Starting phenix.real_space_refine on Sat Oct 31 10:40:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pnb_71749/10_2026/9pnb_71749_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pnb_71749/10_2026/9pnb_71749.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pnb_71749/10_2026/9pnb_71749.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pnb_71749/10_2026/9pnb_71749.map" model { file = "/net/cci-nas-00/data/ceres_data/9pnb_71749/10_2026/9pnb_71749_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pnb_71749/10_2026/9pnb_71749_neut.cif" } resolution = 2.57 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 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= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 99 5.16 5 C 13284 2.51 5 N 3654 2.21 5 O 4041 1.98 5 H 20997 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 42075 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 837 Classifications: {'peptide': 58} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "J" Number of atoms: 3838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 3838 Classifications: {'peptide': 246} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 233} Chain breaks: 1 Restraints were copied for chains: B, C, D, E, F, G, H, I, K, L, M, N, O, P, Q, R Time building chain proxies: 5.93, per 1000 atoms: 0.14 Number of scatterers: 42075 At special positions: 0 Unit cell: (134.274, 131.772, 124.266, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 99 16.00 O 4041 8.00 N 3654 7.00 C 13284 6.00 H 20997 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 24 " - pdb=" SG CYS A 58 " distance=2.03 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 58 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 58 " distance=2.03 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 58 " distance=2.03 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 58 " distance=2.03 Simple disulfide: pdb=" SG CYS F 24 " - pdb=" SG CYS F 58 " distance=2.03 Simple disulfide: pdb=" SG CYS G 24 " - pdb=" SG CYS G 58 " distance=2.03 Simple disulfide: pdb=" SG CYS H 24 " - pdb=" SG CYS H 58 " distance=2.03 Simple disulfide: pdb=" SG CYS I 24 " - pdb=" SG CYS I 58 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.61 Conformation dependent library (CDL) restraints added in 1.4 seconds 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5040 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 1 sheets defined 41.1% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 9 through 13 Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 18 through 41 removed outlier: 3.550A pdb=" N GLN A 29 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU A 34 " --> pdb=" O ASN A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 58 removed outlier: 3.671A pdb=" N ALA A 47 " --> pdb=" O ASP A 43 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N CYS A 58 " --> pdb=" O ILE A 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 13 Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 18 through 41 removed outlier: 3.551A pdb=" N GLN B 29 " --> pdb=" O SER B 25 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU B 34 " --> pdb=" O ASN B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 58 removed outlier: 3.672A pdb=" N ALA B 47 " --> pdb=" O ASP B 43 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N CYS B 58 " --> pdb=" O ILE B 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 13 Processing helix chain 'C' and resid 15 through 17 No H-bonds generated for 'chain 'C' and resid 15 through 17' Processing helix chain 'C' and resid 18 through 41 removed outlier: 3.550A pdb=" N GLN C 29 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU C 34 " --> pdb=" O ASN C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 58 removed outlier: 3.672A pdb=" N ALA C 47 " --> pdb=" O ASP C 43 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N CYS C 58 " --> pdb=" O ILE C 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 13 Processing helix chain 'D' and resid 15 through 17 No H-bonds generated for 'chain 'D' and resid 15 through 17' Processing helix chain 'D' and resid 18 through 41 removed outlier: 3.550A pdb=" N GLN D 29 " --> pdb=" O SER D 25 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU D 34 " --> pdb=" O ASN D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 58 removed outlier: 3.672A pdb=" N ALA D 47 " --> pdb=" O ASP D 43 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N CYS D 58 " --> pdb=" O ILE D 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 13 Processing helix chain 'E' and resid 15 through 17 No H-bonds generated for 'chain 'E' and resid 15 through 17' Processing helix chain 'E' and resid 18 through 41 removed outlier: 3.550A pdb=" N GLN E 29 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU E 34 " --> pdb=" O ASN E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 58 removed outlier: 3.672A pdb=" N ALA E 47 " --> pdb=" O ASP E 43 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N CYS E 58 " --> pdb=" O ILE E 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 13 Processing helix chain 'F' and resid 15 through 17 No H-bonds generated for 'chain 'F' and resid 15 through 17' Processing helix chain 'F' and resid 18 through 41 removed outlier: 3.550A pdb=" N GLN F 29 " --> pdb=" O SER F 25 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU F 34 " --> pdb=" O ASN F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 58 removed outlier: 3.672A pdb=" N ALA F 47 " --> pdb=" O ASP F 43 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N CYS F 58 " --> pdb=" O ILE F 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 13 Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 18 through 41 removed outlier: 3.550A pdb=" N GLN G 29 " --> pdb=" O SER G 25 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU G 34 " --> pdb=" O ASN G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 58 removed outlier: 3.672A pdb=" N ALA G 47 " --> pdb=" O ASP G 43 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N CYS G 58 " --> pdb=" O ILE G 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 13 Processing helix chain 'H' and resid 15 through 17 No H-bonds generated for 'chain 'H' and resid 15 through 17' Processing helix chain 'H' and resid 18 through 41 removed outlier: 3.551A pdb=" N GLN H 29 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU H 34 " --> pdb=" O ASN H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 58 removed outlier: 3.671A pdb=" N ALA H 47 " --> pdb=" O ASP H 43 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N CYS H 58 " --> pdb=" O ILE H 54 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 13 Processing helix chain 'I' and resid 15 through 17 No H-bonds generated for 'chain 'I' and resid 15 through 17' Processing helix chain 'I' and resid 18 through 41 removed outlier: 3.550A pdb=" N GLN I 29 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU I 34 " --> pdb=" O ASN I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 43 through 58 removed outlier: 3.671A pdb=" N ALA I 47 " --> pdb=" O ASP I 43 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N CYS I 58 " --> pdb=" O ILE I 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 25 Processing helix chain 'J' and resid 63 through 75 Processing helix chain 'J' and resid 85 through 99 Processing helix chain 'J' and resid 211 through 234 removed outlier: 3.555A pdb=" N CYS J 215 " --> pdb=" O PRO J 211 " (cutoff:3.500A) Processing helix chain 'J' and resid 241 through 246 removed outlier: 3.804A pdb=" N GLN J 246 " --> pdb=" O ALA J 243 " (cutoff:3.500A) Processing helix chain 'J' and resid 247 through 257 Processing helix chain 'K' and resid 18 through 25 Processing helix chain 'K' and resid 63 through 75 Processing helix chain 'K' and resid 85 through 99 Processing helix chain 'K' and resid 211 through 234 removed outlier: 3.555A pdb=" N CYS K 215 " --> pdb=" O PRO K 211 " (cutoff:3.500A) Processing helix chain 'K' and resid 241 through 246 removed outlier: 3.804A pdb=" N GLN K 246 " --> pdb=" O ALA K 243 " (cutoff:3.500A) Processing helix chain 'K' and resid 247 through 257 Processing helix chain 'L' and resid 18 through 25 Processing helix chain 'L' and resid 63 through 75 Processing helix chain 'L' and resid 85 through 99 Processing helix chain 'L' and resid 211 through 234 removed outlier: 3.555A pdb=" N CYS L 215 " --> pdb=" O PRO L 211 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 246 removed outlier: 3.803A pdb=" N GLN L 246 " --> pdb=" O ALA L 243 " (cutoff:3.500A) Processing helix chain 'L' and resid 247 through 257 Processing helix chain 'M' and resid 18 through 25 Processing helix chain 'M' and resid 63 through 75 Processing helix chain 'M' and resid 85 through 99 Processing helix chain 'M' and resid 211 through 234 removed outlier: 3.555A pdb=" N CYS M 215 " --> pdb=" O PRO M 211 " (cutoff:3.500A) Processing helix chain 'M' and resid 241 through 246 removed outlier: 3.803A pdb=" N GLN M 246 " --> pdb=" O ALA M 243 " (cutoff:3.500A) Processing helix chain 'M' and resid 247 through 257 Processing helix chain 'N' and resid 18 through 25 Processing helix chain 'N' and resid 63 through 75 Processing helix chain 'N' and resid 85 through 99 Processing helix chain 'N' and resid 211 through 234 removed outlier: 3.555A pdb=" N CYS N 215 " --> pdb=" O PRO N 211 " (cutoff:3.500A) Processing helix chain 'N' and resid 241 through 246 removed outlier: 3.804A pdb=" N GLN N 246 " --> pdb=" O ALA N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 247 through 257 Processing helix chain 'O' and resid 18 through 25 Processing helix chain 'O' and resid 63 through 75 Processing helix chain 'O' and resid 85 through 99 Processing helix chain 'O' and resid 211 through 234 removed outlier: 3.556A pdb=" N CYS O 215 " --> pdb=" O PRO O 211 " (cutoff:3.500A) Processing helix chain 'O' and resid 241 through 246 removed outlier: 3.803A pdb=" N GLN O 246 " --> pdb=" O ALA O 243 " (cutoff:3.500A) Processing helix chain 'O' and resid 247 through 257 Processing helix chain 'P' and resid 18 through 25 Processing helix chain 'P' and resid 63 through 75 Processing helix chain 'P' and resid 85 through 99 Processing helix chain 'P' and resid 211 through 234 removed outlier: 3.555A pdb=" N CYS P 215 " --> pdb=" O PRO P 211 " (cutoff:3.500A) Processing helix chain 'P' and resid 241 through 246 removed outlier: 3.803A pdb=" N GLN P 246 " --> pdb=" O ALA P 243 " (cutoff:3.500A) Processing helix chain 'P' and resid 247 through 257 Processing helix chain 'Q' and resid 18 through 25 Processing helix chain 'Q' and resid 63 through 75 Processing helix chain 'Q' and resid 85 through 99 Processing helix chain 'Q' and resid 211 through 234 removed outlier: 3.555A pdb=" N CYS Q 215 " --> pdb=" O PRO Q 211 " (cutoff:3.500A) Processing helix chain 'Q' and resid 241 through 246 removed outlier: 3.803A pdb=" N GLN Q 246 " --> pdb=" O ALA Q 243 " (cutoff:3.500A) Processing helix chain 'Q' and resid 247 through 257 Processing helix chain 'R' and resid 18 through 25 Processing helix chain 'R' and resid 63 through 75 Processing helix chain 'R' and resid 85 through 99 Processing helix chain 'R' and resid 211 through 234 removed outlier: 3.555A pdb=" N CYS R 215 " --> pdb=" O PRO R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 241 through 246 removed outlier: 3.804A pdb=" N GLN R 246 " --> pdb=" O ALA R 243 " (cutoff:3.500A) Processing helix chain 'R' and resid 247 through 257 Processing sheet with id=AA1, first strand: chain 'J' and resid 13 through 14 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 13 through 14 current: chain 'J' and resid 146 through 165 removed outlier: 3.815A pdb=" N SER J 173 " --> pdb=" O VAL J 163 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ASN J 165 " --> pdb=" O ILE J 171 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE J 171 " --> pdb=" O ASN J 165 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE J 194 " --> pdb=" O ARG J 198 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ARG J 198 " --> pdb=" O ILE J 194 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 198 through 209 current: chain 'K' and resid 146 through 165 removed outlier: 3.816A pdb=" N SER K 173 " --> pdb=" O VAL K 163 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASN K 165 " --> pdb=" O ILE K 171 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE K 171 " --> pdb=" O ASN K 165 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE K 194 " --> pdb=" O ARG K 198 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ARG K 198 " --> pdb=" O ILE K 194 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 198 through 209 current: chain 'L' and resid 146 through 165 removed outlier: 3.816A pdb=" N SER L 173 " --> pdb=" O VAL L 163 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ASN L 165 " --> pdb=" O ILE L 171 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE L 171 " --> pdb=" O ASN L 165 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE L 194 " --> pdb=" O ARG L 198 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ARG L 198 " --> pdb=" O ILE L 194 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 198 through 209 current: chain 'M' and resid 146 through 165 removed outlier: 3.815A pdb=" N SER M 173 " --> pdb=" O VAL M 163 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ASN M 165 " --> pdb=" O ILE M 171 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE M 171 " --> pdb=" O ASN M 165 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE M 194 " --> pdb=" O ARG M 198 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ARG M 198 " --> pdb=" O ILE M 194 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 198 through 209 current: chain 'N' and resid 146 through 165 removed outlier: 3.817A pdb=" N SER N 173 " --> pdb=" O VAL N 163 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ASN N 165 " --> pdb=" O ILE N 171 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE N 171 " --> pdb=" O ASN N 165 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE N 194 " --> pdb=" O ARG N 198 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ARG N 198 " --> pdb=" O ILE N 194 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 198 through 209 current: chain 'O' and resid 146 through 165 removed outlier: 3.816A pdb=" N SER O 173 " --> pdb=" O VAL O 163 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ASN O 165 " --> pdb=" O ILE O 171 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE O 171 " --> pdb=" O ASN O 165 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE O 194 " --> pdb=" O ARG O 198 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ARG O 198 " --> pdb=" O ILE O 194 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 198 through 209 current: chain 'P' and resid 146 through 165 removed outlier: 3.815A pdb=" N SER P 173 " --> pdb=" O VAL P 163 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASN P 165 " --> pdb=" O ILE P 171 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE P 171 " --> pdb=" O ASN P 165 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE P 194 " --> pdb=" O ARG P 198 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ARG P 198 " --> pdb=" O ILE P 194 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 198 through 209 current: chain 'Q' and resid 146 through 165 removed outlier: 3.815A pdb=" N SER Q 173 " --> pdb=" O VAL Q 163 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASN Q 165 " --> pdb=" O ILE Q 171 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE Q 171 " --> pdb=" O ASN Q 165 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE Q 194 " --> pdb=" O ARG Q 198 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ARG Q 198 " --> pdb=" O ILE Q 194 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 198 through 209 current: chain 'R' and resid 146 through 165 removed outlier: 3.815A pdb=" N SER R 173 " --> pdb=" O VAL R 163 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ASN R 165 " --> pdb=" O ILE R 171 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE R 171 " --> pdb=" O ASN R 165 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE R 194 " --> pdb=" O ARG R 198 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ARG R 198 " --> pdb=" O ILE R 194 " (cutoff:3.500A) 981 hydrogen bonds defined for protein. 2835 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.69 Time building geometry restraints manager: 6.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 20979 1.03 - 1.23: 21 1.23 - 1.42: 8853 1.42 - 1.62: 12429 1.62 - 1.81: 162 Bond restraints: 42444 Sorted by residual: bond pdb=" N CYS N 1 " pdb=" H1 CYS N 1 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" N CYS Q 1 " pdb=" H1 CYS Q 1 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" N CYS L 1 " pdb=" H1 CYS L 1 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" N CYS K 1 " pdb=" H1 CYS K 1 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" N CYS J 1 " pdb=" H1 CYS J 1 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.52e+01 ... (remaining 42439 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 74442 1.37 - 2.74: 1853 2.74 - 4.12: 232 4.12 - 5.49: 41 5.49 - 6.86: 49 Bond angle restraints: 76617 Sorted by residual: angle pdb=" CG LYS K 22 " pdb=" CD LYS K 22 " pdb=" CE LYS K 22 " ideal model delta sigma weight residual 111.30 117.50 -6.20 2.30e+00 1.89e-01 7.27e+00 angle pdb=" CG LYS M 22 " pdb=" CD LYS M 22 " pdb=" CE LYS M 22 " ideal model delta sigma weight residual 111.30 117.49 -6.19 2.30e+00 1.89e-01 7.25e+00 angle pdb=" CG LYS O 22 " pdb=" CD LYS O 22 " pdb=" CE LYS O 22 " ideal model delta sigma weight residual 111.30 117.49 -6.19 2.30e+00 1.89e-01 7.25e+00 angle pdb=" CG LYS N 22 " pdb=" CD LYS N 22 " pdb=" CE LYS N 22 " ideal model delta sigma weight residual 111.30 117.48 -6.18 2.30e+00 1.89e-01 7.21e+00 angle pdb=" CG LYS R 22 " pdb=" CD LYS R 22 " pdb=" CE LYS R 22 " ideal model delta sigma weight residual 111.30 117.47 -6.17 2.30e+00 1.89e-01 7.20e+00 ... (remaining 76612 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 18090 17.41 - 34.82: 1206 34.82 - 52.23: 513 52.23 - 69.64: 171 69.64 - 87.05: 54 Dihedral angle restraints: 20034 sinusoidal: 11079 harmonic: 8955 Sorted by residual: dihedral pdb=" CB GLU P 82 " pdb=" CG GLU P 82 " pdb=" CD GLU P 82 " pdb=" OE1 GLU P 82 " ideal model delta sinusoidal sigma weight residual 0.00 84.14 -84.14 1 3.00e+01 1.11e-03 9.58e+00 dihedral pdb=" CB GLU M 82 " pdb=" CG GLU M 82 " pdb=" CD GLU M 82 " pdb=" OE1 GLU M 82 " ideal model delta sinusoidal sigma weight residual 0.00 84.11 -84.11 1 3.00e+01 1.11e-03 9.57e+00 dihedral pdb=" CB GLU O 82 " pdb=" CG GLU O 82 " pdb=" CD GLU O 82 " pdb=" OE1 GLU O 82 " ideal model delta sinusoidal sigma weight residual 0.00 84.10 -84.10 1 3.00e+01 1.11e-03 9.57e+00 ... (remaining 20031 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2048 0.028 - 0.056: 800 0.056 - 0.084: 232 0.084 - 0.111: 158 0.111 - 0.139: 65 Chirality restraints: 3303 Sorted by residual: chirality pdb=" CA ILE O 41 " pdb=" N ILE O 41 " pdb=" C ILE O 41 " pdb=" CB ILE O 41 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA ILE N 41 " pdb=" N ILE N 41 " pdb=" C ILE N 41 " pdb=" CB ILE N 41 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA ILE J 41 " pdb=" N ILE J 41 " pdb=" C ILE J 41 " pdb=" CB ILE J 41 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.77e-01 ... (remaining 3300 not shown) Planarity restraints: 6408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU G 33 " -0.023 2.00e-02 2.50e+03 4.64e-02 2.15e+01 pdb=" CD GLU G 33 " 0.080 2.00e-02 2.50e+03 pdb=" OE1 GLU G 33 " -0.029 2.00e-02 2.50e+03 pdb=" OE2 GLU G 33 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU F 33 " -0.023 2.00e-02 2.50e+03 4.63e-02 2.15e+01 pdb=" CD GLU F 33 " 0.080 2.00e-02 2.50e+03 pdb=" OE1 GLU F 33 " -0.029 2.00e-02 2.50e+03 pdb=" OE2 GLU F 33 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU H 33 " 0.023 2.00e-02 2.50e+03 4.63e-02 2.14e+01 pdb=" CD GLU H 33 " -0.080 2.00e-02 2.50e+03 pdb=" OE1 GLU H 33 " 0.029 2.00e-02 2.50e+03 pdb=" OE2 GLU H 33 " 0.029 2.00e-02 2.50e+03 ... (remaining 6405 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.29: 7405 2.29 - 2.87: 96927 2.87 - 3.44: 110020 3.44 - 4.02: 157851 4.02 - 4.60: 240420 Nonbonded interactions: 612623 Sorted by model distance: nonbonded pdb=" HB3 LYS K 22 " pdb=" HZ2 LYS K 22 " model vdw 1.709 2.270 nonbonded pdb=" HB3 LYS Q 22 " pdb=" HZ2 LYS Q 22 " model vdw 1.709 2.270 nonbonded pdb=" HB3 LYS P 22 " pdb=" HZ2 LYS P 22 " model vdw 1.709 2.270 nonbonded pdb=" HB3 LYS R 22 " pdb=" HZ2 LYS R 22 " model vdw 1.709 2.270 nonbonded pdb=" HB3 LYS L 22 " pdb=" HZ2 LYS L 22 " model vdw 1.709 2.270 ... (remaining 612618 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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: 10.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.130 Extract box with map and model: 0.780 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 41.700 Find NCS groups from input model: 0.360 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: 0.000 Load rotamer database and sin/cos tables:6.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9146 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 : 0.004 0.029 21456 Z= 0.173 Angle : 0.562 6.860 29097 Z= 0.302 Chirality : 0.040 0.139 3303 Planarity : 0.005 0.046 3816 Dihedral : 15.027 87.051 7893 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.00 % Allowed : 9.88 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.17), residues: 2682 helix: 2.17 (0.17), residues: 981 sheet: 0.82 (0.20), residues: 675 loop : -0.29 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 162 TYR 0.008 0.001 TYR P 253 PHE 0.011 0.001 PHE C 21 TRP 0.018 0.003 TRP G 39 HIS 0.002 0.001 HIS P 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (21447) covalent geometry : angle 0.56191 / 0.30 (29079) SS BOND : bond 0.00115 / 0.08 ( 9) SS BOND : angle 0.15367 / 0.10 ( 18) hydrogen bonds : bond 0.12595 / 8.65 ( 981) hydrogen bonds : angle 5.87230 / 4.05 ( 2835) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 GLN cc_start: 0.9206 (mm-40) cc_final: 0.8956 (mm110) REVERT: D 27 GLN cc_start: 0.9221 (mm-40) cc_final: 0.8970 (mm110) REVERT: E 27 GLN cc_start: 0.9197 (mm-40) cc_final: 0.8947 (mm110) REVERT: F 27 GLN cc_start: 0.9195 (mm-40) cc_final: 0.8950 (mm110) REVERT: G 27 GLN cc_start: 0.9205 (mm-40) cc_final: 0.8936 (mm110) REVERT: H 27 GLN cc_start: 0.9238 (mm-40) cc_final: 0.8963 (mm110) REVERT: I 27 GLN cc_start: 0.9188 (mm-40) cc_final: 0.8885 (mm110) REVERT: L 230 ASP cc_start: 0.9001 (t70) cc_final: 0.8715 (t0) REVERT: M 230 ASP cc_start: 0.8984 (t70) cc_final: 0.8770 (t0) REVERT: N 230 ASP cc_start: 0.8960 (t70) cc_final: 0.8748 (t0) REVERT: P 230 ASP cc_start: 0.8948 (t70) cc_final: 0.8739 (t0) REVERT: Q 230 ASP cc_start: 0.8935 (t70) cc_final: 0.8636 (t0) outliers start: 0 outliers final: 1 residues processed: 263 average time/residue: 1.2836 time to fit residues: 389.8014 Evaluate side-chains 224 residues out of total 2277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 223 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 238 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: [197, 215, 20, 132, 248, 207, 155, 244, 183, 111, 258] chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.4980 chunk 111 optimal weight: 0.6980 chunk 258 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 ASN B 11 ASN C 11 ASN D 11 ASN D 41 ASN E 11 ASN F 11 ASN G 11 ASN H 11 ASN I 11 ASN J 56 GLN K 56 GLN L 56 GLN M 56 GLN N 56 GLN P 56 GLN R 56 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.058406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2439 r_free = 0.2439 target = 0.045438 restraints weight = 134880.528| |-----------------------------------------------------------------------------| r_work (start): 0.2428 rms_B_bonded: 2.41 r_work: 0.2301 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2182 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9025 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 21456 Z= 0.179 Angle : 0.488 4.114 29097 Z= 0.257 Chirality : 0.041 0.141 3303 Planarity : 0.003 0.028 3816 Dihedral : 4.359 52.389 2936 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 0.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.57 % Allowed : 8.92 % Favored : 90.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.16), residues: 2682 helix: 2.91 (0.17), residues: 999 sheet: 1.14 (0.20), residues: 585 loop : -0.03 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 254 TYR 0.010 0.001 TYR K 253 PHE 0.008 0.001 PHE E 7 TRP 0.010 0.001 TRP B 39 HIS 0.001 0.000 HIS N 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (21447) covalent geometry : angle 0.48769 / 0.26 (29079) SS BOND : bond 0.00079 / 0.05 ( 9) SS BOND : angle 0.35459 / 0.22 ( 18) hydrogen bonds : bond 0.03548 / 2.37 ( 981) hydrogen bonds : angle 4.46731 / 3.08 ( 2835) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 231 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.9001 (t0) cc_final: 0.8689 (t0) REVERT: B 6 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8286 (tm-30) REVERT: B 27 GLN cc_start: 0.9099 (mm-40) cc_final: 0.8853 (mm110) REVERT: B 43 ASP cc_start: 0.9024 (t0) cc_final: 0.8712 (t0) REVERT: C 27 GLN cc_start: 0.9006 (mm-40) cc_final: 0.8776 (mm-40) REVERT: C 43 ASP cc_start: 0.9017 (t0) cc_final: 0.8655 (t0) REVERT: D 3 MET cc_start: 0.9024 (mtp) cc_final: 0.8731 (mtp) REVERT: D 6 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8266 (tm-30) REVERT: D 43 ASP cc_start: 0.9013 (t0) cc_final: 0.8666 (t0) REVERT: D 44 GLU cc_start: 0.8356 (tp30) cc_final: 0.8105 (mm-30) REVERT: E 27 GLN cc_start: 0.9168 (mm-40) cc_final: 0.8875 (mm110) REVERT: F 27 GLN cc_start: 0.9117 (mm-40) cc_final: 0.8912 (mm110) REVERT: F 43 ASP cc_start: 0.9033 (t0) cc_final: 0.8682 (t0) REVERT: G 3 MET cc_start: 0.9033 (mtp) cc_final: 0.8806 (mtp) REVERT: G 27 GLN cc_start: 0.9095 (mm-40) cc_final: 0.8822 (mm110) REVERT: G 33 GLU cc_start: 0.8488 (tt0) cc_final: 0.7958 (tp30) REVERT: G 43 ASP cc_start: 0.9060 (t0) cc_final: 0.8710 (t0) REVERT: H 6 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8264 (tm-30) REVERT: H 27 GLN cc_start: 0.9086 (mm-40) cc_final: 0.8878 (mm110) REVERT: H 43 ASP cc_start: 0.9050 (t0) cc_final: 0.8692 (t0) REVERT: H 44 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8108 (mm-30) REVERT: I 43 ASP cc_start: 0.9048 (t0) cc_final: 0.8702 (t0) REVERT: J 230 ASP cc_start: 0.9087 (t70) cc_final: 0.8852 (t0) REVERT: K 230 ASP cc_start: 0.9064 (t70) cc_final: 0.8785 (t0) REVERT: L 230 ASP cc_start: 0.9052 (t70) cc_final: 0.8802 (t0) REVERT: M 230 ASP cc_start: 0.9031 (t70) cc_final: 0.8831 (t0) REVERT: N 230 ASP cc_start: 0.9014 (t70) cc_final: 0.8808 (t0) REVERT: P 230 ASP cc_start: 0.9016 (t70) cc_final: 0.8815 (t0) REVERT: Q 230 ASP cc_start: 0.9000 (t70) cc_final: 0.8713 (t0) REVERT: R 230 ASP cc_start: 0.9076 (t70) cc_final: 0.8798 (t0) outliers start: 13 outliers final: 2 residues processed: 233 average time/residue: 1.3891 time to fit residues: 369.5265 Evaluate side-chains 217 residues out of total 2277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 211 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 44 GLU Chi-restraints excluded: chain M residue 238 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: [176, 82, 149, 172, 222, 251, 63, 212, 183, 219, 231] chunk 176 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 222 optimal weight: 1.9990 chunk 251 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 212 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 219 optimal weight: 0.3980 chunk 231 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 229 ASN O 229 ASN P 229 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.057349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2421 r_free = 0.2421 target = 0.044728 restraints weight = 135808.335| |-----------------------------------------------------------------------------| r_work (start): 0.2408 rms_B_bonded: 2.34 r_work: 0.2285 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2170 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9050 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 21456 Z= 0.179 Angle : 0.479 3.991 29097 Z= 0.251 Chirality : 0.041 0.139 3303 Planarity : 0.003 0.025 3816 Dihedral : 4.154 14.324 2934 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 0.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.92 % Allowed : 8.56 % Favored : 90.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.17), residues: 2682 helix: 3.17 (0.17), residues: 1008 sheet: 1.23 (0.20), residues: 585 loop : -0.07 (0.19), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 254 TYR 0.010 0.001 TYR L 253 PHE 0.007 0.001 PHE E 7 TRP 0.008 0.001 TRP G 39 HIS 0.001 0.000 HIS N 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (21447) covalent geometry : angle 0.47863 / 0.25 (29079) SS BOND : bond 0.00071 / 0.05 ( 9) SS BOND : angle 0.36922 / 0.23 ( 18) hydrogen bonds : bond 0.03465 / 2.33 ( 981) hydrogen bonds : angle 4.26287 / 2.94 ( 2835) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 249 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8521 (tt0) cc_final: 0.8178 (tp30) REVERT: A 43 ASP cc_start: 0.9010 (t0) cc_final: 0.8645 (t0) REVERT: B 27 GLN cc_start: 0.9135 (mm-40) cc_final: 0.8901 (mm110) REVERT: B 43 ASP cc_start: 0.9024 (t0) cc_final: 0.8643 (t0) REVERT: C 6 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.8383 (tm-30) REVERT: C 27 GLN cc_start: 0.9001 (mm-40) cc_final: 0.8764 (mm-40) REVERT: C 33 GLU cc_start: 0.8560 (tt0) cc_final: 0.8065 (tp30) REVERT: D 6 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8255 (tm-30) REVERT: D 43 ASP cc_start: 0.9023 (t0) cc_final: 0.8674 (t0) REVERT: E 6 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.8247 (tm-30) REVERT: E 27 GLN cc_start: 0.9177 (mm-40) cc_final: 0.8901 (mm110) REVERT: F 6 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.8332 (tm-30) REVERT: G 3 MET cc_start: 0.9130 (mtp) cc_final: 0.8900 (mtp) REVERT: G 6 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8086 (tm-30) REVERT: G 33 GLU cc_start: 0.8543 (tt0) cc_final: 0.8046 (tp30) REVERT: H 6 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8228 (tm-30) REVERT: H 43 ASP cc_start: 0.9092 (t0) cc_final: 0.8713 (t0) REVERT: I 43 ASP cc_start: 0.9087 (t0) cc_final: 0.8732 (t0) REVERT: J 230 ASP cc_start: 0.9085 (t70) cc_final: 0.8839 (t0) REVERT: K 230 ASP cc_start: 0.9088 (t70) cc_final: 0.8802 (t0) REVERT: K 242 LYS cc_start: 0.9157 (mmmm) cc_final: 0.8954 (mmtm) REVERT: L 230 ASP cc_start: 0.9081 (t70) cc_final: 0.8824 (t0) REVERT: M 230 ASP cc_start: 0.9069 (t70) cc_final: 0.8840 (t0) REVERT: N 230 ASP cc_start: 0.9054 (t70) cc_final: 0.8800 (t0) REVERT: O 230 ASP cc_start: 0.9037 (t70) cc_final: 0.8738 (t0) REVERT: Q 230 ASP cc_start: 0.9038 (t70) cc_final: 0.8728 (t0) REVERT: Q 242 LYS cc_start: 0.9051 (mmmm) cc_final: 0.8814 (mmtm) REVERT: R 230 ASP cc_start: 0.9094 (t70) cc_final: 0.8804 (t0) outliers start: 21 outliers final: 9 residues processed: 258 average time/residue: 1.3405 time to fit residues: 394.6955 Evaluate side-chains 234 residues out of total 2277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 219 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 6 GLN Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain M residue 238 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: [125, 183, 142, 215, 175, 255, 116, 64, 257, 34, 87] chunk 125 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 chunk 255 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 257 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 6 GLN D 41 ASN I 6 GLN K 229 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.056541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2398 r_free = 0.2398 target = 0.043815 restraints weight = 136255.022| |-----------------------------------------------------------------------------| r_work (start): 0.2386 rms_B_bonded: 2.37 r_work: 0.2260 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2143 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9038 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 21456 Z= 0.208 Angle : 0.490 3.981 29097 Z= 0.256 Chirality : 0.042 0.139 3303 Planarity : 0.003 0.025 3816 Dihedral : 4.199 14.837 2934 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 1.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.70 % Allowed : 8.83 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.17), residues: 2682 helix: 3.28 (0.17), residues: 1008 sheet: 1.24 (0.20), residues: 585 loop : -0.13 (0.19), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 254 TYR 0.011 0.001 TYR M 253 PHE 0.007 0.001 PHE B 7 TRP 0.009 0.001 TRP D 39 HIS 0.001 0.000 HIS L 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.21 (21447) covalent geometry : angle 0.48978 / 0.26 (29079) SS BOND : bond 0.00082 / 0.06 ( 9) SS BOND : angle 0.37825 / 0.24 ( 18) hydrogen bonds : bond 0.03507 / 2.35 ( 981) hydrogen bonds : angle 4.16107 / 2.87 ( 2835) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 228 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8580 (tt0) cc_final: 0.8217 (tp30) REVERT: B 3 MET cc_start: 0.9284 (mtm) cc_final: 0.8972 (mtp) REVERT: B 33 GLU cc_start: 0.8684 (tt0) cc_final: 0.8141 (tp30) REVERT: B 43 ASP cc_start: 0.9032 (t0) cc_final: 0.8683 (t0) REVERT: C 27 GLN cc_start: 0.8995 (mm-40) cc_final: 0.8757 (mm-40) REVERT: C 33 GLU cc_start: 0.8574 (tt0) cc_final: 0.8117 (tp30) REVERT: D 6 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8269 (tm-30) REVERT: D 43 ASP cc_start: 0.9057 (t0) cc_final: 0.8747 (t0) REVERT: E 6 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8230 (tm-30) REVERT: E 27 GLN cc_start: 0.9167 (mm-40) cc_final: 0.8872 (mm110) REVERT: F 6 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8360 (tm-30) REVERT: G 3 MET cc_start: 0.9091 (mtp) cc_final: 0.8820 (mtp) REVERT: G 6 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8115 (tm-30) REVERT: G 33 GLU cc_start: 0.8602 (tt0) cc_final: 0.8135 (tp30) REVERT: I 33 GLU cc_start: 0.8736 (tt0) cc_final: 0.8291 (tp30) REVERT: J 230 ASP cc_start: 0.9096 (t70) cc_final: 0.8832 (t0) REVERT: K 230 ASP cc_start: 0.9099 (t70) cc_final: 0.8818 (t0) REVERT: K 242 LYS cc_start: 0.9152 (mmmm) cc_final: 0.8930 (mmtm) REVERT: L 230 ASP cc_start: 0.9074 (t70) cc_final: 0.8810 (t0) REVERT: L 242 LYS cc_start: 0.9076 (mmmm) cc_final: 0.8835 (mppt) REVERT: M 230 ASP cc_start: 0.9077 (t70) cc_final: 0.8847 (t0) REVERT: N 230 ASP cc_start: 0.9060 (t70) cc_final: 0.8811 (t0) REVERT: N 242 LYS cc_start: 0.9053 (mmtm) cc_final: 0.8852 (mmtm) REVERT: O 230 ASP cc_start: 0.9039 (t70) cc_final: 0.8744 (t0) REVERT: O 242 LYS cc_start: 0.9096 (mmmm) cc_final: 0.8828 (mmtm) REVERT: Q 230 ASP cc_start: 0.9029 (t70) cc_final: 0.8711 (t0) REVERT: R 230 ASP cc_start: 0.9086 (t70) cc_final: 0.8785 (t0) outliers start: 16 outliers final: 10 residues processed: 237 average time/residue: 1.2896 time to fit residues: 351.1114 Evaluate side-chains 231 residues out of total 2277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 217 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 6 GLN Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain M residue 238 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: [207, 174, 201, 4, 176, 186, 52, 15, 227, 94, 37] chunk 207 optimal weight: 1.9990 chunk 174 optimal weight: 0.9980 chunk 201 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 176 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 227 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 6 GLN B 6 GLN C 6 GLN H 6 GLN I 6 GLN J 229 ASN N 229 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.056915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2410 r_free = 0.2410 target = 0.044252 restraints weight = 135788.479| |-----------------------------------------------------------------------------| r_work (start): 0.2399 rms_B_bonded: 2.37 r_work: 0.2274 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2156 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9028 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 21456 Z= 0.165 Angle : 0.469 4.354 29097 Z= 0.245 Chirality : 0.041 0.140 3303 Planarity : 0.003 0.023 3816 Dihedral : 4.086 14.219 2934 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.75 % Allowed : 9.00 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.36 (0.17), residues: 2682 helix: 3.45 (0.17), residues: 1008 sheet: 1.28 (0.20), residues: 585 loop : -0.11 (0.19), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG N 11 TYR 0.010 0.001 TYR M 253 PHE 0.006 0.001 PHE I 7 TRP 0.007 0.001 TRP D 39 HIS 0.001 0.000 HIS Q 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 (21447) covalent geometry : angle 0.46888 / 0.24 (29079) SS BOND : bond 0.00097 / 0.07 ( 9) SS BOND : angle 0.34322 / 0.21 ( 18) hydrogen bonds : bond 0.03185 / 2.12 ( 981) hydrogen bonds : angle 4.02824 / 2.78 ( 2835) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 234 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8594 (tt0) cc_final: 0.8269 (tp30) REVERT: B 3 MET cc_start: 0.9265 (mtm) cc_final: 0.8966 (mtp) REVERT: B 6 GLN cc_start: 0.9028 (tp40) cc_final: 0.8741 (tm-30) REVERT: B 33 GLU cc_start: 0.8702 (tt0) cc_final: 0.8182 (tp30) REVERT: B 43 ASP cc_start: 0.9014 (t0) cc_final: 0.8663 (t0) REVERT: C 27 GLN cc_start: 0.8994 (mm-40) cc_final: 0.8771 (mm-40) REVERT: C 33 GLU cc_start: 0.8589 (tt0) cc_final: 0.8109 (tp30) REVERT: D 6 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.8217 (tm-30) REVERT: E 6 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8220 (tm-30) REVERT: F 6 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8062 (tm-30) REVERT: G 3 MET cc_start: 0.9089 (mtp) cc_final: 0.8838 (mtp) REVERT: G 33 GLU cc_start: 0.8618 (tt0) cc_final: 0.8145 (tp30) REVERT: H 6 GLN cc_start: 0.9006 (tp40) cc_final: 0.8690 (tm-30) REVERT: I 33 GLU cc_start: 0.8761 (tt0) cc_final: 0.8313 (tp30) REVERT: J 124 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8565 (pt0) REVERT: J 230 ASP cc_start: 0.9085 (t70) cc_final: 0.8820 (t0) REVERT: K 230 ASP cc_start: 0.9094 (t70) cc_final: 0.8824 (t0) REVERT: K 242 LYS cc_start: 0.9171 (mmmm) cc_final: 0.8936 (mptt) REVERT: L 230 ASP cc_start: 0.9069 (t70) cc_final: 0.8798 (t0) REVERT: M 230 ASP cc_start: 0.9070 (t70) cc_final: 0.8840 (t0) REVERT: N 230 ASP cc_start: 0.9059 (t70) cc_final: 0.8807 (t0) REVERT: N 242 LYS cc_start: 0.9066 (mmtm) cc_final: 0.8860 (mmtm) REVERT: O 230 ASP cc_start: 0.9038 (t70) cc_final: 0.8737 (t0) REVERT: O 242 LYS cc_start: 0.9093 (mmmm) cc_final: 0.8808 (mmtm) REVERT: P 155 ASP cc_start: 0.9325 (m-30) cc_final: 0.9106 (m-30) REVERT: Q 230 ASP cc_start: 0.9031 (t70) cc_final: 0.8708 (t0) REVERT: R 230 ASP cc_start: 0.9080 (t70) cc_final: 0.8775 (t0) outliers start: 17 outliers final: 9 residues processed: 243 average time/residue: 1.2941 time to fit residues: 362.8626 Evaluate side-chains 231 residues out of total 2277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 218 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 6 GLN Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain J residue 124 GLU Chi-restraints excluded: chain M residue 238 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: [199, 132, 87, 101, 186, 67, 155, 140, 45, 5, 66] chunk 199 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 186 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 140 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 6 GLN C 6 GLN G 6 GLN I 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.056616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2399 r_free = 0.2399 target = 0.043859 restraints weight = 136405.701| |-----------------------------------------------------------------------------| r_work (start): 0.2387 rms_B_bonded: 2.38 r_work: 0.2266 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2151 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9034 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 21456 Z= 0.185 Angle : 0.475 4.368 29097 Z= 0.248 Chirality : 0.041 0.138 3303 Planarity : 0.003 0.024 3816 Dihedral : 4.080 14.400 2934 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 1.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.92 % Allowed : 9.09 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.17), residues: 2682 helix: 3.50 (0.17), residues: 1008 sheet: 1.24 (0.20), residues: 585 loop : -0.13 (0.19), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 254 TYR 0.010 0.001 TYR N 253 PHE 0.007 0.001 PHE B 7 TRP 0.005 0.001 TRP D 39 HIS 0.001 0.000 HIS O 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 (21447) covalent geometry : angle 0.47546 / 0.25 (29079) SS BOND : bond 0.00082 / 0.06 ( 9) SS BOND : angle 0.32755 / 0.20 ( 18) hydrogen bonds : bond 0.03246 / 2.15 ( 981) hydrogen bonds : angle 3.99415 / 2.75 ( 2835) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 230 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8595 (tt0) cc_final: 0.8310 (tp30) REVERT: B 3 MET cc_start: 0.9273 (mtm) cc_final: 0.8951 (mtp) REVERT: B 33 GLU cc_start: 0.8693 (tt0) cc_final: 0.8245 (tp30) REVERT: C 27 GLN cc_start: 0.9010 (mm-40) cc_final: 0.8795 (mm-40) REVERT: C 33 GLU cc_start: 0.8626 (tt0) cc_final: 0.8166 (tp30) REVERT: D 6 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8227 (tm-30) REVERT: D 43 ASP cc_start: 0.9026 (t0) cc_final: 0.8694 (t0) REVERT: E 6 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.8190 (tm-30) REVERT: E 33 GLU cc_start: 0.8633 (tt0) cc_final: 0.8245 (tp30) REVERT: F 33 GLU cc_start: 0.8700 (tt0) cc_final: 0.8276 (tp30) REVERT: G 3 MET cc_start: 0.9080 (mtp) cc_final: 0.8852 (mtp) REVERT: G 33 GLU cc_start: 0.8654 (tt0) cc_final: 0.8184 (tp30) REVERT: I 33 GLU cc_start: 0.8757 (tt0) cc_final: 0.8363 (tp30) REVERT: J 124 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8543 (pt0) REVERT: J 230 ASP cc_start: 0.9091 (t70) cc_final: 0.8822 (t0) REVERT: K 230 ASP cc_start: 0.9105 (t70) cc_final: 0.8831 (t0) REVERT: K 242 LYS cc_start: 0.9200 (mmmm) cc_final: 0.8971 (mptt) REVERT: L 230 ASP cc_start: 0.9080 (t70) cc_final: 0.8803 (t0) REVERT: M 230 ASP cc_start: 0.9086 (t70) cc_final: 0.8849 (t0) REVERT: N 230 ASP cc_start: 0.9074 (t70) cc_final: 0.8814 (t0) REVERT: O 230 ASP cc_start: 0.9055 (t70) cc_final: 0.8745 (t0) REVERT: P 155 ASP cc_start: 0.9324 (m-30) cc_final: 0.9104 (m-30) REVERT: Q 230 ASP cc_start: 0.9045 (t70) cc_final: 0.8720 (t0) REVERT: R 230 ASP cc_start: 0.9086 (t70) cc_final: 0.8780 (t0) outliers start: 21 outliers final: 8 residues processed: 247 average time/residue: 1.3374 time to fit residues: 378.4981 Evaluate side-chains 229 residues out of total 2277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 218 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain J residue 124 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: [220, 255, 97, 19, 235, 51, 111, 244, 145, 209, 178] chunk 220 optimal weight: 1.9990 chunk 255 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 235 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 209 optimal weight: 0.9980 chunk 178 optimal weight: 2.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 6 GLN B 6 GLN C 6 GLN F 6 GLN G 6 GLN H 6 GLN I 6 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.056763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2404 r_free = 0.2404 target = 0.044039 restraints weight = 136018.886| |-----------------------------------------------------------------------------| r_work (start): 0.2393 rms_B_bonded: 2.37 r_work: 0.2272 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2157 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9031 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 21456 Z= 0.170 Angle : 0.477 5.017 29097 Z= 0.247 Chirality : 0.041 0.139 3303 Planarity : 0.003 0.023 3816 Dihedral : 4.033 13.874 2934 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.92 % Allowed : 9.13 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.40 (0.17), residues: 2682 helix: 3.53 (0.16), residues: 1008 sheet: 1.25 (0.20), residues: 585 loop : -0.11 (0.19), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 192 TYR 0.010 0.001 TYR M 253 PHE 0.006 0.001 PHE F 5 TRP 0.005 0.001 TRP D 39 HIS 0.001 0.000 HIS P 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (21447) covalent geometry : angle 0.47755 / 0.25 (29079) SS BOND : bond 0.00093 / 0.07 ( 9) SS BOND : angle 0.31744 / 0.20 ( 18) hydrogen bonds : bond 0.03130 / 2.07 ( 981) hydrogen bonds : angle 3.94745 / 2.71 ( 2835) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 227 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8609 (tt0) cc_final: 0.8327 (tp30) REVERT: B 3 MET cc_start: 0.9266 (mtm) cc_final: 0.8903 (mtp) REVERT: B 33 GLU cc_start: 0.8694 (tt0) cc_final: 0.8247 (tp30) REVERT: B 43 ASP cc_start: 0.8993 (t0) cc_final: 0.8661 (t0) REVERT: C 27 GLN cc_start: 0.9013 (mm-40) cc_final: 0.8773 (mm-40) REVERT: C 33 GLU cc_start: 0.8644 (tt0) cc_final: 0.8173 (tp30) REVERT: D 6 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8137 (tm-30) REVERT: E 6 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8128 (tm-30) REVERT: E 33 GLU cc_start: 0.8632 (tt0) cc_final: 0.8243 (tp30) REVERT: F 6 GLN cc_start: 0.9044 (tp40) cc_final: 0.8731 (tm-30) REVERT: F 33 GLU cc_start: 0.8689 (tt0) cc_final: 0.8289 (tp30) REVERT: G 3 MET cc_start: 0.9071 (mtp) cc_final: 0.8849 (mtp) REVERT: G 33 GLU cc_start: 0.8647 (tt0) cc_final: 0.8174 (tp30) REVERT: I 33 GLU cc_start: 0.8766 (tt0) cc_final: 0.8368 (tp30) REVERT: J 230 ASP cc_start: 0.9097 (t70) cc_final: 0.8812 (t0) REVERT: J 242 LYS cc_start: 0.9087 (mmmm) cc_final: 0.8812 (mmtm) REVERT: K 230 ASP cc_start: 0.9102 (t70) cc_final: 0.8828 (t0) REVERT: K 242 LYS cc_start: 0.9217 (mmmm) cc_final: 0.8985 (mptt) REVERT: L 230 ASP cc_start: 0.9087 (t70) cc_final: 0.8809 (t0) REVERT: M 230 ASP cc_start: 0.9088 (t70) cc_final: 0.8849 (t0) REVERT: N 230 ASP cc_start: 0.9082 (t70) cc_final: 0.8806 (t0) REVERT: O 230 ASP cc_start: 0.9062 (t70) cc_final: 0.8751 (t0) REVERT: P 192 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.8233 (ptp-170) REVERT: Q 124 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8570 (pt0) REVERT: Q 230 ASP cc_start: 0.9053 (t70) cc_final: 0.8724 (t0) REVERT: Q 242 LYS cc_start: 0.9042 (mmmm) cc_final: 0.8834 (mmtm) REVERT: R 230 ASP cc_start: 0.9088 (t70) cc_final: 0.8782 (t0) outliers start: 21 outliers final: 9 residues processed: 243 average time/residue: 1.3453 time to fit residues: 375.0431 Evaluate side-chains 234 residues out of total 2277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 221 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain M residue 238 ASP Chi-restraints excluded: chain P residue 192 ARG Chi-restraints excluded: chain Q residue 124 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: [244, 144, 195, 75, 19, 201, 68, 226, 93, 256, 65] chunk 244 optimal weight: 1.9990 chunk 144 optimal weight: 0.7980 chunk 195 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 201 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 226 optimal weight: 2.9990 chunk 93 optimal weight: 0.0070 chunk 256 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 6 GLN C 6 GLN G 6 GLN H 6 GLN I 6 GLN M 229 ASN Q 229 ASN R 229 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.057518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2423 r_free = 0.2423 target = 0.044761 restraints weight = 135986.341| |-----------------------------------------------------------------------------| r_work (start): 0.2410 rms_B_bonded: 2.41 r_work: 0.2289 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2175 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9043 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21456 Z= 0.120 Angle : 0.459 5.659 29097 Z= 0.237 Chirality : 0.041 0.140 3303 Planarity : 0.003 0.023 3816 Dihedral : 3.927 15.356 2934 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.48 % Allowed : 9.71 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.48 (0.17), residues: 2682 helix: 3.58 (0.16), residues: 1008 sheet: 1.40 (0.20), residues: 594 loop : -0.14 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 11 TYR 0.009 0.001 TYR R 253 PHE 0.005 0.001 PHE B 7 TRP 0.005 0.001 TRP M 237 HIS 0.001 0.000 HIS P 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (21447) covalent geometry : angle 0.45936 / 0.24 (29079) SS BOND : bond 0.00107 / 0.08 ( 9) SS BOND : angle 0.30885 / 0.19 ( 18) hydrogen bonds : bond 0.02858 / 1.89 ( 981) hydrogen bonds : angle 3.84912 / 2.64 ( 2835) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 236 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8622 (tt0) cc_final: 0.8334 (tp30) REVERT: B 3 MET cc_start: 0.9271 (mtm) cc_final: 0.8962 (mtp) REVERT: B 33 GLU cc_start: 0.8709 (tt0) cc_final: 0.8264 (tp30) REVERT: B 43 ASP cc_start: 0.9009 (t0) cc_final: 0.8656 (t0) REVERT: C 27 GLN cc_start: 0.9027 (mm-40) cc_final: 0.8799 (mm-40) REVERT: C 33 GLU cc_start: 0.8640 (tt0) cc_final: 0.8170 (tp30) REVERT: D 6 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8150 (tm-30) REVERT: D 43 ASP cc_start: 0.9012 (t0) cc_final: 0.8690 (t0) REVERT: E 6 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8136 (tm-30) REVERT: E 33 GLU cc_start: 0.8632 (tt0) cc_final: 0.8251 (tp30) REVERT: F 33 GLU cc_start: 0.8706 (tt0) cc_final: 0.8309 (tp30) REVERT: G 3 MET cc_start: 0.9077 (mtp) cc_final: 0.8864 (mtp) REVERT: G 33 GLU cc_start: 0.8654 (tt0) cc_final: 0.8175 (tp30) REVERT: I 33 GLU cc_start: 0.8761 (tt0) cc_final: 0.8370 (tp30) REVERT: J 230 ASP cc_start: 0.9126 (t70) cc_final: 0.8832 (t0) REVERT: K 242 LYS cc_start: 0.9233 (mmmm) cc_final: 0.9022 (mptt) REVERT: L 230 ASP cc_start: 0.9113 (t70) cc_final: 0.8829 (t0) REVERT: M 44 GLU cc_start: 0.9130 (mt-10) cc_final: 0.8923 (mt-10) REVERT: M 230 ASP cc_start: 0.9115 (t70) cc_final: 0.8869 (t0) REVERT: N 230 ASP cc_start: 0.9095 (t70) cc_final: 0.8812 (t0) REVERT: O 230 ASP cc_start: 0.9079 (t70) cc_final: 0.8765 (t0) REVERT: O 242 LYS cc_start: 0.9103 (mmmm) cc_final: 0.8832 (mmtm) REVERT: P 192 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8278 (ptp-170) REVERT: Q 230 ASP cc_start: 0.9078 (t70) cc_final: 0.8742 (t0) REVERT: Q 242 LYS cc_start: 0.9059 (mmmm) cc_final: 0.8848 (mmtm) REVERT: R 230 ASP cc_start: 0.9112 (t70) cc_final: 0.8800 (t0) outliers start: 11 outliers final: 8 residues processed: 245 average time/residue: 1.3009 time to fit residues: 366.5912 Evaluate side-chains 236 residues out of total 2277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 225 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain P residue 192 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: [110, 3, 49, 136, 62, 207, 182, 8, 240, 172, 31] chunk 110 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 207 optimal weight: 1.9990 chunk 182 optimal weight: 0.6980 chunk 8 optimal weight: 4.9990 chunk 240 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 31 optimal weight: 0.3980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 6 GLN B 6 GLN C 6 GLN D 11 ASN F 6 GLN G 6 GLN H 6 GLN I 6 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.057812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2434 r_free = 0.2434 target = 0.045141 restraints weight = 135700.794| |-----------------------------------------------------------------------------| r_work (start): 0.2424 rms_B_bonded: 2.38 r_work: 0.2300 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2183 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9015 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 21456 Z= 0.115 Angle : 0.453 4.458 29097 Z= 0.234 Chirality : 0.040 0.140 3303 Planarity : 0.003 0.023 3816 Dihedral : 3.826 14.289 2934 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.57 % Allowed : 9.75 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.53 (0.17), residues: 2682 helix: 3.62 (0.16), residues: 1008 sheet: 1.42 (0.20), residues: 594 loop : -0.10 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG Q 192 TYR 0.009 0.001 TYR R 253 PHE 0.005 0.001 PHE B 7 TRP 0.004 0.001 TRP D 39 HIS 0.001 0.000 HIS O 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.11 (21447) covalent geometry : angle 0.45264 / 0.23 (29079) SS BOND : bond 0.00112 / 0.08 ( 9) SS BOND : angle 0.30011 / 0.19 ( 18) hydrogen bonds : bond 0.02750 / 1.81 ( 981) hydrogen bonds : angle 3.78656 / 2.60 ( 2835) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 232 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8607 (tt0) cc_final: 0.8311 (tp30) REVERT: B 3 MET cc_start: 0.9252 (mtm) cc_final: 0.8955 (mtp) REVERT: B 33 GLU cc_start: 0.8707 (tt0) cc_final: 0.8277 (tp30) REVERT: B 43 ASP cc_start: 0.8998 (t0) cc_final: 0.8632 (t0) REVERT: C 27 GLN cc_start: 0.9003 (mm-40) cc_final: 0.8777 (mm-40) REVERT: C 33 GLU cc_start: 0.8643 (tt0) cc_final: 0.8151 (tp30) REVERT: D 6 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8136 (tm-30) REVERT: D 43 ASP cc_start: 0.9015 (t0) cc_final: 0.8679 (t0) REVERT: E 6 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8128 (tm-30) REVERT: E 33 GLU cc_start: 0.8654 (tt0) cc_final: 0.8247 (tp30) REVERT: F 6 GLN cc_start: 0.9028 (tp40) cc_final: 0.8625 (tp40) REVERT: F 33 GLU cc_start: 0.8710 (tt0) cc_final: 0.8300 (tp30) REVERT: G 33 GLU cc_start: 0.8655 (tt0) cc_final: 0.8167 (tp30) REVERT: I 33 GLU cc_start: 0.8758 (tt0) cc_final: 0.8364 (tp30) REVERT: J 230 ASP cc_start: 0.9116 (t70) cc_final: 0.8830 (t0) REVERT: K 242 LYS cc_start: 0.9237 (mmmm) cc_final: 0.9032 (mptt) REVERT: L 192 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8285 (ptp-170) REVERT: L 230 ASP cc_start: 0.9090 (t70) cc_final: 0.8812 (t0) REVERT: L 242 LYS cc_start: 0.9057 (mmmm) cc_final: 0.8795 (mppt) REVERT: M 44 GLU cc_start: 0.9124 (mt-10) cc_final: 0.8878 (mt-10) REVERT: M 230 ASP cc_start: 0.9096 (t70) cc_final: 0.8856 (t0) REVERT: N 230 ASP cc_start: 0.9080 (t70) cc_final: 0.8803 (t0) REVERT: O 230 ASP cc_start: 0.9062 (t70) cc_final: 0.8745 (t0) REVERT: O 242 LYS cc_start: 0.9101 (mmmm) cc_final: 0.8811 (mppt) REVERT: P 192 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8254 (ptp-170) REVERT: Q 230 ASP cc_start: 0.9059 (t70) cc_final: 0.8734 (t0) REVERT: Q 242 LYS cc_start: 0.9063 (mmmm) cc_final: 0.8853 (mmtm) REVERT: R 230 ASP cc_start: 0.9091 (t70) cc_final: 0.8803 (t0) outliers start: 13 outliers final: 11 residues processed: 243 average time/residue: 1.2608 time to fit residues: 353.3552 Evaluate side-chains 240 residues out of total 2277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 225 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain L residue 192 ARG Chi-restraints excluded: chain P residue 43 ASP Chi-restraints excluded: chain P residue 192 ARG Chi-restraints excluded: chain Q residue 132 SER Chi-restraints excluded: chain Q residue 238 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: [149, 90, 222, 243, 236, 2, 156, 16, 32, 121, 53] chunk 149 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 222 optimal weight: 1.9990 chunk 243 optimal weight: 0.9990 chunk 236 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 156 optimal weight: 0.6980 chunk 16 optimal weight: 0.0670 chunk 32 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 6 GLN B 6 GLN C 6 GLN G 6 GLN H 6 GLN I 6 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.058098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2445 r_free = 0.2445 target = 0.045574 restraints weight = 135290.751| |-----------------------------------------------------------------------------| r_work (start): 0.2433 rms_B_bonded: 2.33 r_work: 0.2314 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2199 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9030 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21456 Z= 0.099 Angle : 0.450 4.378 29097 Z= 0.232 Chirality : 0.040 0.140 3303 Planarity : 0.003 0.023 3816 Dihedral : 3.777 13.299 2934 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.66 % Allowed : 10.06 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.58 (0.17), residues: 2682 helix: 3.65 (0.16), residues: 1008 sheet: 1.45 (0.20), residues: 594 loop : -0.07 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG Q 192 TYR 0.008 0.001 TYR M 253 PHE 0.005 0.001 PHE B 7 TRP 0.004 0.001 TRP Q 237 HIS 0.001 0.000 HIS K 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 (21447) covalent geometry : angle 0.44961 / 0.23 (29079) SS BOND : bond 0.00117 / 0.08 ( 9) SS BOND : angle 0.29821 / 0.18 ( 18) hydrogen bonds : bond 0.02657 / 1.75 ( 981) hydrogen bonds : angle 3.73971 / 2.57 ( 2835) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 234 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8584 (tt0) cc_final: 0.8314 (tp30) REVERT: B 3 MET cc_start: 0.9266 (mtm) cc_final: 0.8970 (mtp) REVERT: B 33 GLU cc_start: 0.8691 (tt0) cc_final: 0.8281 (tp30) REVERT: B 43 ASP cc_start: 0.9005 (t0) cc_final: 0.8636 (t0) REVERT: C 27 GLN cc_start: 0.9017 (mm-40) cc_final: 0.8797 (mm-40) REVERT: C 33 GLU cc_start: 0.8636 (tt0) cc_final: 0.8164 (tp30) REVERT: D 6 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8124 (tm-30) REVERT: D 43 ASP cc_start: 0.9028 (t0) cc_final: 0.8689 (t0) REVERT: E 6 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8116 (tm-30) REVERT: E 33 GLU cc_start: 0.8640 (tt0) cc_final: 0.8258 (tp30) REVERT: F 6 GLN cc_start: 0.9031 (tp40) cc_final: 0.8597 (tp40) REVERT: F 33 GLU cc_start: 0.8693 (tt0) cc_final: 0.8300 (tp30) REVERT: G 33 GLU cc_start: 0.8643 (tt0) cc_final: 0.8172 (tp30) REVERT: I 33 GLU cc_start: 0.8756 (tt0) cc_final: 0.8369 (tp30) REVERT: J 230 ASP cc_start: 0.9130 (t70) cc_final: 0.8832 (t0) REVERT: L 124 GLU cc_start: 0.8556 (pt0) cc_final: 0.8239 (pt0) REVERT: L 192 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.8345 (ptp-170) REVERT: L 230 ASP cc_start: 0.9103 (t70) cc_final: 0.8817 (t0) REVERT: L 242 LYS cc_start: 0.9074 (mmmm) cc_final: 0.8818 (mppt) REVERT: M 44 GLU cc_start: 0.9106 (mt-10) cc_final: 0.8860 (mt-10) REVERT: M 230 ASP cc_start: 0.9107 (t70) cc_final: 0.8862 (t0) REVERT: N 230 ASP cc_start: 0.9096 (t70) cc_final: 0.8814 (t0) REVERT: O 192 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.8304 (ptp-170) REVERT: O 230 ASP cc_start: 0.9076 (t70) cc_final: 0.8755 (t0) REVERT: O 242 LYS cc_start: 0.9112 (mmmm) cc_final: 0.8857 (mppt) REVERT: P 192 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.8295 (ptp-170) REVERT: Q 230 ASP cc_start: 0.9070 (t70) cc_final: 0.8743 (t0) REVERT: R 230 ASP cc_start: 0.9106 (t70) cc_final: 0.8811 (t0) outliers start: 15 outliers final: 10 residues processed: 247 average time/residue: 1.3115 time to fit residues: 372.1456 Evaluate side-chains 242 residues out of total 2277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 227 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain L residue 192 ARG Chi-restraints excluded: chain O residue 192 ARG Chi-restraints excluded: chain P residue 192 ARG Chi-restraints excluded: chain Q residue 132 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: [252, 18, 71, 32, 13, 19, 218, 131, 179, 125, 204] chunk 252 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 218 optimal weight: 0.4980 chunk 131 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 204 optimal weight: 0.5980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 6 GLN B 6 GLN C 6 GLN G 6 GLN H 6 GLN I 6 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.057217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2423 r_free = 0.2423 target = 0.044659 restraints weight = 137014.607| |-----------------------------------------------------------------------------| r_work (start): 0.2411 rms_B_bonded: 2.37 r_work: 0.2291 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2176 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9021 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21456 Z= 0.146 Angle : 0.466 5.724 29097 Z= 0.241 Chirality : 0.041 0.139 3303 Planarity : 0.003 0.023 3816 Dihedral : 3.825 13.691 2934 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.66 % Allowed : 10.14 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.54 (0.17), residues: 2682 helix: 3.65 (0.16), residues: 1008 sheet: 1.40 (0.20), residues: 594 loop : -0.11 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Q 192 TYR 0.009 0.001 TYR M 253 PHE 0.006 0.001 PHE B 7 TRP 0.006 0.001 TRP I 39 HIS 0.001 0.000 HIS P 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (21447) covalent geometry : angle 0.46626 / 0.24 (29079) SS BOND : bond 0.00108 / 0.08 ( 9) SS BOND : angle 0.30408 / 0.19 ( 18) hydrogen bonds : bond 0.02899 / 1.92 ( 981) hydrogen bonds : angle 3.79184 / 2.61 ( 2835) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12517.19 seconds wall clock time: 212 minutes 16.77 seconds (12736.77 seconds total)