048 2669 Dihedral : 3.651 44.388 2120 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.93 % Favored : 95.02 % Rotamer: Outliers : 1.60 % Allowed : 10.28 % Favored : 88.12 % 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: 1.00 (0.20), residues: 1919 helix: 2.69 (0.19), residues: 787 sheet: 0.27 (0.37), residues: 197 loop : -1.11 (0.21), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 571 HIS 0.002 0.000 HIS B 660 PHE 0.009 0.001 PHE A 585 TYR 0.010 0.001 TYR B 802 ARG 0.004 0.000 ARG B 77 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 54 time to evaluate : 1.784 Fit side-chains REVERT: A 791 MET cc_start: 0.8753 (mpp) cc_final: 0.8468 (mpp) REVERT: B 574 MET cc_start: 0.8247 (mpt) cc_final: 0.7909 (mmt) REVERT: B 681 MET cc_start: 0.9174 (tmm) cc_final: 0.8760 (tmm) REVERT: B 791 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.7159 (pmm) REVERT: C 16 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8081 (mm-30) outliers start: 18 outliers final: 16 residues processed: 69 average time/residue: 0.2823 time to fit residues: 29.5509 Evaluate side-chains 71 residues out of total 1426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 54 time to evaluate : 2.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 255 LYS Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 592 CYS Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 571 TRP Chi-restraints excluded: chain B residue 791 MET Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain C residue 167 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 0.8980 chunk 170 optimal weight: 0.9990 chunk 175 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 74 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 154 optimal weight: 0.1980 chunk 161 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 180 optimal weight: 5.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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: 0.8457 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14557 Z= 0.187 Angle : 0.486 9.163 19813 Z= 0.245 Chirality : 0.041 0.180 2228 Planarity : 0.004 0.048 2669 Dihedral : 3.650 38.724 2120 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.25 % Favored : 94.70 % Rotamer: Outliers : 1.67 % Allowed : 10.35 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.20), residues: 1919 helix: 2.69 (0.19), residues: 787 sheet: 0.22 (0.37), residues: 200 loop : -1.11 (0.21), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 571 HIS 0.002 0.001 HIS A 660 PHE 0.009 0.001 PHE B 264 TYR 0.010 0.001 TYR B 802 ARG 0.004 0.000 ARG C 23 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 54 time to evaluate : 1.620 Fit side-chains REVERT: A 791 MET cc_start: 0.8718 (mpp) cc_final: 0.8429 (mpp) REVERT: B 681 MET cc_start: 0.9193 (tmm) cc_final: 0.8771 (tmm) REVERT: B 791 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.7155 (pmm) REVERT: C 16 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8111 (mm-30) outliers start: 19 outliers final: 16 residues processed: 70 average time/residue: 0.2837 time to fit residues: 30.1936 Evaluate side-chains 71 residues out of total 1426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 54 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 255 LYS Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 592 CYS Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 571 TRP Chi-restraints excluded: chain B residue 791 MET Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain C residue 167 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 110 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 189 optimal weight: 0.9990 chunk 174 optimal weight: 1.9990 chunk 150 optimal weight: 0.7980 chunk 15 optimal weight: 0.0370 chunk 116 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 160 optimal weight: 0.8980 overall best weight: 0.6458 ------------------------------------------------------------------------------- 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: 0.8453 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14557 Z= 0.175 Angle : 0.483 9.122 19813 Z= 0.242 Chirality : 0.041 0.176 2228 Planarity : 0.004 0.048 2669 Dihedral : 3.631 38.508 2120 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.20 % Favored : 94.75 % Rotamer: Outliers : 1.60 % Allowed : 10.49 % Favored : 87.92 % 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: 0.99 (0.20), residues: 1919 helix: 2.68 (0.19), residues: 787 sheet: 0.28 (0.37), residues: 197 loop : -1.11 (0.21), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 571 HIS 0.002 0.001 HIS B 660 PHE 0.009 0.001 PHE A 585 TYR 0.010 0.001 TYR B 802 ARG 0.004 0.000 ARG B 77 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 55 time to evaluate : 1.584 Fit side-chains REVERT: A 791 MET cc_start: 0.8732 (mpp) cc_final: 0.8447 (mpp) REVERT: B 574 MET cc_start: 0.7865 (mmt) cc_final: 0.7655 (mmt) REVERT: B 681 MET cc_start: 0.9192 (tmm) cc_final: 0.8769 (tmm) REVERT: B 791 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.7162 (pmm) REVERT: C 16 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8112 (mm-30) outliers start: 18 outliers final: 16 residues processed: 70 average time/residue: 0.2875 time to fit residues: 30.4242 Evaluate side-chains 70 residues out of total 1426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 53 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 255 LYS Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 592 CYS Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 571 TRP Chi-restraints excluded: chain B residue 791 MET Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain C residue 167 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 46 optimal weight: 0.7980 chunk 138 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 41 optimal weight: 0.4980 chunk 150 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 155 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.067380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.042541 restraints weight = 210170.620| |-----------------------------------------------------------------------------| r_work (start): 0.2640 rms_B_bonded: 7.02 r_work: 0.2437 rms_B_bonded: 6.14 restraints_weight: 2.0000 r_work (final): 0.2437 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2423 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2423 r_free = 0.2423 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2423 r_free = 0.2423 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.2423 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14557 Z= 0.177 Angle : 0.483 8.976 19813 Z= 0.242 Chirality : 0.041 0.180 2228 Planarity : 0.004 0.048 2669 Dihedral : 3.658 38.549 2120 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.14 % Favored : 94.80 % Rotamer: Outliers : 1.60 % Allowed : 10.35 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.20), residues: 1919 helix: 2.70 (0.19), residues: 787 sheet: 0.28 (0.37), residues: 197 loop : -1.11 (0.21), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 571 HIS 0.002 0.001 HIS B 660 PHE 0.009 0.001 PHE A 585 TYR 0.009 0.001 TYR B 802 ARG 0.004 0.000 ARG B 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2967.27 seconds wall clock time: 53 minutes 35.15 seconds (3215.15 seconds total)