Starting phenix.real_space_refine on Thu Mar 21 02:14:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxe_13700/03_2024/7pxe_13700_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxe_13700/03_2024/7pxe_13700.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxe_13700/03_2024/7pxe_13700.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxe_13700/03_2024/7pxe_13700.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxe_13700/03_2024/7pxe_13700_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxe_13700/03_2024/7pxe_13700_updated.pdb" } resolution = 2.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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: 8 Type Number sf(0) Gaussians Ca 8 9.91 5 K 4 8.98 5 P 16 5.49 5 Mg 4 5.21 5 S 192 5.16 5 C 18724 2.51 5 N 4604 2.21 5 O 5376 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 113": "OD1" <-> "OD2" Residue "A TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 380": "OE1" <-> "OE2" Residue "A ASP 448": "OD1" <-> "OD2" Residue "A TYR 960": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 986": "OD1" <-> "OD2" Residue "A TYR 1071": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 113": "OD1" <-> "OD2" Residue "B TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 380": "OE1" <-> "OE2" Residue "B ASP 448": "OD1" <-> "OD2" Residue "B TYR 960": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 986": "OD1" <-> "OD2" Residue "B TYR 1071": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 113": "OD1" <-> "OD2" Residue "C TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 380": "OE1" <-> "OE2" Residue "C ASP 448": "OD1" <-> "OD2" Residue "C TYR 960": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 986": "OD1" <-> "OD2" Residue "C TYR 1071": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 113": "OD1" <-> "OD2" Residue "D TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 380": "OE1" <-> "OE2" Residue "D ASP 448": "OD1" <-> "OD2" Residue "D TYR 960": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 986": "OD1" <-> "OD2" Residue "D TYR 1071": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28928 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 885, 7023 Classifications: {'peptide': 885} Link IDs: {'PTRANS': 32, 'TRANS': 852} Chain breaks: 5 Chain: "B" Number of atoms: 7023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 885, 7023 Classifications: {'peptide': 885} Link IDs: {'PTRANS': 32, 'TRANS': 852} Chain breaks: 5 Chain: "C" Number of atoms: 7023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 885, 7023 Classifications: {'peptide': 885} Link IDs: {'PTRANS': 32, 'TRANS': 852} Chain breaks: 5 Chain: "D" Number of atoms: 7023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 885, 7023 Classifications: {'peptide': 885} Link IDs: {'PTRANS': 32, 'TRANS': 852} Chain breaks: 5 Chain: "A" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 178 Unusual residues: {' K': 4, ' CA': 2, ' MG': 1, '6PL': 4, 'CLR': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 66 Planarities with less than four sites: {'6PL:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 174 Unusual residues: {' CA': 2, ' MG': 1, '6PL': 4, 'CLR': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 66 Planarities with less than four sites: {'6PL:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 174 Unusual residues: {' CA': 2, ' MG': 1, '6PL': 4, 'CLR': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 66 Planarities with less than four sites: {'6PL:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 174 Unusual residues: {' CA': 2, ' MG': 1, '6PL': 4, 'CLR': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 66 Planarities with less than four sites: {'6PL:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" K K A1209 " occ=0.25 residue: pdb=" K K A1210 " occ=0.25 residue: pdb=" K K A1211 " occ=0.50 residue: pdb=" K K A1212 " occ=0.50 Time building chain proxies: 16.04, per 1000 atoms: 0.55 Number of scatterers: 28928 At special positions: 0 Unit cell: (165.9, 165.9, 130.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Ca 8 19.99 K 4 19.00 S 192 16.00 P 16 15.00 Mg 4 11.99 O 5376 8.00 N 4604 7.00 C 18724 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: 11.99 Conformation dependent library (CDL) restraints added in 5.4 seconds 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6696 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 164 helices and 20 sheets defined 48.6% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.46 Creating SS restraints... Processing helix chain 'A' and resid 49 through 76 Processing helix chain 'A' and resid 107 through 119 Processing helix chain 'A' and resid 124 through 148 Processing helix chain 'A' and resid 163 through 185 removed outlier: 3.692A pdb=" N PHE A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 193 Processing helix chain 'A' and resid 196 through 202 Processing helix chain 'A' and resid 205 through 214 Processing helix chain 'A' and resid 222 through 238 Proline residue: A 233 - end of helix Processing helix chain 'A' and resid 245 through 274 Processing helix chain 'A' and resid 288 through 299 Processing helix chain 'A' and resid 312 through 340 removed outlier: 3.516A pdb=" N PHE A 320 " --> pdb=" O THR A 316 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU A 326 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ALA A 327 " --> pdb=" O LEU A 323 " (cutoff:3.500A) Proline residue: A 334 - end of helix Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 399 through 407 Processing helix chain 'A' and resid 422 through 427 Processing helix chain 'A' and resid 430 through 432 No H-bonds generated for 'chain 'A' and resid 430 through 432' Processing helix chain 'A' and resid 447 through 464 Processing helix chain 'A' and resid 477 through 484 removed outlier: 3.906A pdb=" N ALA A 481 " --> pdb=" O HIS A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 513 removed outlier: 3.751A pdb=" N LEU A 513 " --> pdb=" O ALA A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 524 Processing helix chain 'A' and resid 538 through 548 Processing helix chain 'A' and resid 558 through 560 No H-bonds generated for 'chain 'A' and resid 558 through 560' Processing helix chain 'A' and resid 565 through 574 Processing helix chain 'A' and resid 618 through 625 removed outlier: 3.777A pdb=" N LYS A 622 " --> pdb=" O ALA A 618 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ARG A 623 " --> pdb=" O ASP A 619 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ALA A 624 " --> pdb=" O GLU A 620 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N TRP A 625 " --> pdb=" O VAL A 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 618 through 625' Processing helix chain 'A' and resid 795 through 797 No H-bonds generated for 'chain 'A' and resid 795 through 797' Processing helix chain 'A' and resid 801 through 805 Processing helix chain 'A' and resid 828 through 836 Proline residue: A 834 - end of helix Processing helix chain 'A' and resid 854 through 863 removed outlier: 3.838A pdb=" N ARG A 859 " --> pdb=" O ASP A 855 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU A 860 " --> pdb=" O TYR A 856 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LYS A 862 " --> pdb=" O ARG A 858 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N MET A 863 " --> pdb=" O ARG A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 885 Processing helix chain 'A' and resid 888 through 890 No H-bonds generated for 'chain 'A' and resid 888 through 890' Processing helix chain 'A' and resid 907 through 909 No H-bonds generated for 'chain 'A' and resid 907 through 909' Processing helix chain 'A' and resid 912 through 922 Processing helix chain 'A' and resid 961 through 963 No H-bonds generated for 'chain 'A' and resid 961 through 963' Processing helix chain 'A' and resid 973 through 978 removed outlier: 3.975A pdb=" N GLN A 977 " --> pdb=" O GLY A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 993 No H-bonds generated for 'chain 'A' and resid 991 through 993' Processing helix chain 'A' and resid 995 through 998 No H-bonds generated for 'chain 'A' and resid 995 through 998' Processing helix chain 'A' and resid 1005 through 1017 removed outlier: 3.574A pdb=" N ASP A1009 " --> pdb=" O SER A1006 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER A1010 " --> pdb=" O VAL A1007 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N MET A1012 " --> pdb=" O ASP A1009 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER A1013 " --> pdb=" O SER A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1029 Processing helix chain 'A' and resid 1035 through 1043 Processing helix chain 'A' and resid 1058 through 1060 No H-bonds generated for 'chain 'A' and resid 1058 through 1060' Processing helix chain 'A' and resid 1074 through 1081 removed outlier: 3.991A pdb=" N GLN A1077 " --> pdb=" O PRO A1074 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N CYS A1081 " --> pdb=" O PHE A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1095 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 107 through 119 Processing helix chain 'B' and resid 124 through 148 Processing helix chain 'B' and resid 163 through 185 removed outlier: 3.693A pdb=" N PHE B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 193 Processing helix chain 'B' and resid 196 through 202 Processing helix chain 'B' and resid 205 through 214 Processing helix chain 'B' and resid 222 through 238 Proline residue: B 233 - end of helix Processing helix chain 'B' and resid 245 through 274 Processing helix chain 'B' and resid 288 through 299 Processing helix chain 'B' and resid 312 through 340 removed outlier: 3.516A pdb=" N PHE B 320 " --> pdb=" O THR B 316 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ALA B 327 " --> pdb=" O LEU B 323 " (cutoff:3.500A) Proline residue: B 334 - end of helix Processing helix chain 'B' and resid 367 through 377 Processing helix chain 'B' and resid 399 through 407 Processing helix chain 'B' and resid 422 through 427 Processing helix chain 'B' and resid 430 through 432 No H-bonds generated for 'chain 'B' and resid 430 through 432' Processing helix chain 'B' and resid 447 through 464 Processing helix chain 'B' and resid 477 through 484 removed outlier: 3.906A pdb=" N ALA B 481 " --> pdb=" O HIS B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 513 removed outlier: 3.750A pdb=" N LEU B 513 " --> pdb=" O ALA B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 524 Processing helix chain 'B' and resid 538 through 548 Processing helix chain 'B' and resid 558 through 560 No H-bonds generated for 'chain 'B' and resid 558 through 560' Processing helix chain 'B' and resid 565 through 574 Processing helix chain 'B' and resid 618 through 625 removed outlier: 3.777A pdb=" N LYS B 622 " --> pdb=" O ALA B 618 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ARG B 623 " --> pdb=" O ASP B 619 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ALA B 624 " --> pdb=" O GLU B 620 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N TRP B 625 " --> pdb=" O VAL B 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 618 through 625' Processing helix chain 'B' and resid 795 through 797 No H-bonds generated for 'chain 'B' and resid 795 through 797' Processing helix chain 'B' and resid 801 through 805 Processing helix chain 'B' and resid 828 through 836 Proline residue: B 834 - end of helix Processing helix chain 'B' and resid 854 through 863 removed outlier: 3.838A pdb=" N ARG B 859 " --> pdb=" O ASP B 855 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU B 860 " --> pdb=" O TYR B 856 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LYS B 862 " --> pdb=" O ARG B 858 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N MET B 863 " --> pdb=" O ARG B 859 " (cutoff:3.500A) Processing helix chain 'B' and resid 880 through 885 Processing helix chain 'B' and resid 888 through 890 No H-bonds generated for 'chain 'B' and resid 888 through 890' Processing helix chain 'B' and resid 907 through 909 No H-bonds generated for 'chain 'B' and resid 907 through 909' Processing helix chain 'B' and resid 912 through 922 Processing helix chain 'B' and resid 961 through 963 No H-bonds generated for 'chain 'B' and resid 961 through 963' Processing helix chain 'B' and resid 973 through 978 removed outlier: 3.975A pdb=" N GLN B 977 " --> pdb=" O GLY B 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 993 No H-bonds generated for 'chain 'B' and resid 991 through 993' Processing helix chain 'B' and resid 995 through 998 No H-bonds generated for 'chain 'B' and resid 995 through 998' Processing helix chain 'B' and resid 1005 through 1017 removed outlier: 3.575A pdb=" N ASP B1009 " --> pdb=" O SER B1006 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N SER B1010 " --> pdb=" O VAL B1007 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N MET B1012 " --> pdb=" O ASP B1009 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B1013 " --> pdb=" O SER B1010 " (cutoff:3.500A) Processing helix chain 'B' and resid 1019 through 1029 Processing helix chain 'B' and resid 1035 through 1043 Processing helix chain 'B' and resid 1058 through 1060 No H-bonds generated for 'chain 'B' and resid 1058 through 1060' Processing helix chain 'B' and resid 1074 through 1081 removed outlier: 3.990A pdb=" N GLN B1077 " --> pdb=" O PRO B1074 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N CYS B1081 " --> pdb=" O PHE B1078 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1095 Processing helix chain 'C' and resid 49 through 76 Processing helix chain 'C' and resid 107 through 119 Processing helix chain 'C' and resid 124 through 148 Processing helix chain 'C' and resid 163 through 185 removed outlier: 3.693A pdb=" N PHE C 174 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 193 Processing helix chain 'C' and resid 196 through 202 Processing helix chain 'C' and resid 205 through 214 Processing helix chain 'C' and resid 222 through 238 Proline residue: C 233 - end of helix Processing helix chain 'C' and resid 245 through 274 Processing helix chain 'C' and resid 288 through 299 Processing helix chain 'C' and resid 312 through 340 removed outlier: 3.516A pdb=" N PHE C 320 " --> pdb=" O THR C 316 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU C 326 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ALA C 327 " --> pdb=" O LEU C 323 " (cutoff:3.500A) Proline residue: C 334 - end of helix Processing helix chain 'C' and resid 367 through 377 Processing helix chain 'C' and resid 399 through 407 Processing helix chain 'C' and resid 422 through 427 Processing helix chain 'C' and resid 430 through 432 No H-bonds generated for 'chain 'C' and resid 430 through 432' Processing helix chain 'C' and resid 447 through 464 Processing helix chain 'C' and resid 477 through 484 removed outlier: 3.907A pdb=" N ALA C 481 " --> pdb=" O HIS C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 513 removed outlier: 3.750A pdb=" N LEU C 513 " --> pdb=" O ALA C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 517 through 524 Processing helix chain 'C' and resid 538 through 548 Processing helix chain 'C' and resid 558 through 560 No H-bonds generated for 'chain 'C' and resid 558 through 560' Processing helix chain 'C' and resid 565 through 574 Processing helix chain 'C' and resid 618 through 625 removed outlier: 3.777A pdb=" N LYS C 622 " --> pdb=" O ALA C 618 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ARG C 623 " --> pdb=" O ASP C 619 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ALA C 624 " --> pdb=" O GLU C 620 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N TRP C 625 " --> pdb=" O VAL C 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 618 through 625' Processing helix chain 'C' and resid 795 through 797 No H-bonds generated for 'chain 'C' and resid 795 through 797' Processing helix chain 'C' and resid 801 through 805 Processing helix chain 'C' and resid 828 through 836 Proline residue: C 834 - end of helix Processing helix chain 'C' and resid 854 through 863 removed outlier: 3.838A pdb=" N ARG C 859 " --> pdb=" O ASP C 855 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU C 860 " --> pdb=" O TYR C 856 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LYS C 862 " --> pdb=" O ARG C 858 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N MET C 863 " --> pdb=" O ARG C 859 " (cutoff:3.500A) Processing helix chain 'C' and resid 880 through 885 Processing helix chain 'C' and resid 888 through 890 No H-bonds generated for 'chain 'C' and resid 888 through 890' Processing helix chain 'C' and resid 907 through 909 No H-bonds generated for 'chain 'C' and resid 907 through 909' Processing helix chain 'C' and resid 912 through 922 Processing helix chain 'C' and resid 961 through 963 No H-bonds generated for 'chain 'C' and resid 961 through 963' Processing helix chain 'C' and resid 973 through 978 removed outlier: 3.975A pdb=" N GLN C 977 " --> pdb=" O GLY C 974 " (cutoff:3.500A) Processing helix chain 'C' and resid 991 through 993 No H-bonds generated for 'chain 'C' and resid 991 through 993' Processing helix chain 'C' and resid 995 through 998 No H-bonds generated for 'chain 'C' and resid 995 through 998' Processing helix chain 'C' and resid 1005 through 1017 removed outlier: 3.575A pdb=" N ASP C1009 " --> pdb=" O SER C1006 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER C1010 " --> pdb=" O VAL C1007 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N MET C1012 " --> pdb=" O ASP C1009 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER C1013 " --> pdb=" O SER C1010 " (cutoff:3.500A) Processing helix chain 'C' and resid 1019 through 1029 Processing helix chain 'C' and resid 1035 through 1043 Processing helix chain 'C' and resid 1058 through 1060 No H-bonds generated for 'chain 'C' and resid 1058 through 1060' Processing helix chain 'C' and resid 1074 through 1081 removed outlier: 3.991A pdb=" N GLN C1077 " --> pdb=" O PRO C1074 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N CYS C1081 " --> pdb=" O PHE C1078 " (cutoff:3.500A) Processing helix chain 'C' and resid 1084 through 1095 Processing helix chain 'D' and resid 49 through 76 Processing helix chain 'D' and resid 107 through 119 Processing helix chain 'D' and resid 124 through 148 Processing helix chain 'D' and resid 163 through 185 removed outlier: 3.692A pdb=" N PHE D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 193 Processing helix chain 'D' and resid 196 through 202 Processing helix chain 'D' and resid 205 through 214 Processing helix chain 'D' and resid 222 through 238 Proline residue: D 233 - end of helix Processing helix chain 'D' and resid 245 through 274 Processing helix chain 'D' and resid 288 through 299 Processing helix chain 'D' and resid 312 through 340 removed outlier: 3.516A pdb=" N PHE D 320 " --> pdb=" O THR D 316 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ALA D 327 " --> pdb=" O LEU D 323 " (cutoff:3.500A) Proline residue: D 334 - end of helix Processing helix chain 'D' and resid 367 through 377 Processing helix chain 'D' and resid 399 through 407 Processing helix chain 'D' and resid 422 through 427 Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 447 through 464 Processing helix chain 'D' and resid 477 through 484 removed outlier: 3.906A pdb=" N ALA D 481 " --> pdb=" O HIS D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 513 removed outlier: 3.751A pdb=" N LEU D 513 " --> pdb=" O ALA D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 524 Processing helix chain 'D' and resid 538 through 548 Processing helix chain 'D' and resid 558 through 560 No H-bonds generated for 'chain 'D' and resid 558 through 560' Processing helix chain 'D' and resid 565 through 574 Processing helix chain 'D' and resid 618 through 625 removed outlier: 3.777A pdb=" N LYS D 622 " --> pdb=" O ALA D 618 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ARG D 623 " --> pdb=" O ASP D 619 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ALA D 624 " --> pdb=" O GLU D 620 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N TRP D 625 " --> pdb=" O VAL D 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 618 through 625' Processing helix chain 'D' and resid 795 through 797 No H-bonds generated for 'chain 'D' and resid 795 through 797' Processing helix chain 'D' and resid 801 through 805 Processing helix chain 'D' and resid 828 through 836 Proline residue: D 834 - end of helix Processing helix chain 'D' and resid 854 through 863 removed outlier: 3.837A pdb=" N ARG D 859 " --> pdb=" O ASP D 855 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU D 860 " --> pdb=" O TYR D 856 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LYS D 862 " --> pdb=" O ARG D 858 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N MET D 863 " --> pdb=" O ARG D 859 " (cutoff:3.500A) Processing helix chain 'D' and resid 880 through 885 Processing helix chain 'D' and resid 888 through 890 No H-bonds generated for 'chain 'D' and resid 888 through 890' Processing helix chain 'D' and resid 907 through 909 No H-bonds generated for 'chain 'D' and resid 907 through 909' Processing helix chain 'D' and resid 912 through 922 Processing helix chain 'D' and resid 961 through 963 No H-bonds generated for 'chain 'D' and resid 961 through 963' Processing helix chain 'D' and resid 973 through 978 removed outlier: 3.975A pdb=" N GLN D 977 " --> pdb=" O GLY D 974 " (cutoff:3.500A) Processing helix chain 'D' and resid 991 through 993 No H-bonds generated for 'chain 'D' and resid 991 through 993' Processing helix chain 'D' and resid 995 through 998 No H-bonds generated for 'chain 'D' and resid 995 through 998' Processing helix chain 'D' and resid 1005 through 1017 removed outlier: 3.575A pdb=" N ASP D1009 " --> pdb=" O SER D1006 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N SER D1010 " --> pdb=" O VAL D1007 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N MET D1012 " --> pdb=" O ASP D1009 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER D1013 " --> pdb=" O SER D1010 " (cutoff:3.500A) Processing helix chain 'D' and resid 1019 through 1029 Processing helix chain 'D' and resid 1035 through 1043 Processing helix chain 'D' and resid 1058 through 1060 No H-bonds generated for 'chain 'D' and resid 1058 through 1060' Processing helix chain 'D' and resid 1074 through 1081 removed outlier: 3.991A pdb=" N GLN D1077 " --> pdb=" O PRO D1074 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N CYS D1081 " --> pdb=" O PHE D1078 " (cutoff:3.500A) Processing helix chain 'D' and resid 1084 through 1095 Processing sheet with id= A, first strand: chain 'A' and resid 154 through 156 Processing sheet with id= B, first strand: chain 'A' and resid 496 through 499 removed outlier: 7.337A pdb=" N HIS A 358 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N LEU A 437 " --> pdb=" O HIS A 358 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL A 360 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N LEU A 439 " --> pdb=" O VAL A 360 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N CYS A 362 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLY A 363 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 550 through 555 removed outlier: 4.456A pdb=" N GLN A 610 " --> pdb=" O GLU A 584 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA A 582 " --> pdb=" O PHE A 612 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ILE A 614 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LEU A 580 " --> pdb=" O ILE A 614 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 966 through 968 removed outlier: 6.285A pdb=" N CYS A 894 " --> pdb=" O ILE A 967 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1064 through 1069 removed outlier: 3.707A pdb=" N GLY A1101 " --> pdb=" O PHE A1137 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU A1139 " --> pdb=" O CYS A1099 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N CYS A1099 " --> pdb=" O LEU A1139 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 154 through 156 Processing sheet with id= G, first strand: chain 'B' and resid 496 through 499 removed outlier: 7.336A pdb=" N HIS B 358 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N LEU B 437 " --> pdb=" O HIS B 358 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL B 360 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N LEU B 439 " --> pdb=" O VAL B 360 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N CYS B 362 " --> pdb=" O LEU B 439 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLY B 363 " --> pdb=" O LEU B 392 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 550 through 555 removed outlier: 4.455A pdb=" N GLN B 610 " --> pdb=" O GLU B 584 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA B 582 " --> pdb=" O PHE B 612 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ILE B 614 " --> pdb=" O LEU B 580 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LEU B 580 " --> pdb=" O ILE B 614 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 966 through 968 removed outlier: 6.284A pdb=" N CYS B 894 " --> pdb=" O ILE B 967 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 1064 through 1069 removed outlier: 3.707A pdb=" N GLY B1101 " --> pdb=" O PHE B1137 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU B1139 " --> pdb=" O CYS B1099 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N CYS B1099 " --> pdb=" O LEU B1139 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 154 through 156 Processing sheet with id= L, first strand: chain 'C' and resid 496 through 499 removed outlier: 7.336A pdb=" N HIS C 358 " --> pdb=" O ALA C 435 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N LEU C 437 " --> pdb=" O HIS C 358 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL C 360 " --> pdb=" O LEU C 437 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N LEU C 439 " --> pdb=" O VAL C 360 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N CYS C 362 " --> pdb=" O LEU C 439 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLY C 363 " --> pdb=" O LEU C 392 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 550 through 555 removed outlier: 4.456A pdb=" N GLN C 610 " --> pdb=" O GLU C 584 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA C 582 " --> pdb=" O PHE C 612 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ILE C 614 " --> pdb=" O LEU C 580 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LEU C 580 " --> pdb=" O ILE C 614 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 966 through 968 removed outlier: 6.284A pdb=" N CYS C 894 " --> pdb=" O ILE C 967 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 1064 through 1069 removed outlier: 3.707A pdb=" N GLY C1101 " --> pdb=" O PHE C1137 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU C1139 " --> pdb=" O CYS C1099 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N CYS C1099 " --> pdb=" O LEU C1139 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 154 through 156 Processing sheet with id= Q, first strand: chain 'D' and resid 496 through 499 removed outlier: 7.337A pdb=" N HIS D 358 " --> pdb=" O ALA D 435 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N LEU D 437 " --> pdb=" O HIS D 358 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL D 360 " --> pdb=" O LEU D 437 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N LEU D 439 " --> pdb=" O VAL D 360 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N CYS D 362 " --> pdb=" O LEU D 439 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLY D 363 " --> pdb=" O LEU D 392 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 550 through 555 removed outlier: 4.457A pdb=" N GLN D 610 " --> pdb=" O GLU D 584 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA D 582 " --> pdb=" O PHE D 612 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ILE D 614 " --> pdb=" O LEU D 580 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N LEU D 580 " --> pdb=" O ILE D 614 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 966 through 968 removed outlier: 6.285A pdb=" N CYS D 894 " --> pdb=" O ILE D 967 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 1064 through 1069 removed outlier: 3.706A pdb=" N GLY D1101 " --> pdb=" O PHE D1137 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU D1139 " --> pdb=" O CYS D1099 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N CYS D1099 " --> pdb=" O LEU D1139 " (cutoff:3.500A) 1224 hydrogen bonds defined for protein. 3300 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: 11.24 Time building geometry restraints manager: 12.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4576 1.31 - 1.43: 7861 1.43 - 1.56: 16631 1.56 - 1.69: 40 1.69 - 1.81: 296 Bond restraints: 29404 Sorted by residual: bond pdb=" C11 6PL C1206 " pdb=" O3 6PL C1206 " ideal model delta sigma weight residual 1.327 1.444 -0.117 2.00e-02 2.50e+03 3.44e+01 bond pdb=" C11 6PL B1206 " pdb=" O3 6PL B1206 " ideal model delta sigma weight residual 1.327 1.443 -0.116 2.00e-02 2.50e+03 3.39e+01 bond pdb=" C11 6PL D1206 " pdb=" O3 6PL D1206 " ideal model delta sigma weight residual 1.327 1.443 -0.116 2.00e-02 2.50e+03 3.39e+01 bond pdb=" C11 6PL A1206 " pdb=" O3 6PL A1206 " ideal model delta sigma weight residual 1.327 1.443 -0.116 2.00e-02 2.50e+03 3.38e+01 bond pdb=" C11 6PL B1205 " pdb=" O3 6PL B1205 " ideal model delta sigma weight residual 1.327 1.443 -0.116 2.00e-02 2.50e+03 3.38e+01 ... (remaining 29399 not shown) Histogram of bond angle deviations from ideal: 100.42 - 107.13: 756 107.13 - 113.85: 16846 113.85 - 120.56: 11662 120.56 - 127.27: 10275 127.27 - 133.98: 293 Bond angle restraints: 39832 Sorted by residual: angle pdb=" O3P 6PL D1207 " pdb=" P 6PL D1207 " pdb=" O4P 6PL D1207 " ideal model delta sigma weight residual 93.65 109.54 -15.89 3.00e+00 1.11e-01 2.80e+01 angle pdb=" O3P 6PL C1207 " pdb=" P 6PL C1207 " pdb=" O4P 6PL C1207 " ideal model delta sigma weight residual 93.65 109.54 -15.89 3.00e+00 1.11e-01 2.80e+01 angle pdb=" O3P 6PL B1207 " pdb=" P 6PL B1207 " pdb=" O4P 6PL B1207 " ideal model delta sigma weight residual 93.65 109.51 -15.86 3.00e+00 1.11e-01 2.79e+01 angle pdb=" O3P 6PL A1207 " pdb=" P 6PL A1207 " pdb=" O4P 6PL A1207 " ideal model delta sigma weight residual 93.65 109.49 -15.84 3.00e+00 1.11e-01 2.79e+01 angle pdb=" O3P 6PL C1205 " pdb=" P 6PL C1205 " pdb=" O4P 6PL C1205 " ideal model delta sigma weight residual 93.65 109.43 -15.78 3.00e+00 1.11e-01 2.77e+01 ... (remaining 39827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 15354 17.54 - 35.07: 1681 35.07 - 52.61: 609 52.61 - 70.15: 100 70.15 - 87.69: 20 Dihedral angle restraints: 17764 sinusoidal: 7424 harmonic: 10340 Sorted by residual: dihedral pdb=" CG ARG B 623 " pdb=" CD ARG B 623 " pdb=" NE ARG B 623 " pdb=" CZ ARG B 623 " ideal model delta sinusoidal sigma weight residual 90.00 133.90 -43.90 2 1.50e+01 4.44e-03 1.03e+01 dihedral pdb=" CG ARG A 623 " pdb=" CD ARG A 623 " pdb=" NE ARG A 623 " pdb=" CZ ARG A 623 " ideal model delta sinusoidal sigma weight residual 90.00 133.90 -43.90 2 1.50e+01 4.44e-03 1.03e+01 dihedral pdb=" CG ARG C 623 " pdb=" CD ARG C 623 " pdb=" NE ARG C 623 " pdb=" CZ ARG C 623 " ideal model delta sinusoidal sigma weight residual 90.00 133.89 -43.89 2 1.50e+01 4.44e-03 1.03e+01 ... (remaining 17761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 4083 0.066 - 0.132: 408 0.132 - 0.198: 4 0.198 - 0.264: 21 0.264 - 0.329: 4 Chirality restraints: 4520 Sorted by residual: chirality pdb=" C14 CLR A1208 " pdb=" C13 CLR A1208 " pdb=" C15 CLR A1208 " pdb=" C8 CLR A1208 " both_signs ideal model delta sigma weight residual False -2.32 -2.65 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" C14 CLR B1208 " pdb=" C13 CLR B1208 " pdb=" C15 CLR B1208 " pdb=" C8 CLR B1208 " both_signs ideal model delta sigma weight residual False -2.32 -2.64 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" C14 CLR D1208 " pdb=" C13 CLR D1208 " pdb=" C15 CLR D1208 " pdb=" C8 CLR D1208 " both_signs ideal model delta sigma weight residual False -2.32 -2.64 0.33 2.00e-01 2.50e+01 2.68e+00 ... (remaining 4517 not shown) Planarity restraints: 4932 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 206 " 0.024 5.00e-02 4.00e+02 3.52e-02 1.99e+00 pdb=" N PRO B 207 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 207 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 207 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 206 " -0.023 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO D 207 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO D 207 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 207 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 206 " 0.023 5.00e-02 4.00e+02 3.51e-02 1.97e+00 pdb=" N PRO C 207 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO C 207 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 207 " 0.020 5.00e-02 4.00e+02 ... (remaining 4929 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.75: 3115 2.75 - 3.35: 32473 3.35 - 3.94: 55494 3.94 - 4.54: 78523 4.54 - 5.14: 114173 Nonbonded interactions: 283778 Sorted by model distance: nonbonded pdb=" OH TYR A 304 " pdb=" OG1 THR C 298 " model vdw 2.151 2.440 nonbonded pdb=" O ALA D 526 " pdb="MG MG D1203 " model vdw 2.280 2.170 nonbonded pdb=" O ALA A 526 " pdb="MG MG A1203 " model vdw 2.281 2.170 nonbonded pdb=" O ALA B 526 " pdb="MG MG B1203 " model vdw 2.281 2.170 nonbonded pdb=" O ALA C 526 " pdb="MG MG C1203 " model vdw 2.281 2.170 ... (remaining 283773 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' and (resid 44 through 1145 or resid 1201 through 1208)) selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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=0.25 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.460 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: 0.020 Extract box with map and model: 20.000 Check model and map are aligned: 0.550 Set scattering table: 0.260 Process input model: 81.120 Find NCS groups from input model: 2.260 Set up NCS constraints: 0.180 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:14.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 29404 Z= 0.356 Angle : 0.730 15.888 39832 Z= 0.287 Chirality : 0.042 0.329 4520 Planarity : 0.003 0.035 4932 Dihedral : 16.772 87.686 11068 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.94 % Allowed : 19.93 % Favored : 78.13 % 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: 1.17 (0.14), residues: 3492 helix: 0.81 (0.12), residues: 1716 sheet: 1.22 (0.26), residues: 420 loop : 0.85 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 861 HIS 0.003 0.001 HIS A 379 PHE 0.011 0.001 PHE D 525 TYR 0.006 0.001 TYR C 346 ARG 0.002 0.000 ARG D 382 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 254 time to evaluate : 3.518 Fit side-chains REVERT: B 388 GLU cc_start: 0.8022 (pt0) cc_final: 0.7819 (pt0) outliers start: 60 outliers final: 32 residues processed: 290 average time/residue: 1.3144 time to fit residues: 453.3412 Evaluate side-chains 267 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 235 time to evaluate : 3.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 778 MET Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 1036 GLU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 778 MET Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 1036 GLU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 1036 GLU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 488 SER Chi-restraints excluded: chain D residue 778 MET Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 1036 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 297 optimal weight: 3.9990 chunk 266 optimal weight: 10.0000 chunk 148 optimal weight: 0.7980 chunk 91 optimal weight: 20.0000 chunk 179 optimal weight: 20.0000 chunk 142 optimal weight: 4.9990 chunk 275 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 167 optimal weight: 9.9990 chunk 205 optimal weight: 3.9990 chunk 319 optimal weight: 8.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN B 122 GLN B 802 ASN C 122 GLN D 122 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 29404 Z= 0.385 Angle : 0.542 6.238 39832 Z= 0.285 Chirality : 0.044 0.138 4520 Planarity : 0.004 0.043 4932 Dihedral : 9.341 61.397 4600 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 3.49 % Allowed : 16.86 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.14), residues: 3492 helix: 0.97 (0.12), residues: 1688 sheet: 0.85 (0.26), residues: 420 loop : 1.05 (0.18), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 289 HIS 0.005 0.001 HIS C 478 PHE 0.023 0.002 PHE D 525 TYR 0.015 0.002 TYR B1016 ARG 0.003 0.000 ARG C 545 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 255 time to evaluate : 3.365 Fit side-chains REVERT: B 375 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8458 (mtmt) REVERT: B 475 MET cc_start: 0.8910 (mmm) cc_final: 0.8641 (mmm) REVERT: C 1001 THR cc_start: 0.9226 (m) cc_final: 0.8805 (p) REVERT: D 375 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8172 (mtmt) REVERT: D 475 MET cc_start: 0.8910 (mmm) cc_final: 0.8636 (mmm) outliers start: 108 outliers final: 45 residues processed: 330 average time/residue: 1.2748 time to fit residues: 498.9716 Evaluate side-chains 281 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 234 time to evaluate : 3.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 971 VAL Chi-restraints excluded: chain A residue 973 ASP Chi-restraints excluded: chain A residue 1036 GLU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 971 VAL Chi-restraints excluded: chain B residue 973 ASP Chi-restraints excluded: chain B residue 1036 GLU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 351 LYS Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain C residue 973 ASP Chi-restraints excluded: chain C residue 1036 GLU Chi-restraints excluded: chain C residue 1037 LEU Chi-restraints excluded: chain C residue 1077 GLN Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain D residue 375 LYS Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 971 VAL Chi-restraints excluded: chain D residue 973 ASP Chi-restraints excluded: chain D residue 1001 THR Chi-restraints excluded: chain D residue 1012 MET Chi-restraints excluded: chain D residue 1036 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 177 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 266 optimal weight: 10.0000 chunk 217 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 320 optimal weight: 6.9990 chunk 345 optimal weight: 4.9990 chunk 285 optimal weight: 3.9990 chunk 317 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 256 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN B 122 GLN C 122 GLN D 122 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 29404 Z= 0.381 Angle : 0.515 5.329 39832 Z= 0.270 Chirality : 0.044 0.136 4520 Planarity : 0.004 0.040 4932 Dihedral : 9.001 59.978 4574 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 3.26 % Allowed : 16.18 % Favored : 80.56 % 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: 1.23 (0.14), residues: 3492 helix: 0.98 (0.12), residues: 1688 sheet: 0.66 (0.25), residues: 420 loop : 0.91 (0.18), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 289 HIS 0.005 0.001 HIS D 478 PHE 0.021 0.002 PHE B 525 TYR 0.014 0.002 TYR D1016 ARG 0.002 0.000 ARG D 829 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 235 time to evaluate : 3.449 Fit side-chains REVERT: A 1140 MET cc_start: 0.8700 (mtp) cc_final: 0.8499 (mtm) REVERT: B 375 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8540 (mtmt) REVERT: C 1001 THR cc_start: 0.9253 (m) cc_final: 0.8895 (p) REVERT: D 375 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8502 (mtmt) outliers start: 101 outliers final: 62 residues processed: 307 average time/residue: 1.3020 time to fit residues: 473.9732 Evaluate side-chains 297 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 233 time to evaluate : 3.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 971 VAL Chi-restraints excluded: chain A residue 1036 GLU Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1077 GLN Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 971 VAL Chi-restraints excluded: chain B residue 1036 GLU Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1077 GLN Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain C residue 1036 GLU Chi-restraints excluded: chain C residue 1039 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 375 LYS Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 971 VAL Chi-restraints excluded: chain D residue 1012 MET Chi-restraints excluded: chain D residue 1036 GLU Chi-restraints excluded: chain D residue 1037 LEU Chi-restraints excluded: chain D residue 1039 LEU Chi-restraints excluded: chain D residue 1077 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 316 optimal weight: 0.0570 chunk 240 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 chunk 215 optimal weight: 0.9980 chunk 321 optimal weight: 2.9990 chunk 340 optimal weight: 0.5980 chunk 167 optimal weight: 0.0000 chunk 304 optimal weight: 0.8980 chunk 91 optimal weight: 20.0000 overall best weight: 0.5102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN B 122 GLN C 122 GLN D 122 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 29404 Z= 0.123 Angle : 0.413 5.385 39832 Z= 0.216 Chirality : 0.039 0.134 4520 Planarity : 0.003 0.037 4932 Dihedral : 8.496 59.920 4574 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.94 % Allowed : 16.54 % Favored : 80.52 % 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: 1.40 (0.14), residues: 3492 helix: 1.20 (0.13), residues: 1680 sheet: 0.62 (0.26), residues: 420 loop : 0.92 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 289 HIS 0.002 0.000 HIS D 478 PHE 0.015 0.001 PHE A 321 TYR 0.008 0.001 TYR B 197 ARG 0.001 0.000 ARG C1118 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 242 time to evaluate : 3.752 Fit side-chains REVERT: A 801 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7482 (mtt-85) REVERT: A 1140 MET cc_start: 0.8668 (mtp) cc_final: 0.8450 (mtm) REVERT: C 1001 THR cc_start: 0.9175 (m) cc_final: 0.8821 (p) outliers start: 91 outliers final: 41 residues processed: 299 average time/residue: 1.3067 time to fit residues: 463.3249 Evaluate side-chains 276 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 234 time to evaluate : 3.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 801 ARG Chi-restraints excluded: chain A residue 1036 GLU Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1077 GLN Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 973 ASP Chi-restraints excluded: chain B residue 1036 GLU Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1077 GLN Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 1036 GLU Chi-restraints excluded: chain C residue 1037 LEU Chi-restraints excluded: chain C residue 1077 GLN Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 1036 GLU Chi-restraints excluded: chain D residue 1037 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 283 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 253 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 290 optimal weight: 0.0970 chunk 235 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 173 optimal weight: 7.9990 chunk 305 optimal weight: 0.8980 chunk 85 optimal weight: 0.0670 overall best weight: 1.0120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN B 122 GLN B 802 ASN C 122 GLN D 122 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 29404 Z= 0.175 Angle : 0.428 8.109 39832 Z= 0.222 Chirality : 0.039 0.131 4520 Planarity : 0.003 0.037 4932 Dihedral : 8.255 59.461 4568 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.94 % Allowed : 16.86 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.14), residues: 3492 helix: 1.29 (0.13), residues: 1684 sheet: 0.67 (0.26), residues: 420 loop : 0.92 (0.17), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 289 HIS 0.002 0.001 HIS D 358 PHE 0.015 0.001 PHE A 321 TYR 0.011 0.001 TYR D1016 ARG 0.002 0.000 ARG D1064 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 251 time to evaluate : 3.559 Fit side-chains REVERT: A 551 MET cc_start: 0.8177 (ttp) cc_final: 0.7894 (ttp) REVERT: A 801 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.7490 (mtt-85) REVERT: B 375 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8477 (mtmt) REVERT: B 551 MET cc_start: 0.8170 (ttp) cc_final: 0.7858 (ttp) REVERT: C 551 MET cc_start: 0.8171 (ttp) cc_final: 0.7952 (ttm) REVERT: C 1001 THR cc_start: 0.9209 (m) cc_final: 0.8886 (p) REVERT: D 375 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8492 (mtmt) outliers start: 91 outliers final: 45 residues processed: 311 average time/residue: 1.2894 time to fit residues: 475.6944 Evaluate side-chains 288 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 240 time to evaluate : 3.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 801 ARG Chi-restraints excluded: chain A residue 1036 GLU Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1077 GLN Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 971 VAL Chi-restraints excluded: chain B residue 973 ASP Chi-restraints excluded: chain B residue 1036 GLU Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1077 GLN Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain C residue 1036 GLU Chi-restraints excluded: chain C residue 1037 LEU Chi-restraints excluded: chain C residue 1077 GLN Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 375 LYS Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 1036 GLU Chi-restraints excluded: chain D residue 1037 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 114 optimal weight: 0.3980 chunk 306 optimal weight: 3.9990 chunk 67 optimal weight: 0.0170 chunk 199 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 340 optimal weight: 1.9990 chunk 282 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 178 optimal weight: 8.9990 overall best weight: 1.0422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN B 122 GLN B 802 ASN C 122 GLN D 122 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 29404 Z= 0.173 Angle : 0.425 7.102 39832 Z= 0.221 Chirality : 0.039 0.132 4520 Planarity : 0.003 0.037 4932 Dihedral : 7.978 59.951 4568 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.58 % Allowed : 17.09 % Favored : 80.33 % 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: 1.51 (0.14), residues: 3492 helix: 1.33 (0.13), residues: 1680 sheet: 0.68 (0.26), residues: 420 loop : 0.92 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 289 HIS 0.003 0.001 HIS D 358 PHE 0.015 0.001 PHE A 321 TYR 0.010 0.001 TYR C1016 ARG 0.001 0.000 ARG D 829 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 249 time to evaluate : 3.767 Fit side-chains REVERT: A 801 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7505 (mtt-85) REVERT: B 551 MET cc_start: 0.8170 (ttp) cc_final: 0.7909 (ttm) REVERT: C 551 MET cc_start: 0.8167 (ttp) cc_final: 0.7954 (tmm) REVERT: C 1001 THR cc_start: 0.9209 (m) cc_final: 0.8913 (p) REVERT: D 375 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8492 (mtmt) outliers start: 80 outliers final: 55 residues processed: 301 average time/residue: 1.4296 time to fit residues: 508.2413 Evaluate side-chains 298 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 241 time to evaluate : 3.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 801 ARG Chi-restraints excluded: chain A residue 971 VAL Chi-restraints excluded: chain A residue 973 ASP Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain A residue 1036 GLU Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1077 GLN Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 973 ASP Chi-restraints excluded: chain B residue 1012 MET Chi-restraints excluded: chain B residue 1036 GLU Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1077 GLN Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain C residue 973 ASP Chi-restraints excluded: chain C residue 1012 MET Chi-restraints excluded: chain C residue 1036 GLU Chi-restraints excluded: chain C residue 1037 LEU Chi-restraints excluded: chain C residue 1077 GLN Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 375 LYS Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 971 VAL Chi-restraints excluded: chain D residue 973 ASP Chi-restraints excluded: chain D residue 1036 GLU Chi-restraints excluded: chain D residue 1037 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 328 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 194 optimal weight: 4.9990 chunk 248 optimal weight: 0.7980 chunk 192 optimal weight: 0.6980 chunk 286 optimal weight: 0.8980 chunk 190 optimal weight: 9.9990 chunk 339 optimal weight: 2.9990 chunk 212 optimal weight: 4.9990 chunk 206 optimal weight: 1.9990 chunk 156 optimal weight: 7.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN B 122 GLN C 122 GLN D 122 GLN D 802 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 29404 Z= 0.201 Angle : 0.437 6.813 39832 Z= 0.227 Chirality : 0.040 0.132 4520 Planarity : 0.003 0.037 4932 Dihedral : 7.781 58.583 4568 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.75 % Allowed : 16.99 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.14), residues: 3492 helix: 1.35 (0.13), residues: 1676 sheet: 0.67 (0.26), residues: 420 loop : 0.92 (0.17), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 289 HIS 0.003 0.001 HIS A 358 PHE 0.017 0.001 PHE A 525 TYR 0.012 0.001 TYR C1016 ARG 0.001 0.000 ARG C 801 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 243 time to evaluate : 3.443 Fit side-chains REVERT: A 801 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7511 (mtt-85) REVERT: A 1036 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7744 (mp0) REVERT: B 551 MET cc_start: 0.8173 (ttp) cc_final: 0.7960 (tmm) REVERT: B 801 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7565 (mtt-85) REVERT: C 551 MET cc_start: 0.8174 (ttp) cc_final: 0.7965 (tmm) REVERT: C 1001 THR cc_start: 0.9231 (m) cc_final: 0.8962 (p) REVERT: D 375 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8494 (mtmt) REVERT: D 475 MET cc_start: 0.8874 (mmm) cc_final: 0.8582 (mmm) REVERT: D 1036 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7741 (mp0) outliers start: 85 outliers final: 58 residues processed: 305 average time/residue: 1.3978 time to fit residues: 502.7116 Evaluate side-chains 304 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 241 time to evaluate : 3.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 801 ARG Chi-restraints excluded: chain A residue 971 VAL Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain A residue 1036 GLU Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1077 GLN Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 801 ARG Chi-restraints excluded: chain B residue 971 VAL Chi-restraints excluded: chain B residue 973 ASP Chi-restraints excluded: chain B residue 1012 MET Chi-restraints excluded: chain B residue 1036 GLU Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1077 GLN Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain C residue 1012 MET Chi-restraints excluded: chain C residue 1036 GLU Chi-restraints excluded: chain C residue 1037 LEU Chi-restraints excluded: chain C residue 1077 GLN Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 155 ARG Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 375 LYS Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 971 VAL Chi-restraints excluded: chain D residue 1036 GLU Chi-restraints excluded: chain D residue 1037 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 209 optimal weight: 0.9990 chunk 135 optimal weight: 3.9990 chunk 202 optimal weight: 2.9990 chunk 102 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 65 optimal weight: 0.0270 chunk 215 optimal weight: 0.0470 chunk 231 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 266 optimal weight: 7.9990 overall best weight: 1.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN B 122 GLN C 122 GLN D 122 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 29404 Z= 0.170 Angle : 0.425 6.564 39832 Z= 0.220 Chirality : 0.039 0.131 4520 Planarity : 0.003 0.036 4932 Dihedral : 7.589 57.782 4568 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.58 % Allowed : 17.15 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.14), residues: 3492 helix: 1.42 (0.13), residues: 1656 sheet: 0.66 (0.26), residues: 420 loop : 1.03 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 289 HIS 0.003 0.001 HIS B 358 PHE 0.015 0.001 PHE D 321 TYR 0.010 0.001 TYR A1016 ARG 0.001 0.000 ARG C 801 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 251 time to evaluate : 3.343 Fit side-chains REVERT: A 801 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.7543 (mtt-85) REVERT: A 1036 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7765 (mp0) REVERT: B 551 MET cc_start: 0.8148 (ttp) cc_final: 0.7886 (ttm) REVERT: B 801 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7574 (mtt-85) REVERT: B 1036 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7757 (mp0) REVERT: C 551 MET cc_start: 0.8164 (ttp) cc_final: 0.7890 (ttm) REVERT: C 1001 THR cc_start: 0.9240 (m) cc_final: 0.8977 (p) REVERT: C 1036 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7755 (mp0) REVERT: D 147 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7605 (t0) REVERT: D 551 MET cc_start: 0.8193 (ttp) cc_final: 0.7986 (tmm) REVERT: D 1036 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7772 (mp0) outliers start: 80 outliers final: 60 residues processed: 310 average time/residue: 1.3751 time to fit residues: 503.3941 Evaluate side-chains 305 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 238 time to evaluate : 2.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 801 ARG Chi-restraints excluded: chain A residue 971 VAL Chi-restraints excluded: chain A residue 973 ASP Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain A residue 1036 GLU Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1077 GLN Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 801 ARG Chi-restraints excluded: chain B residue 971 VAL Chi-restraints excluded: chain B residue 973 ASP Chi-restraints excluded: chain B residue 1012 MET Chi-restraints excluded: chain B residue 1036 GLU Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1077 GLN Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain C residue 973 ASP Chi-restraints excluded: chain C residue 1012 MET Chi-restraints excluded: chain C residue 1036 GLU Chi-restraints excluded: chain C residue 1037 LEU Chi-restraints excluded: chain C residue 1077 GLN Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 155 ARG Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 971 VAL Chi-restraints excluded: chain D residue 973 ASP Chi-restraints excluded: chain D residue 1036 GLU Chi-restraints excluded: chain D residue 1037 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 308 optimal weight: 4.9990 chunk 325 optimal weight: 1.9990 chunk 296 optimal weight: 0.6980 chunk 316 optimal weight: 0.9990 chunk 324 optimal weight: 2.9990 chunk 190 optimal weight: 10.0000 chunk 137 optimal weight: 0.7980 chunk 248 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 285 optimal weight: 5.9990 chunk 299 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN B 122 GLN C 122 GLN D 122 GLN D 802 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 29404 Z= 0.176 Angle : 0.432 8.893 39832 Z= 0.222 Chirality : 0.039 0.132 4520 Planarity : 0.003 0.037 4932 Dihedral : 7.449 56.775 4568 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.42 % Allowed : 17.41 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.14), residues: 3492 helix: 1.43 (0.13), residues: 1664 sheet: 0.66 (0.26), residues: 420 loop : 1.06 (0.17), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 289 HIS 0.003 0.001 HIS B 358 PHE 0.015 0.001 PHE C 525 TYR 0.011 0.001 TYR C1016 ARG 0.002 0.000 ARG A 801 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 246 time to evaluate : 3.326 Fit side-chains REVERT: A 155 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.6877 (ptm-80) REVERT: A 1036 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7758 (mp0) REVERT: B 551 MET cc_start: 0.8149 (ttp) cc_final: 0.7882 (ttm) REVERT: B 1036 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7748 (mp0) REVERT: C 551 MET cc_start: 0.8157 (ttp) cc_final: 0.7894 (ttm) REVERT: C 1001 THR cc_start: 0.9236 (m) cc_final: 0.8977 (p) REVERT: C 1036 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7752 (mp0) REVERT: D 147 ASP cc_start: 0.8013 (OUTLIER) cc_final: 0.7605 (t0) REVERT: D 801 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7578 (mtt-85) REVERT: D 1036 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7759 (mp0) outliers start: 75 outliers final: 62 residues processed: 303 average time/residue: 1.3937 time to fit residues: 495.8579 Evaluate side-chains 310 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 241 time to evaluate : 3.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 971 VAL Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain A residue 1036 GLU Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1077 GLN Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 971 VAL Chi-restraints excluded: chain B residue 973 ASP Chi-restraints excluded: chain B residue 1012 MET Chi-restraints excluded: chain B residue 1036 GLU Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1077 GLN Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain C residue 973 ASP Chi-restraints excluded: chain C residue 1012 MET Chi-restraints excluded: chain C residue 1036 GLU Chi-restraints excluded: chain C residue 1037 LEU Chi-restraints excluded: chain C residue 1077 GLN Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 155 ARG Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 801 ARG Chi-restraints excluded: chain D residue 971 VAL Chi-restraints excluded: chain D residue 973 ASP Chi-restraints excluded: chain D residue 1036 GLU Chi-restraints excluded: chain D residue 1037 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 315 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 334 optimal weight: 5.9990 chunk 204 optimal weight: 0.0270 chunk 158 optimal weight: 7.9990 chunk 232 optimal weight: 7.9990 chunk 350 optimal weight: 5.9990 chunk 322 optimal weight: 5.9990 chunk 279 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 215 optimal weight: 0.7980 overall best weight: 1.5442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN B 122 GLN C 122 GLN D 122 GLN D 802 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 29404 Z= 0.232 Angle : 0.456 8.322 39832 Z= 0.236 Chirality : 0.041 0.149 4520 Planarity : 0.003 0.037 4932 Dihedral : 7.459 58.354 4568 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.20 % Allowed : 17.64 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.15), residues: 3492 helix: 1.37 (0.13), residues: 1684 sheet: 0.64 (0.26), residues: 420 loop : 1.06 (0.18), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 861 HIS 0.003 0.001 HIS A 358 PHE 0.018 0.001 PHE C 525 TYR 0.014 0.001 TYR C1016 ARG 0.001 0.000 ARG A 545 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 248 time to evaluate : 4.087 Fit side-chains REVERT: A 108 MET cc_start: 0.2272 (mmm) cc_final: 0.2061 (mmm) REVERT: A 155 ARG cc_start: 0.7191 (OUTLIER) cc_final: 0.6879 (ptm-80) REVERT: A 1036 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7737 (mp0) REVERT: B 551 MET cc_start: 0.8167 (ttp) cc_final: 0.7898 (ttm) REVERT: B 1036 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7732 (mp0) REVERT: C 551 MET cc_start: 0.8174 (ttp) cc_final: 0.7908 (ttm) REVERT: C 1001 THR cc_start: 0.9247 (m) cc_final: 0.8997 (p) REVERT: C 1036 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7744 (mp0) REVERT: D 147 ASP cc_start: 0.8033 (OUTLIER) cc_final: 0.7617 (t0) REVERT: D 1036 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7754 (mp0) outliers start: 68 outliers final: 62 residues processed: 303 average time/residue: 1.3751 time to fit residues: 491.0420 Evaluate side-chains 309 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 241 time to evaluate : 3.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 971 VAL Chi-restraints excluded: chain A residue 973 ASP Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain A residue 1036 GLU Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1077 GLN Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 971 VAL Chi-restraints excluded: chain B residue 1012 MET Chi-restraints excluded: chain B residue 1036 GLU Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1077 GLN Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain C residue 1012 MET Chi-restraints excluded: chain C residue 1036 GLU Chi-restraints excluded: chain C residue 1037 LEU Chi-restraints excluded: chain C residue 1077 GLN Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 155 ARG Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 971 VAL Chi-restraints excluded: chain D residue 973 ASP Chi-restraints excluded: chain D residue 1036 GLU Chi-restraints excluded: chain D residue 1037 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 171 optimal weight: 0.8980 chunk 221 optimal weight: 2.9990 chunk 297 optimal weight: 0.9980 chunk 85 optimal weight: 0.4980 chunk 257 optimal weight: 2.9990 chunk 41 optimal weight: 0.3980 chunk 77 optimal weight: 2.9990 chunk 279 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 chunk 287 optimal weight: 0.0870 chunk 35 optimal weight: 0.9980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN B 122 GLN C 122 GLN D 122 GLN D 802 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.112601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.076655 restraints weight = 41484.334| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.51 r_work: 0.2804 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2658 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2658 r_free = 0.2658 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2657 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 29404 Z= 0.134 Angle : 0.422 8.501 39832 Z= 0.217 Chirality : 0.039 0.153 4520 Planarity : 0.003 0.036 4932 Dihedral : 7.255 58.787 4568 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.94 % Allowed : 17.93 % Favored : 80.14 % 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: 1.72 (0.15), residues: 3492 helix: 1.47 (0.13), residues: 1660 sheet: 0.64 (0.26), residues: 420 loop : 1.13 (0.18), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 289 HIS 0.002 0.000 HIS D 478 PHE 0.013 0.001 PHE A 321 TYR 0.010 0.001 TYR A 477 ARG 0.006 0.000 ARG B 829 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10147.27 seconds wall clock time: 180 minutes 23.35 seconds (10823.35 seconds total)