Starting phenix.real_space_refine on Wed Apr 10 09:43:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnh_33315/04_2024/7xnh_33315_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnh_33315/04_2024/7xnh_33315.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnh_33315/04_2024/7xnh_33315.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnh_33315/04_2024/7xnh_33315.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnh_33315/04_2024/7xnh_33315_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnh_33315/04_2024/7xnh_33315_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 156 5.16 5 C 13212 2.51 5 N 2820 2.21 5 O 3036 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 19224 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "B" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "C" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "D" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "E" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "F" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "G" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "H" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "I" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "J" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "K" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "L" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "A" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 158 Unusual residues: {'MC3': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 394 Unresolved non-hydrogen angles: 502 Unresolved non-hydrogen dihedrals: 346 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'MC3:plan-2': 12, 'MC3:plan-1': 12} Unresolved non-hydrogen planarities: 74 Chain: "B" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 144 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 461 Unresolved non-hydrogen dihedrals: 318 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-2': 11, 'MC3:plan-1': 11} Unresolved non-hydrogen planarities: 68 Chain: "C" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 144 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 461 Unresolved non-hydrogen dihedrals: 318 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-2': 11, 'MC3:plan-1': 11} Unresolved non-hydrogen planarities: 68 Chain: "D" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 144 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 461 Unresolved non-hydrogen dihedrals: 318 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-2': 11, 'MC3:plan-1': 11} Unresolved non-hydrogen planarities: 68 Chain: "E" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 144 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 461 Unresolved non-hydrogen dihedrals: 318 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-2': 11, 'MC3:plan-1': 11} Unresolved non-hydrogen planarities: 68 Chain: "F" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 130 Unusual residues: {'MC3': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 330 Unresolved non-hydrogen angles: 420 Unresolved non-hydrogen dihedrals: 290 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'MC3:plan-2': 10, 'MC3:plan-1': 10} Unresolved non-hydrogen planarities: 62 Chain: "G" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 158 Unusual residues: {'MC3': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 394 Unresolved non-hydrogen angles: 502 Unresolved non-hydrogen dihedrals: 346 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'MC3:plan-2': 12, 'MC3:plan-1': 12} Unresolved non-hydrogen planarities: 74 Chain: "H" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 144 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 461 Unresolved non-hydrogen dihedrals: 318 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-2': 11, 'MC3:plan-1': 11} Unresolved non-hydrogen planarities: 68 Chain: "I" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 144 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 461 Unresolved non-hydrogen dihedrals: 318 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-2': 11, 'MC3:plan-1': 11} Unresolved non-hydrogen planarities: 68 Chain: "J" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 144 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 461 Unresolved non-hydrogen dihedrals: 318 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-2': 11, 'MC3:plan-1': 11} Unresolved non-hydrogen planarities: 68 Chain: "K" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 144 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 461 Unresolved non-hydrogen dihedrals: 318 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-2': 11, 'MC3:plan-1': 11} Unresolved non-hydrogen planarities: 68 Chain: "L" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 130 Unusual residues: {'MC3': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 330 Unresolved non-hydrogen angles: 420 Unresolved non-hydrogen dihedrals: 290 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'MC3:plan-2': 10, 'MC3:plan-1': 10} Unresolved non-hydrogen planarities: 62 Time building chain proxies: 10.15, per 1000 atoms: 0.53 Number of scatterers: 19224 At special positions: 0 Unit cell: (94.752, 100.674, 145.418, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 156 16.00 O 3036 8.00 N 2820 7.00 C 13212 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 242 " distance=2.04 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 236 " distance=2.04 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 242 " distance=2.04 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 236 " distance=2.04 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 242 " distance=2.04 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 236 " distance=2.04 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 231 " distance=2.03 Simple disulfide: pdb=" SG CYS D 55 " - pdb=" SG CYS D 242 " distance=2.04 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 236 " distance=2.04 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 231 " distance=2.03 Simple disulfide: pdb=" SG CYS E 55 " - pdb=" SG CYS E 242 " distance=2.04 Simple disulfide: pdb=" SG CYS E 62 " - pdb=" SG CYS E 236 " distance=2.04 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 231 " distance=2.03 Simple disulfide: pdb=" SG CYS F 55 " - pdb=" SG CYS F 242 " distance=2.04 Simple disulfide: pdb=" SG CYS F 62 " - pdb=" SG CYS F 236 " distance=2.04 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 231 " distance=2.03 Simple disulfide: pdb=" SG CYS G 55 " - pdb=" SG CYS G 242 " distance=2.04 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 236 " distance=2.04 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 231 " distance=2.03 Simple disulfide: pdb=" SG CYS H 55 " - pdb=" SG CYS H 242 " distance=2.04 Simple disulfide: pdb=" SG CYS H 62 " - pdb=" SG CYS H 236 " distance=2.04 Simple disulfide: pdb=" SG CYS H 66 " - pdb=" SG CYS H 231 " distance=2.03 Simple disulfide: pdb=" SG CYS I 55 " - pdb=" SG CYS I 242 " distance=2.04 Simple disulfide: pdb=" SG CYS I 62 " - pdb=" SG CYS I 236 " distance=2.04 Simple disulfide: pdb=" SG CYS I 66 " - pdb=" SG CYS I 231 " distance=2.03 Simple disulfide: pdb=" SG CYS J 55 " - pdb=" SG CYS J 242 " distance=2.04 Simple disulfide: pdb=" SG CYS J 62 " - pdb=" SG CYS J 236 " distance=2.04 Simple disulfide: pdb=" SG CYS J 66 " - pdb=" SG CYS J 231 " distance=2.03 Simple disulfide: pdb=" SG CYS K 55 " - pdb=" SG CYS K 242 " distance=2.04 Simple disulfide: pdb=" SG CYS K 62 " - pdb=" SG CYS K 236 " distance=2.04 Simple disulfide: pdb=" SG CYS K 66 " - pdb=" SG CYS K 231 " distance=2.03 Simple disulfide: pdb=" SG CYS L 55 " - pdb=" SG CYS L 242 " distance=2.04 Simple disulfide: pdb=" SG CYS L 62 " - pdb=" SG CYS L 236 " distance=2.04 Simple disulfide: pdb=" SG CYS L 66 " - pdb=" SG CYS L 231 " distance=2.03 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.19 Conformation dependent library (CDL) restraints added in 3.3 seconds 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4104 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 108 helices and 12 sheets defined 64.6% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.37 Creating SS restraints... Processing helix chain 'A' and resid 4 through 12 Processing helix chain 'A' and resid 21 through 33 Processing helix chain 'A' and resid 35 through 38 No H-bonds generated for 'chain 'A' and resid 35 through 38' Processing helix chain 'A' and resid 42 through 45 No H-bonds generated for 'chain 'A' and resid 42 through 45' Processing helix chain 'A' and resid 62 through 70 Processing helix chain 'A' and resid 75 through 86 Processing helix chain 'A' and resid 88 through 100 removed outlier: 4.104A pdb=" N PHE A 93 " --> pdb=" O PRO A 89 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ILE A 94 " --> pdb=" O SER A 90 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N THR A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL A 98 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS A 99 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN A 100 " --> pdb=" O TYR A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 220 Processing helix chain 'A' and resid 247 through 275 removed outlier: 3.652A pdb=" N PHE A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 12 Processing helix chain 'B' and resid 21 through 33 Processing helix chain 'B' and resid 35 through 38 No H-bonds generated for 'chain 'B' and resid 35 through 38' Processing helix chain 'B' and resid 42 through 45 No H-bonds generated for 'chain 'B' and resid 42 through 45' Processing helix chain 'B' and resid 62 through 70 Processing helix chain 'B' and resid 75 through 86 Processing helix chain 'B' and resid 88 through 100 removed outlier: 4.104A pdb=" N PHE B 93 " --> pdb=" O PRO B 89 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ILE B 94 " --> pdb=" O SER B 90 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N THR B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL B 98 " --> pdb=" O ILE B 94 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS B 99 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN B 100 " --> pdb=" O TYR B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 220 Processing helix chain 'B' and resid 247 through 275 removed outlier: 3.653A pdb=" N PHE B 253 " --> pdb=" O GLU B 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 12 Processing helix chain 'C' and resid 21 through 33 Processing helix chain 'C' and resid 35 through 38 No H-bonds generated for 'chain 'C' and resid 35 through 38' Processing helix chain 'C' and resid 42 through 45 No H-bonds generated for 'chain 'C' and resid 42 through 45' Processing helix chain 'C' and resid 62 through 70 Processing helix chain 'C' and resid 75 through 86 Processing helix chain 'C' and resid 88 through 100 removed outlier: 4.104A pdb=" N PHE C 93 " --> pdb=" O PRO C 89 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ILE C 94 " --> pdb=" O SER C 90 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N THR C 95 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL C 98 " --> pdb=" O ILE C 94 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS C 99 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN C 100 " --> pdb=" O TYR C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 220 Processing helix chain 'C' and resid 247 through 275 removed outlier: 3.651A pdb=" N PHE C 253 " --> pdb=" O GLU C 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 12 Processing helix chain 'D' and resid 21 through 33 Processing helix chain 'D' and resid 35 through 38 No H-bonds generated for 'chain 'D' and resid 35 through 38' Processing helix chain 'D' and resid 42 through 45 No H-bonds generated for 'chain 'D' and resid 42 through 45' Processing helix chain 'D' and resid 62 through 70 Processing helix chain 'D' and resid 75 through 86 Processing helix chain 'D' and resid 88 through 100 removed outlier: 4.104A pdb=" N PHE D 93 " --> pdb=" O PRO D 89 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ILE D 94 " --> pdb=" O SER D 90 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N THR D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL D 98 " --> pdb=" O ILE D 94 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS D 99 " --> pdb=" O THR D 95 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN D 100 " --> pdb=" O TYR D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 220 Processing helix chain 'D' and resid 247 through 275 removed outlier: 3.651A pdb=" N PHE D 253 " --> pdb=" O GLU D 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 12 Processing helix chain 'E' and resid 21 through 33 Processing helix chain 'E' and resid 35 through 38 No H-bonds generated for 'chain 'E' and resid 35 through 38' Processing helix chain 'E' and resid 42 through 45 No H-bonds generated for 'chain 'E' and resid 42 through 45' Processing helix chain 'E' and resid 62 through 70 Processing helix chain 'E' and resid 75 through 86 Processing helix chain 'E' and resid 88 through 100 removed outlier: 4.105A pdb=" N PHE E 93 " --> pdb=" O PRO E 89 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ILE E 94 " --> pdb=" O SER E 90 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N THR E 95 " --> pdb=" O LEU E 91 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL E 98 " --> pdb=" O ILE E 94 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS E 99 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN E 100 " --> pdb=" O TYR E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 220 Processing helix chain 'E' and resid 247 through 275 removed outlier: 3.652A pdb=" N PHE E 253 " --> pdb=" O GLU E 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 12 Processing helix chain 'F' and resid 21 through 33 Processing helix chain 'F' and resid 35 through 38 No H-bonds generated for 'chain 'F' and resid 35 through 38' Processing helix chain 'F' and resid 42 through 45 No H-bonds generated for 'chain 'F' and resid 42 through 45' Processing helix chain 'F' and resid 62 through 70 Processing helix chain 'F' and resid 75 through 86 Processing helix chain 'F' and resid 88 through 100 removed outlier: 4.104A pdb=" N PHE F 93 " --> pdb=" O PRO F 89 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ILE F 94 " --> pdb=" O SER F 90 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N THR F 95 " --> pdb=" O LEU F 91 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL F 98 " --> pdb=" O ILE F 94 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS F 99 " --> pdb=" O THR F 95 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN F 100 " --> pdb=" O TYR F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 220 Processing helix chain 'F' and resid 247 through 275 removed outlier: 3.652A pdb=" N PHE F 253 " --> pdb=" O GLU F 249 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 12 Processing helix chain 'G' and resid 21 through 33 Processing helix chain 'G' and resid 35 through 38 No H-bonds generated for 'chain 'G' and resid 35 through 38' Processing helix chain 'G' and resid 42 through 45 No H-bonds generated for 'chain 'G' and resid 42 through 45' Processing helix chain 'G' and resid 62 through 70 Processing helix chain 'G' and resid 75 through 86 Processing helix chain 'G' and resid 88 through 100 removed outlier: 4.104A pdb=" N PHE G 93 " --> pdb=" O PRO G 89 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ILE G 94 " --> pdb=" O SER G 90 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N THR G 95 " --> pdb=" O LEU G 91 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL G 98 " --> pdb=" O ILE G 94 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN G 100 " --> pdb=" O TYR G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 220 Processing helix chain 'G' and resid 247 through 275 removed outlier: 3.651A pdb=" N PHE G 253 " --> pdb=" O GLU G 249 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 12 Processing helix chain 'H' and resid 21 through 33 Processing helix chain 'H' and resid 35 through 38 No H-bonds generated for 'chain 'H' and resid 35 through 38' Processing helix chain 'H' and resid 42 through 45 No H-bonds generated for 'chain 'H' and resid 42 through 45' Processing helix chain 'H' and resid 62 through 70 Processing helix chain 'H' and resid 75 through 86 Processing helix chain 'H' and resid 88 through 100 removed outlier: 4.105A pdb=" N PHE H 93 " --> pdb=" O PRO H 89 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ILE H 94 " --> pdb=" O SER H 90 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N THR H 95 " --> pdb=" O LEU H 91 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL H 98 " --> pdb=" O ILE H 94 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS H 99 " --> pdb=" O THR H 95 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN H 100 " --> pdb=" O TYR H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 220 Processing helix chain 'H' and resid 247 through 275 removed outlier: 3.652A pdb=" N PHE H 253 " --> pdb=" O GLU H 249 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 12 Processing helix chain 'I' and resid 21 through 33 Processing helix chain 'I' and resid 35 through 38 No H-bonds generated for 'chain 'I' and resid 35 through 38' Processing helix chain 'I' and resid 42 through 45 No H-bonds generated for 'chain 'I' and resid 42 through 45' Processing helix chain 'I' and resid 62 through 70 Processing helix chain 'I' and resid 75 through 86 Processing helix chain 'I' and resid 88 through 100 removed outlier: 4.105A pdb=" N PHE I 93 " --> pdb=" O PRO I 89 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ILE I 94 " --> pdb=" O SER I 90 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N THR I 95 " --> pdb=" O LEU I 91 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL I 98 " --> pdb=" O ILE I 94 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS I 99 " --> pdb=" O THR I 95 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN I 100 " --> pdb=" O TYR I 96 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 220 Processing helix chain 'I' and resid 247 through 275 removed outlier: 3.652A pdb=" N PHE I 253 " --> pdb=" O GLU I 249 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 12 Processing helix chain 'J' and resid 21 through 33 Processing helix chain 'J' and resid 35 through 38 No H-bonds generated for 'chain 'J' and resid 35 through 38' Processing helix chain 'J' and resid 42 through 45 No H-bonds generated for 'chain 'J' and resid 42 through 45' Processing helix chain 'J' and resid 62 through 70 Processing helix chain 'J' and resid 75 through 86 Processing helix chain 'J' and resid 88 through 100 removed outlier: 4.104A pdb=" N PHE J 93 " --> pdb=" O PRO J 89 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ILE J 94 " --> pdb=" O SER J 90 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N THR J 95 " --> pdb=" O LEU J 91 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL J 98 " --> pdb=" O ILE J 94 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS J 99 " --> pdb=" O THR J 95 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN J 100 " --> pdb=" O TYR J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 220 Processing helix chain 'J' and resid 247 through 275 removed outlier: 3.652A pdb=" N PHE J 253 " --> pdb=" O GLU J 249 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 12 Processing helix chain 'K' and resid 21 through 33 Processing helix chain 'K' and resid 35 through 38 No H-bonds generated for 'chain 'K' and resid 35 through 38' Processing helix chain 'K' and resid 42 through 45 No H-bonds generated for 'chain 'K' and resid 42 through 45' Processing helix chain 'K' and resid 62 through 70 Processing helix chain 'K' and resid 75 through 86 Processing helix chain 'K' and resid 88 through 100 removed outlier: 4.105A pdb=" N PHE K 93 " --> pdb=" O PRO K 89 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ILE K 94 " --> pdb=" O SER K 90 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N THR K 95 " --> pdb=" O LEU K 91 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL K 98 " --> pdb=" O ILE K 94 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS K 99 " --> pdb=" O THR K 95 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN K 100 " --> pdb=" O TYR K 96 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 220 Processing helix chain 'K' and resid 247 through 275 removed outlier: 3.651A pdb=" N PHE K 253 " --> pdb=" O GLU K 249 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 12 Processing helix chain 'L' and resid 21 through 33 Processing helix chain 'L' and resid 35 through 38 No H-bonds generated for 'chain 'L' and resid 35 through 38' Processing helix chain 'L' and resid 42 through 45 No H-bonds generated for 'chain 'L' and resid 42 through 45' Processing helix chain 'L' and resid 62 through 70 Processing helix chain 'L' and resid 75 through 86 Processing helix chain 'L' and resid 88 through 100 removed outlier: 4.104A pdb=" N PHE L 93 " --> pdb=" O PRO L 89 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ILE L 94 " --> pdb=" O SER L 90 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N THR L 95 " --> pdb=" O LEU L 91 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL L 98 " --> pdb=" O ILE L 94 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS L 99 " --> pdb=" O THR L 95 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN L 100 " --> pdb=" O TYR L 96 " (cutoff:3.500A) Processing helix chain 'L' and resid 197 through 220 Processing helix chain 'L' and resid 247 through 275 removed outlier: 3.651A pdb=" N PHE L 253 " --> pdb=" O GLU L 249 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 228 through 231 Processing sheet with id= B, first strand: chain 'B' and resid 228 through 231 Processing sheet with id= C, first strand: chain 'C' and resid 228 through 231 Processing sheet with id= D, first strand: chain 'D' and resid 228 through 231 Processing sheet with id= E, first strand: chain 'E' and resid 228 through 231 Processing sheet with id= F, first strand: chain 'F' and resid 228 through 231 Processing sheet with id= G, first strand: chain 'G' and resid 228 through 231 Processing sheet with id= H, first strand: chain 'H' and resid 228 through 231 Processing sheet with id= I, first strand: chain 'I' and resid 228 through 231 Processing sheet with id= J, first strand: chain 'J' and resid 228 through 231 Processing sheet with id= K, first strand: chain 'K' and resid 228 through 231 Processing sheet with id= L, first strand: chain 'L' and resid 228 through 231 936 hydrogen bonds defined for protein. 2772 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.05 Time building geometry restraints manager: 7.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5389 1.34 - 1.46: 4167 1.46 - 1.58: 9752 1.58 - 1.70: 0 1.70 - 1.82: 204 Bond restraints: 19512 Sorted by residual: bond pdb=" CB PRO B 235 " pdb=" CG PRO B 235 " ideal model delta sigma weight residual 1.506 1.456 0.050 3.90e-02 6.57e+02 1.61e+00 bond pdb=" CB PRO L 235 " pdb=" CG PRO L 235 " ideal model delta sigma weight residual 1.506 1.457 0.049 3.90e-02 6.57e+02 1.60e+00 bond pdb=" CB PRO H 235 " pdb=" CG PRO H 235 " ideal model delta sigma weight residual 1.506 1.457 0.049 3.90e-02 6.57e+02 1.59e+00 bond pdb=" CB PRO C 235 " pdb=" CG PRO C 235 " ideal model delta sigma weight residual 1.506 1.457 0.049 3.90e-02 6.57e+02 1.58e+00 bond pdb=" CB PRO J 235 " pdb=" CG PRO J 235 " ideal model delta sigma weight residual 1.506 1.457 0.049 3.90e-02 6.57e+02 1.58e+00 ... (remaining 19507 not shown) Histogram of bond angle deviations from ideal: 100.05 - 106.85: 408 106.85 - 113.64: 11438 113.64 - 120.44: 7563 120.44 - 127.24: 6259 127.24 - 134.03: 168 Bond angle restraints: 25836 Sorted by residual: angle pdb=" N PHE G 253 " pdb=" CA PHE G 253 " pdb=" CB PHE G 253 " ideal model delta sigma weight residual 110.12 114.24 -4.12 1.47e+00 4.63e-01 7.84e+00 angle pdb=" N PHE H 253 " pdb=" CA PHE H 253 " pdb=" CB PHE H 253 " ideal model delta sigma weight residual 110.12 114.24 -4.12 1.47e+00 4.63e-01 7.84e+00 angle pdb=" N PHE A 253 " pdb=" CA PHE A 253 " pdb=" CB PHE A 253 " ideal model delta sigma weight residual 110.12 114.23 -4.11 1.47e+00 4.63e-01 7.81e+00 angle pdb=" N PHE D 253 " pdb=" CA PHE D 253 " pdb=" CB PHE D 253 " ideal model delta sigma weight residual 110.12 114.22 -4.10 1.47e+00 4.63e-01 7.80e+00 angle pdb=" N PHE J 253 " pdb=" CA PHE J 253 " pdb=" CB PHE J 253 " ideal model delta sigma weight residual 110.12 114.22 -4.10 1.47e+00 4.63e-01 7.79e+00 ... (remaining 25831 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.58: 10692 14.58 - 29.17: 720 29.17 - 43.75: 228 43.75 - 58.34: 180 58.34 - 72.92: 36 Dihedral angle restraints: 11856 sinusoidal: 5484 harmonic: 6372 Sorted by residual: dihedral pdb=" CB GLU I 239 " pdb=" CG GLU I 239 " pdb=" CD GLU I 239 " pdb=" OE1 GLU I 239 " ideal model delta sinusoidal sigma weight residual 0.00 -72.92 72.92 1 3.00e+01 1.11e-03 7.53e+00 dihedral pdb=" CB GLU F 239 " pdb=" CG GLU F 239 " pdb=" CD GLU F 239 " pdb=" OE1 GLU F 239 " ideal model delta sinusoidal sigma weight residual 0.00 -72.89 72.89 1 3.00e+01 1.11e-03 7.53e+00 dihedral pdb=" CB GLU L 239 " pdb=" CG GLU L 239 " pdb=" CD GLU L 239 " pdb=" OE1 GLU L 239 " ideal model delta sinusoidal sigma weight residual 0.00 -72.89 72.89 1 3.00e+01 1.11e-03 7.53e+00 ... (remaining 11853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1765 0.038 - 0.076: 773 0.076 - 0.114: 212 0.114 - 0.153: 82 0.153 - 0.191: 12 Chirality restraints: 2844 Sorted by residual: chirality pdb=" CA PHE A 253 " pdb=" N PHE A 253 " pdb=" C PHE A 253 " pdb=" CB PHE A 253 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.10e-01 chirality pdb=" CA PHE G 253 " pdb=" N PHE G 253 " pdb=" C PHE G 253 " pdb=" CB PHE G 253 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.81e-01 chirality pdb=" CA PHE B 253 " pdb=" N PHE B 253 " pdb=" C PHE B 253 " pdb=" CB PHE B 253 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.79e-01 ... (remaining 2841 not shown) Planarity restraints: 3024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY L 23 " 0.011 2.00e-02 2.50e+03 2.19e-02 4.79e+00 pdb=" C GLY L 23 " -0.038 2.00e-02 2.50e+03 pdb=" O GLY L 23 " 0.014 2.00e-02 2.50e+03 pdb=" N ARG L 24 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY H 23 " -0.011 2.00e-02 2.50e+03 2.19e-02 4.78e+00 pdb=" C GLY H 23 " 0.038 2.00e-02 2.50e+03 pdb=" O GLY H 23 " -0.014 2.00e-02 2.50e+03 pdb=" N ARG H 24 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 23 " 0.011 2.00e-02 2.50e+03 2.19e-02 4.78e+00 pdb=" C GLY B 23 " -0.038 2.00e-02 2.50e+03 pdb=" O GLY B 23 " 0.014 2.00e-02 2.50e+03 pdb=" N ARG B 24 " 0.013 2.00e-02 2.50e+03 ... (remaining 3021 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 379 2.70 - 3.25: 16997 3.25 - 3.80: 28980 3.80 - 4.35: 39771 4.35 - 4.90: 68284 Nonbonded interactions: 154411 Sorted by model distance: nonbonded pdb=" OE1 GLU E 230 " pdb=" NZ LYS L 238 " model vdw 2.144 2.520 nonbonded pdb=" OE1 GLU F 230 " pdb=" NZ LYS K 238 " model vdw 2.157 2.520 nonbonded pdb=" NZ LYS E 238 " pdb=" OE1 GLU L 230 " model vdw 2.190 2.520 nonbonded pdb=" NZ LYS D 238 " pdb=" OE1 GLU G 230 " model vdw 2.228 2.520 nonbonded pdb=" NZ LYS F 238 " pdb=" OE1 GLU K 230 " model vdw 2.239 2.520 ... (remaining 154406 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 2 through 276 or resid 401 through 402 or (resid 403 throu \ gh 405 and (name C31 or name C32 or name C33 or name C34 or name C35 or name C36 \ or name C37 or name C38 or name C39 or name C40)) or (resid 406 and (name C33 o \ r name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C \ 40 or name C41 or name C42 or name C43 or name C44)) or resid 407 through 408 or \ (resid 409 through 410 and (name C31 or name C32 or name C33 or name C34 or nam \ e C35 or name C36 or name C37 or name C38 or name C39 or name C40)))) selection = (chain 'B' and (resid 2 through 276 or resid 401 through 404 or (resid 405 and ( \ name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name C40)) or (resid 406 and (name C33 or name C34 o \ r name C35 or name C36 or name C37 or name C38 or name C39 or name C40 or name C \ 41 or name C42 or name C43 or name C44)) or resid 407 through 408 or (resid 409 \ through 410 and (name C31 or name C32 or name C33 or name C34 or name C35 or nam \ e C36 or name C37 or name C38 or name C39 or name C40)))) selection = (chain 'C' and (resid 2 through 276 or resid 401 through 404 or (resid 405 and ( \ name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name C40)) or (resid 406 and (name C33 or name C34 o \ r name C35 or name C36 or name C37 or name C38 or name C39 or name C40 or name C \ 41 or name C42 or name C43 or name C44)) or resid 407 through 408 or (resid 409 \ through 410 and (name C31 or name C32 or name C33 or name C34 or name C35 or nam \ e C36 or name C37 or name C38 or name C39 or name C40)))) selection = (chain 'D' and (resid 2 through 276 or resid 401 through 404 or (resid 405 and ( \ name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name C40)) or (resid 406 and (name C33 or name C34 o \ r name C35 or name C36 or name C37 or name C38 or name C39 or name C40 or name C \ 41 or name C42 or name C43 or name C44)) or resid 407 through 408 or (resid 409 \ through 410 and (name C31 or name C32 or name C33 or name C34 or name C35 or nam \ e C36 or name C37 or name C38 or name C39 or name C40)))) selection = (chain 'E' and (resid 2 through 276 or resid 401 through 404 or (resid 405 and ( \ name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name C40)) or (resid 406 and (name C33 or name C34 o \ r name C35 or name C36 or name C37 or name C38 or name C39 or name C40 or name C \ 41 or name C42 or name C43 or name C44)) or resid 407 through 408 or (resid 409 \ through 410 and (name C31 or name C32 or name C33 or name C34 or name C35 or nam \ e C36 or name C37 or name C38 or name C39 or name C40)))) selection = (chain 'F' and (resid 2 through 276 or resid 401 through 402 or (resid 403 throu \ gh 405 and (name C31 or name C32 or name C33 or name C34 or name C35 or name C36 \ or name C37 or name C38 or name C39 or name C40)) or resid 406 through 410)) selection = (chain 'G' and (resid 2 through 276 or resid 401 through 402 or (resid 403 throu \ gh 405 and (name C31 or name C32 or name C33 or name C34 or name C35 or name C36 \ or name C37 or name C38 or name C39 or name C40)) or (resid 406 and (name C33 o \ r name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C \ 40 or name C41 or name C42 or name C43 or name C44)) or resid 407 through 408 or \ (resid 409 through 410 and (name C31 or name C32 or name C33 or name C34 or nam \ e C35 or name C36 or name C37 or name C38 or name C39 or name C40)))) selection = (chain 'H' and (resid 2 through 276 or resid 401 through 404 or (resid 405 and ( \ name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name C40)) or (resid 406 and (name C33 or name C34 o \ r name C35 or name C36 or name C37 or name C38 or name C39 or name C40 or name C \ 41 or name C42 or name C43 or name C44)) or resid 407 through 408 or (resid 409 \ through 410 and (name C31 or name C32 or name C33 or name C34 or name C35 or nam \ e C36 or name C37 or name C38 or name C39 or name C40)))) selection = (chain 'I' and (resid 2 through 276 or resid 401 through 404 or (resid 405 and ( \ name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name C40)) or (resid 406 and (name C33 or name C34 o \ r name C35 or name C36 or name C37 or name C38 or name C39 or name C40 or name C \ 41 or name C42 or name C43 or name C44)) or resid 407 through 408 or (resid 409 \ through 410 and (name C31 or name C32 or name C33 or name C34 or name C35 or nam \ e C36 or name C37 or name C38 or name C39 or name C40)))) selection = (chain 'J' and (resid 2 through 276 or resid 401 through 404 or (resid 405 and ( \ name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name C40)) or (resid 406 and (name C33 or name C34 o \ r name C35 or name C36 or name C37 or name C38 or name C39 or name C40 or name C \ 41 or name C42 or name C43 or name C44)) or resid 407 through 408 or (resid 409 \ through 410 and (name C31 or name C32 or name C33 or name C34 or name C35 or nam \ e C36 or name C37 or name C38 or name C39 or name C40)))) selection = (chain 'K' and (resid 2 through 276 or resid 401 through 404 or (resid 405 and ( \ name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name C40)) or (resid 406 and (name C33 or name C34 o \ r name C35 or name C36 or name C37 or name C38 or name C39 or name C40 or name C \ 41 or name C42 or name C43 or name C44)) or resid 407 through 408 or (resid 409 \ through 410 and (name C31 or name C32 or name C33 or name C34 or name C35 or nam \ e C36 or name C37 or name C38 or name C39 or name C40)))) selection = (chain 'L' and (resid 2 through 276 or resid 401 through 402 or (resid 403 throu \ gh 405 and (name C31 or name C32 or name C33 or name C34 or name C35 or name C36 \ or name C37 or name C38 or name C39 or name C40)) or resid 406 through 410)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 17.450 Check model and map are aligned: 0.300 Set scattering table: 0.190 Process input model: 49.820 Find NCS groups from input model: 1.610 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 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 : 0.006 0.050 19512 Z= 0.359 Angle : 1.119 5.704 25836 Z= 0.494 Chirality : 0.048 0.191 2844 Planarity : 0.006 0.053 3024 Dihedral : 13.571 72.920 7644 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 0.61 % Allowed : 0.61 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.16), residues: 2124 helix: 0.23 (0.13), residues: 1392 sheet: 1.30 (0.47), residues: 144 loop : -1.23 (0.20), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 79 HIS 0.002 0.001 HIS G 75 PHE 0.017 0.002 PHE F 253 TYR 0.016 0.003 TYR A 67 ARG 0.006 0.001 ARG F 77 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 416 time to evaluate : 2.263 Fit side-chains REVERT: C 27 LEU cc_start: 0.7889 (mp) cc_final: 0.7456 (mt) REVERT: I 257 MET cc_start: 0.8901 (mmt) cc_final: 0.8320 (mmt) outliers start: 12 outliers final: 9 residues processed: 419 average time/residue: 0.3339 time to fit residues: 209.6393 Evaluate side-chains 371 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 362 time to evaluate : 2.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain F residue 238 LYS Chi-restraints excluded: chain H residue 238 LYS Chi-restraints excluded: chain I residue 238 LYS Chi-restraints excluded: chain K residue 238 LYS Chi-restraints excluded: chain L residue 238 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 6.9990 chunk 163 optimal weight: 9.9990 chunk 90 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 169 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 chunk 196 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN B 50 GLN C 50 GLN C 99 HIS D 50 GLN D 99 HIS E 50 GLN E 99 HIS F 50 GLN F 99 HIS G 50 GLN H 50 GLN I 50 GLN ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 50 GLN J 63 ASN K 50 GLN L 50 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 19512 Z= 0.164 Angle : 0.446 4.645 25836 Z= 0.231 Chirality : 0.040 0.134 2844 Planarity : 0.004 0.031 3024 Dihedral : 14.138 59.083 3744 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.87 % Allowed : 4.19 % Favored : 94.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.43 (0.17), residues: 2124 helix: 1.60 (0.14), residues: 1392 sheet: 1.56 (0.45), residues: 144 loop : -0.74 (0.20), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 79 HIS 0.002 0.000 HIS D 75 PHE 0.010 0.001 PHE C 253 TYR 0.011 0.002 TYR G 67 ARG 0.002 0.000 ARG H 77 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 368 time to evaluate : 1.970 Fit side-chains REVERT: B 3 GLU cc_start: 0.7493 (mm-30) cc_final: 0.6952 (mm-30) REVERT: I 257 MET cc_start: 0.8879 (mmt) cc_final: 0.8415 (mmt) REVERT: L 257 MET cc_start: 0.9014 (mmt) cc_final: 0.8475 (mmt) outliers start: 17 outliers final: 10 residues processed: 371 average time/residue: 0.2355 time to fit residues: 132.8911 Evaluate side-chains 357 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 347 time to evaluate : 2.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain F residue 3 GLU Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 44 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 10.0000 chunk 60 optimal weight: 0.7980 chunk 163 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 196 optimal weight: 0.7980 chunk 212 optimal weight: 0.2980 chunk 175 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 19512 Z= 0.136 Angle : 0.403 4.591 25836 Z= 0.210 Chirality : 0.038 0.132 2844 Planarity : 0.003 0.022 3024 Dihedral : 12.780 59.496 3708 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.12 % Allowed : 6.08 % Favored : 92.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.18), residues: 2124 helix: 2.13 (0.14), residues: 1392 sheet: 0.28 (0.38), residues: 204 loop : -0.39 (0.22), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 4 HIS 0.001 0.000 HIS D 75 PHE 0.005 0.001 PHE E 198 TYR 0.010 0.001 TYR G 67 ARG 0.002 0.000 ARG C 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 362 time to evaluate : 2.215 Fit side-chains REVERT: B 3 GLU cc_start: 0.7529 (mm-30) cc_final: 0.6976 (mm-30) REVERT: B 34 ARG cc_start: 0.8726 (mtt180) cc_final: 0.8483 (mtt180) REVERT: F 257 MET cc_start: 0.9032 (mmt) cc_final: 0.8515 (mmt) REVERT: I 257 MET cc_start: 0.8894 (mmt) cc_final: 0.8463 (mmt) REVERT: L 257 MET cc_start: 0.9013 (mmt) cc_final: 0.8577 (mmt) outliers start: 22 outliers final: 15 residues processed: 367 average time/residue: 0.3141 time to fit residues: 175.4171 Evaluate side-chains 365 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 350 time to evaluate : 2.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain H residue 253 PHE Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain L residue 41 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 0.9980 chunk 147 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 131 optimal weight: 0.0770 chunk 197 optimal weight: 0.9980 chunk 208 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 186 optimal weight: 0.3980 chunk 56 optimal weight: 5.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 207 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 19512 Z= 0.125 Angle : 0.387 4.587 25836 Z= 0.201 Chirality : 0.038 0.126 2844 Planarity : 0.003 0.020 3024 Dihedral : 12.091 59.953 3708 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 1.33 % Allowed : 6.70 % Favored : 91.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.18), residues: 2124 helix: 2.43 (0.14), residues: 1392 sheet: 0.14 (0.37), residues: 204 loop : -0.26 (0.22), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 4 HIS 0.001 0.000 HIS D 75 PHE 0.004 0.001 PHE E 198 TYR 0.009 0.001 TYR J 67 ARG 0.002 0.000 ARG H 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 358 time to evaluate : 2.003 Fit side-chains REVERT: B 3 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7033 (mm-30) REVERT: B 34 ARG cc_start: 0.8739 (mtt180) cc_final: 0.8517 (mtt180) REVERT: C 3 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7516 (mm-30) REVERT: F 257 MET cc_start: 0.9057 (mmt) cc_final: 0.8515 (mmt) REVERT: I 257 MET cc_start: 0.8915 (mmt) cc_final: 0.8485 (mmt) REVERT: J 85 MET cc_start: 0.7475 (mmp) cc_final: 0.7229 (mmp) REVERT: L 257 MET cc_start: 0.9004 (mmt) cc_final: 0.8543 (mmt) outliers start: 26 outliers final: 19 residues processed: 360 average time/residue: 0.3135 time to fit residues: 172.7276 Evaluate side-chains 361 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 342 time to evaluate : 1.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 253 PHE Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 253 PHE Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain G residue 12 GLU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain H residue 253 PHE Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 253 PHE Chi-restraints excluded: chain L residue 41 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 178 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 106 optimal weight: 0.8980 chunk 187 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 ASN K 207 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19512 Z= 0.251 Angle : 0.478 4.621 25836 Z= 0.246 Chirality : 0.042 0.144 2844 Planarity : 0.004 0.033 3024 Dihedral : 12.401 58.876 3708 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.53 % Allowed : 7.41 % Favored : 91.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.18), residues: 2124 helix: 2.32 (0.14), residues: 1392 sheet: 0.08 (0.36), residues: 204 loop : -0.23 (0.21), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 79 HIS 0.001 0.000 HIS D 75 PHE 0.006 0.001 PHE G 71 TYR 0.015 0.002 TYR L 67 ARG 0.002 0.000 ARG K 77 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 353 time to evaluate : 1.900 Fit side-chains REVERT: C 3 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7463 (mm-30) REVERT: F 257 MET cc_start: 0.9052 (mmt) cc_final: 0.8536 (mmt) outliers start: 30 outliers final: 20 residues processed: 360 average time/residue: 0.3185 time to fit residues: 174.1410 Evaluate side-chains 367 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 346 time to evaluate : 2.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 253 PHE Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 253 PHE Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 253 PHE Chi-restraints excluded: chain L residue 41 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 0.8980 chunk 188 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 122 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 208 optimal weight: 6.9990 chunk 173 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 109 optimal weight: 8.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 19512 Z= 0.145 Angle : 0.395 4.609 25836 Z= 0.207 Chirality : 0.038 0.123 2844 Planarity : 0.003 0.019 3024 Dihedral : 11.815 59.589 3708 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.38 % Allowed : 7.92 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.18), residues: 2124 helix: 2.48 (0.14), residues: 1392 sheet: 0.09 (0.36), residues: 204 loop : -0.15 (0.22), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP I 79 HIS 0.001 0.000 HIS D 75 PHE 0.004 0.001 PHE H 198 TYR 0.010 0.001 TYR E 243 ARG 0.002 0.000 ARG H 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 355 time to evaluate : 2.123 Fit side-chains REVERT: B 3 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7053 (mm-30) REVERT: C 3 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7465 (mm-30) REVERT: F 257 MET cc_start: 0.9068 (mmt) cc_final: 0.8600 (mmt) outliers start: 27 outliers final: 18 residues processed: 360 average time/residue: 0.3191 time to fit residues: 173.9192 Evaluate side-chains 361 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 343 time to evaluate : 2.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 253 PHE Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain G residue 12 GLU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 253 PHE Chi-restraints excluded: chain L residue 41 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 chunk 119 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 175 optimal weight: 0.3980 chunk 116 optimal weight: 1.9990 chunk 208 optimal weight: 5.9990 chunk 130 optimal weight: 0.0070 chunk 126 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 19512 Z= 0.109 Angle : 0.366 4.613 25836 Z= 0.192 Chirality : 0.037 0.121 2844 Planarity : 0.002 0.018 3024 Dihedral : 11.110 59.909 3708 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.07 % Allowed : 8.38 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.18), residues: 2124 helix: 2.70 (0.14), residues: 1392 sheet: 0.04 (0.36), residues: 204 loop : -0.05 (0.22), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP H 79 HIS 0.001 0.000 HIS D 75 PHE 0.004 0.001 PHE H 198 TYR 0.008 0.001 TYR I 243 ARG 0.001 0.000 ARG D 34 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 345 time to evaluate : 2.194 Fit side-chains REVERT: B 3 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7081 (mm-30) REVERT: C 3 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7459 (mm-30) REVERT: F 257 MET cc_start: 0.9078 (mmt) cc_final: 0.8623 (mmt) REVERT: I 34 ARG cc_start: 0.8597 (mtt180) cc_final: 0.8391 (mtt180) outliers start: 21 outliers final: 18 residues processed: 348 average time/residue: 0.3174 time to fit residues: 167.7503 Evaluate side-chains 355 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 337 time to evaluate : 2.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 253 PHE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain G residue 12 GLU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain J residue 12 GLU Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 253 PHE Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 269 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 chunk 102 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 163 optimal weight: 4.9990 chunk 189 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 19512 Z= 0.147 Angle : 0.395 4.621 25836 Z= 0.206 Chirality : 0.039 0.130 2844 Planarity : 0.003 0.019 3024 Dihedral : 11.011 59.858 3708 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.33 % Allowed : 8.59 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.18), residues: 2124 helix: 2.71 (0.14), residues: 1392 sheet: 0.03 (0.36), residues: 204 loop : -0.04 (0.22), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 79 HIS 0.001 0.000 HIS D 75 PHE 0.004 0.001 PHE B 53 TYR 0.011 0.001 TYR C 243 ARG 0.001 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 340 time to evaluate : 2.316 Fit side-chains REVERT: C 3 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7423 (mm-30) REVERT: F 257 MET cc_start: 0.9075 (mmt) cc_final: 0.8597 (mmt) REVERT: I 34 ARG cc_start: 0.8623 (mtt180) cc_final: 0.8420 (mtt180) outliers start: 26 outliers final: 21 residues processed: 346 average time/residue: 0.3190 time to fit residues: 167.4215 Evaluate side-chains 354 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 333 time to evaluate : 2.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 253 PHE Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 253 PHE Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain J residue 12 GLU Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 253 PHE Chi-restraints excluded: chain L residue 41 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 4.9990 chunk 181 optimal weight: 4.9990 chunk 194 optimal weight: 0.8980 chunk 116 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 152 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 175 optimal weight: 1.9990 chunk 183 optimal weight: 6.9990 chunk 193 optimal weight: 3.9990 chunk 127 optimal weight: 8.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19512 Z= 0.173 Angle : 0.422 4.594 25836 Z= 0.219 Chirality : 0.039 0.133 2844 Planarity : 0.003 0.022 3024 Dihedral : 11.057 59.782 3708 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.12 % Allowed : 8.95 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.18), residues: 2124 helix: 2.64 (0.14), residues: 1392 sheet: 0.07 (0.36), residues: 204 loop : -0.06 (0.22), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 79 HIS 0.001 0.000 HIS D 75 PHE 0.005 0.001 PHE J 71 TYR 0.012 0.002 TYR A 67 ARG 0.001 0.000 ARG B 77 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 337 time to evaluate : 2.258 Fit side-chains REVERT: C 3 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7406 (mm-30) REVERT: F 257 MET cc_start: 0.9077 (mmt) cc_final: 0.8606 (mmt) REVERT: I 34 ARG cc_start: 0.8637 (mtt180) cc_final: 0.8435 (mtt180) outliers start: 22 outliers final: 22 residues processed: 340 average time/residue: 0.3241 time to fit residues: 166.8688 Evaluate side-chains 355 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 333 time to evaluate : 2.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 253 PHE Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 253 PHE Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain J residue 12 GLU Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 253 PHE Chi-restraints excluded: chain L residue 41 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 215 optimal weight: 0.3980 chunk 198 optimal weight: 0.9990 chunk 171 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 chunk 136 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 19512 Z= 0.133 Angle : 0.386 4.601 25836 Z= 0.202 Chirality : 0.038 0.125 2844 Planarity : 0.003 0.018 3024 Dihedral : 10.613 59.686 3708 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 1.12 % Allowed : 8.79 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.18), residues: 2124 helix: 2.72 (0.14), residues: 1392 sheet: 0.06 (0.36), residues: 204 loop : -0.04 (0.22), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP L 79 HIS 0.001 0.000 HIS D 75 PHE 0.004 0.001 PHE F 198 TYR 0.009 0.001 TYR E 243 ARG 0.001 0.000 ARG C 206 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 343 time to evaluate : 2.094 Fit side-chains REVERT: C 3 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7414 (mm-30) REVERT: F 257 MET cc_start: 0.9084 (mmt) cc_final: 0.8639 (mmt) outliers start: 22 outliers final: 22 residues processed: 346 average time/residue: 0.3407 time to fit residues: 179.9878 Evaluate side-chains 362 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 340 time to evaluate : 2.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 253 PHE Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 253 PHE Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain J residue 12 GLU Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 253 PHE Chi-restraints excluded: chain L residue 41 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 158 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 171 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 176 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 chunk 150 optimal weight: 7.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.151893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.144822 restraints weight = 16990.158| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 0.25 r_work: 0.3372 rms_B_bonded: 0.70 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 1.22 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19512 Z= 0.166 Angle : 0.415 4.612 25836 Z= 0.215 Chirality : 0.039 0.132 2844 Planarity : 0.003 0.019 3024 Dihedral : 10.636 59.597 3708 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.18 % Allowed : 8.90 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.18), residues: 2124 helix: 2.68 (0.14), residues: 1392 sheet: 0.09 (0.37), residues: 204 loop : -0.07 (0.22), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 79 HIS 0.001 0.000 HIS D 75 PHE 0.005 0.001 PHE J 71 TYR 0.012 0.002 TYR A 67 ARG 0.001 0.000 ARG L 206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4125.79 seconds wall clock time: 81 minutes 2.29 seconds (4862.29 seconds total)