Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 02:46:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnh_33315/04_2023/7xnh_33315_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnh_33315/04_2023/7xnh_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_2023/7xnh_33315.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnh_33315/04_2023/7xnh_33315.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnh_33315/04_2023/7xnh_33315_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnh_33315/04_2023/7xnh_33315_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 226 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: 208 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: 208 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: 208 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: 208 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: 190 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: 226 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: 208 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: 208 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: 208 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: 208 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: 190 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: 9.76, per 1000 atoms: 0.51 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: 6.24 Conformation dependent library (CDL) restraints added in 2.4 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: 1.17 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: 4.89 Time building geometry restraints manager: 6.90 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: 3.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 14.410 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 43.310 Find NCS groups from input model: 1.550 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.650 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 2.131 Fit side-chains outliers start: 12 outliers final: 9 residues processed: 419 average time/residue: 0.3292 time to fit residues: 206.4213 Evaluate side-chains 371 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 362 time to evaluate : 2.244 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.4955 time to fit residues: 8.4943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** L 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 19512 Z= 0.166 Angle : 0.448 4.631 25836 Z= 0.232 Chirality : 0.040 0.136 2844 Planarity : 0.004 0.032 3024 Dihedral : 14.159 59.451 3708 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer Outliers : 0.87 % 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: 1.41 (0.17), residues: 2124 helix: 1.58 (0.14), residues: 1392 sheet: 1.61 (0.46), residues: 144 loop : -0.75 (0.20), residues: 588 *********************** 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 387 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 370 time to evaluate : 2.175 Fit side-chains outliers start: 17 outliers final: 10 residues processed: 373 average time/residue: 0.3206 time to fit residues: 180.8864 Evaluate side-chains 361 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 351 time to evaluate : 2.049 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1748 time to fit residues: 6.0629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.1980 chunk 163 optimal weight: 0.7980 chunk 133 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 196 optimal weight: 0.6980 chunk 212 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 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: 0.1421 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= 0.136 Angle : 0.402 4.590 25836 Z= 0.210 Chirality : 0.039 0.133 2844 Planarity : 0.003 0.022 3024 Dihedral : 12.861 59.645 3708 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer Outliers : 0.72 % 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: 1.98 (0.18), residues: 2124 helix: 2.11 (0.14), residues: 1392 sheet: 0.31 (0.38), residues: 204 loop : -0.40 (0.22), residues: 528 *********************** 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 386 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 372 time to evaluate : 1.986 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 377 average time/residue: 0.3215 time to fit residues: 183.6134 Evaluate side-chains 365 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 357 time to evaluate : 2.144 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1940 time to fit residues: 5.7493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 0.8980 chunk 147 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 131 optimal weight: 0.3980 chunk 197 optimal weight: 0.9990 chunk 208 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 186 optimal weight: 0.1980 chunk 56 optimal weight: 3.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- 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: 0.8464 moved from start: 0.1625 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= 0.130 Angle : 0.391 4.589 25836 Z= 0.203 Chirality : 0.038 0.127 2844 Planarity : 0.003 0.020 3024 Dihedral : 12.155 59.831 3708 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer Outliers : 0.77 % 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: 2.35 (0.18), residues: 2124 helix: 2.44 (0.14), residues: 1392 sheet: 0.16 (0.37), residues: 204 loop : -0.25 (0.22), residues: 528 *********************** 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 378 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 363 time to evaluate : 2.259 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 366 average time/residue: 0.3157 time to fit residues: 175.6224 Evaluate side-chains 364 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 355 time to evaluate : 2.265 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1774 time to fit residues: 6.0740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 chunk 144 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 chunk 187 optimal weight: 0.0170 chunk 52 optimal weight: 4.9990 overall best weight: 1.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 19512 Z= 0.231 Angle : 0.470 4.613 25836 Z= 0.242 Chirality : 0.041 0.143 2844 Planarity : 0.004 0.032 3024 Dihedral : 12.355 58.959 3708 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer Outliers : 0.56 % 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: 2.26 (0.18), residues: 2124 helix: 2.34 (0.14), residues: 1392 sheet: 0.06 (0.36), residues: 204 loop : -0.18 (0.22), residues: 528 *********************** 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 374 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 363 time to evaluate : 2.133 Fit side-chains outliers start: 11 outliers final: 3 residues processed: 367 average time/residue: 0.3253 time to fit residues: 180.2460 Evaluate side-chains 356 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 353 time to evaluate : 2.051 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1875 time to fit residues: 3.8537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 0.9980 chunk 188 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 122 optimal weight: 0.6980 chunk 51 optimal weight: 0.0980 chunk 208 optimal weight: 5.9990 chunk 173 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 109 optimal weight: 8.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 19512 Z= 0.127 Angle : 0.386 4.596 25836 Z= 0.202 Chirality : 0.038 0.122 2844 Planarity : 0.003 0.018 3024 Dihedral : 11.712 59.671 3708 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer Outliers : 0.36 % 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: 2.47 (0.18), residues: 2124 helix: 2.52 (0.14), residues: 1392 sheet: 0.08 (0.36), residues: 204 loop : -0.12 (0.22), residues: 528 *********************** 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 359 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 352 time to evaluate : 1.914 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 355 average time/residue: 0.3176 time to fit residues: 170.4795 Evaluate side-chains 352 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 348 time to evaluate : 1.972 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1640 time to fit residues: 4.3291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 7.9990 chunk 23 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 175 optimal weight: 0.3980 chunk 116 optimal weight: 0.7980 chunk 208 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 126 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1908 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 : 0.387 4.606 25836 Z= 0.202 Chirality : 0.038 0.127 2844 Planarity : 0.003 0.018 3024 Dihedral : 11.225 59.933 3708 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer Outliers : 0.72 % 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: 2.61 (0.18), residues: 2124 helix: 2.64 (0.14), residues: 1392 sheet: 0.06 (0.36), residues: 204 loop : -0.07 (0.22), residues: 528 *********************** 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 360 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 346 time to evaluate : 2.006 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 349 average time/residue: 0.3131 time to fit residues: 165.7498 Evaluate side-chains 353 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 343 time to evaluate : 1.922 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1685 time to fit residues: 5.8241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 40 optimal weight: 0.0050 chunk 132 optimal weight: 3.9990 chunk 141 optimal weight: 0.6980 chunk 102 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 163 optimal weight: 9.9990 chunk 189 optimal weight: 0.7980 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1956 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= 0.142 Angle : 0.394 4.612 25836 Z= 0.205 Chirality : 0.038 0.128 2844 Planarity : 0.003 0.018 3024 Dihedral : 10.981 59.947 3708 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer Outliers : 0.31 % 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: 0.07 (0.36), residues: 204 loop : -0.05 (0.22), residues: 528 *********************** 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 348 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 342 time to evaluate : 2.171 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 343 average time/residue: 0.3186 time to fit residues: 165.1617 Evaluate side-chains 340 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 337 time to evaluate : 2.089 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1767 time to fit residues: 3.7734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 2.9990 chunk 181 optimal weight: 6.9990 chunk 194 optimal weight: 0.5980 chunk 116 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 chunk 59 optimal weight: 0.0570 chunk 175 optimal weight: 0.6980 chunk 183 optimal weight: 5.9990 chunk 193 optimal weight: 4.9990 chunk 127 optimal weight: 6.9990 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2003 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= 0.143 Angle : 0.394 4.622 25836 Z= 0.205 Chirality : 0.038 0.128 2844 Planarity : 0.003 0.018 3024 Dihedral : 10.779 59.553 3708 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer Outliers : 0.05 % 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: 2.68 (0.18), residues: 2124 helix: 2.70 (0.14), residues: 1392 sheet: 0.08 (0.37), residues: 204 loop : -0.06 (0.22), residues: 528 *********************** 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 343 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 342 time to evaluate : 2.213 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 343 average time/residue: 0.3257 time to fit residues: 168.9380 Evaluate side-chains 337 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 337 time to evaluate : 2.158 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 97 optimal weight: 0.8980 chunk 142 optimal weight: 5.9990 chunk 215 optimal weight: 0.0010 chunk 198 optimal weight: 2.9990 chunk 171 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 overall best weight: 0.9190 ------------------------------------------------------------------------------- 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: 0.8483 moved from start: 0.2028 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= 0.151 Angle : 0.401 4.617 25836 Z= 0.208 Chirality : 0.039 0.129 2844 Planarity : 0.003 0.018 3024 Dihedral : 10.645 59.662 3708 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer Outliers : 0.00 % 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: 0.09 (0.37), residues: 204 loop : -0.05 (0.22), residues: 528 ********************** 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 342 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 342 time to evaluate : 2.214 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.3264 time to fit residues: 168.9075 Evaluate side-chains 339 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 339 time to evaluate : 2.166 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 158 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 171 optimal weight: 0.0980 chunk 71 optimal weight: 1.9990 chunk 176 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 chunk 150 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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** F 99 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.153295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.146446 restraints weight = 16946.689| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 0.24 r_work: 0.3393 rms_B_bonded: 0.67 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 1.14 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 19512 Z= 0.126 Angle : 0.382 4.620 25836 Z= 0.200 Chirality : 0.038 0.125 2844 Planarity : 0.003 0.018 3024 Dihedral : 10.358 59.936 3708 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer Outliers : 0.15 % 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: 2.76 (0.18), residues: 2124 helix: 2.77 (0.14), residues: 1392 sheet: 0.10 (0.37), residues: 204 loop : -0.04 (0.22), residues: 528 =============================================================================== Job complete usr+sys time: 3957.59 seconds wall clock time: 72 minutes 52.15 seconds (4372.15 seconds total)