Starting phenix.real_space_refine on Tue Aug 26 00:19:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xge_38319/08_2025/8xge_38319.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xge_38319/08_2025/8xge_38319.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xge_38319/08_2025/8xge_38319.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xge_38319/08_2025/8xge_38319.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xge_38319/08_2025/8xge_38319.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xge_38319/08_2025/8xge_38319.map" } resolution = 2.89 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= 0.001 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 156 5.16 5 C 10932 2.51 5 N 2544 2.21 5 O 2748 1.98 5 H 16008 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32388 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 2664 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Unusual residues: {'MC3': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 185 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'MC3:plan-1': 4, 'MC3:plan-2': 4} Unresolved non-hydrogen planarities: 29 Restraints were copied for chains: C, B, D, E, F, G, H, I, J, K, L Time building chain proxies: 3.22, per 1000 atoms: 0.10 Number of scatterers: 32388 At special positions: 0 Unit cell: (99.246, 100.914, 149.286, 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 156 16.00 O 2748 8.00 N 2544 7.00 C 10932 6.00 H 16008 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 242 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 231 " distance=2.04 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 242 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 242 " distance=2.04 Simple disulfide: pdb=" SG CYS D 55 " - pdb=" SG CYS D 242 " distance=2.03 Simple disulfide: pdb=" SG CYS E 55 " - pdb=" SG CYS E 242 " distance=2.04 Simple disulfide: pdb=" SG CYS F 55 " - pdb=" SG CYS F 242 " distance=2.03 Simple disulfide: pdb=" SG CYS G 55 " - pdb=" SG CYS G 242 " distance=2.03 Simple disulfide: pdb=" SG CYS H 55 " - pdb=" SG CYS H 242 " distance=2.03 Simple disulfide: pdb=" SG CYS I 55 " - pdb=" SG CYS I 242 " distance=2.04 Simple disulfide: pdb=" SG CYS J 55 " - pdb=" SG CYS J 242 " distance=2.03 Simple disulfide: pdb=" SG CYS K 55 " - pdb=" SG CYS K 242 " distance=2.03 Simple disulfide: pdb=" SG CYS L 55 " - pdb=" SG CYS L 242 " distance=2.03 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 236 " distance=2.03 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 236 " distance=2.03 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 236 " distance=2.03 Simple disulfide: pdb=" SG CYS E 62 " - pdb=" SG CYS E 236 " distance=2.03 Simple disulfide: pdb=" SG CYS F 62 " - pdb=" SG CYS F 236 " distance=2.03 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 236 " distance=2.03 Simple disulfide: pdb=" SG CYS H 62 " - pdb=" SG CYS H 236 " distance=2.03 Simple disulfide: pdb=" SG CYS I 62 " - pdb=" SG CYS I 236 " distance=2.03 Simple disulfide: pdb=" SG CYS J 62 " - pdb=" SG CYS J 236 " distance=2.03 Simple disulfide: pdb=" SG CYS K 62 " - pdb=" SG CYS K 236 " distance=2.03 Simple disulfide: pdb=" SG CYS L 62 " - pdb=" SG CYS L 236 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 231 " distance=2.04 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 231 " distance=2.04 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 231 " distance=2.04 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 231 " distance=2.04 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 231 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 231 " distance=2.04 Simple disulfide: pdb=" SG CYS H 66 " - pdb=" SG CYS H 231 " distance=2.04 Simple disulfide: pdb=" SG CYS I 66 " - pdb=" SG CYS I 231 " distance=2.03 Simple disulfide: pdb=" SG CYS J 66 " - pdb=" SG CYS J 231 " distance=2.04 Simple disulfide: pdb=" SG CYS K 66 " - pdb=" SG CYS K 231 " distance=2.04 Simple disulfide: pdb=" SG CYS L 66 " - pdb=" SG CYS L 231 " distance=2.04 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.55 Conformation dependent library (CDL) restraints added in 816.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3744 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 12 sheets defined 76.0% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 19 through 41 removed outlier: 3.838A pdb=" N GLY A 23 " --> pdb=" O SER A 19 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ARG A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE A 25 " --> pdb=" O MET A 21 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL A 41 " --> pdb=" O ILE A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 46 removed outlier: 3.870A pdb=" N VAL A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR A 46 " --> pdb=" O GLY A 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 41 through 46' Processing helix chain 'A' and resid 61 through 71 Processing helix chain 'A' and resid 74 through 86 Processing helix chain 'A' and resid 87 through 101 removed outlier: 3.631A pdb=" N LEU A 91 " --> pdb=" O CYS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 222 Processing helix chain 'A' and resid 246 through 276 Processing helix chain 'C' and resid 20 through 41 removed outlier: 4.096A pdb=" N ARG C 24 " --> pdb=" O THR C 20 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE C 25 " --> pdb=" O MET C 21 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL C 41 " --> pdb=" O ILE C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 46 removed outlier: 3.869A pdb=" N VAL C 45 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR C 46 " --> pdb=" O GLY C 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 41 through 46' Processing helix chain 'C' and resid 61 through 71 Processing helix chain 'C' and resid 74 through 86 Processing helix chain 'C' and resid 87 through 101 removed outlier: 3.632A pdb=" N LEU C 91 " --> pdb=" O CYS C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 222 Processing helix chain 'C' and resid 246 through 276 Processing helix chain 'B' and resid 20 through 41 removed outlier: 4.095A pdb=" N ARG B 24 " --> pdb=" O THR B 20 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE B 25 " --> pdb=" O MET B 21 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL B 41 " --> pdb=" O ILE B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 46 removed outlier: 3.869A pdb=" N VAL B 45 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR B 46 " --> pdb=" O GLY B 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 41 through 46' Processing helix chain 'B' and resid 61 through 71 Processing helix chain 'B' and resid 74 through 86 Processing helix chain 'B' and resid 87 through 101 removed outlier: 3.632A pdb=" N LEU B 91 " --> pdb=" O CYS B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 222 Processing helix chain 'B' and resid 246 through 276 Processing helix chain 'D' and resid 20 through 41 removed outlier: 4.096A pdb=" N ARG D 24 " --> pdb=" O THR D 20 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE D 25 " --> pdb=" O MET D 21 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL D 41 " --> pdb=" O ILE D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 46 removed outlier: 3.870A pdb=" N VAL D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR D 46 " --> pdb=" O GLY D 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 41 through 46' Processing helix chain 'D' and resid 61 through 71 Processing helix chain 'D' and resid 74 through 86 Processing helix chain 'D' and resid 87 through 101 removed outlier: 3.631A pdb=" N LEU D 91 " --> pdb=" O CYS D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 222 Processing helix chain 'D' and resid 246 through 276 Processing helix chain 'E' and resid 20 through 41 removed outlier: 4.096A pdb=" N ARG E 24 " --> pdb=" O THR E 20 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE E 25 " --> pdb=" O MET E 21 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL E 41 " --> pdb=" O ILE E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 46 removed outlier: 3.870A pdb=" N VAL E 45 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR E 46 " --> pdb=" O GLY E 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 41 through 46' Processing helix chain 'E' and resid 61 through 71 Processing helix chain 'E' and resid 74 through 86 Processing helix chain 'E' and resid 87 through 101 removed outlier: 3.632A pdb=" N LEU E 91 " --> pdb=" O CYS E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 222 Processing helix chain 'E' and resid 246 through 276 Processing helix chain 'F' and resid 20 through 41 removed outlier: 4.095A pdb=" N ARG F 24 " --> pdb=" O THR F 20 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE F 25 " --> pdb=" O MET F 21 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL F 41 " --> pdb=" O ILE F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 46 removed outlier: 3.870A pdb=" N VAL F 45 " --> pdb=" O VAL F 41 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR F 46 " --> pdb=" O GLY F 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 41 through 46' Processing helix chain 'F' and resid 61 through 71 Processing helix chain 'F' and resid 74 through 86 Processing helix chain 'F' and resid 87 through 101 removed outlier: 3.632A pdb=" N LEU F 91 " --> pdb=" O CYS F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 222 Processing helix chain 'F' and resid 246 through 276 Processing helix chain 'G' and resid 20 through 41 removed outlier: 4.095A pdb=" N ARG G 24 " --> pdb=" O THR G 20 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE G 25 " --> pdb=" O MET G 21 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL G 41 " --> pdb=" O ILE G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 46 removed outlier: 3.869A pdb=" N VAL G 45 " --> pdb=" O VAL G 41 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR G 46 " --> pdb=" O GLY G 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 41 through 46' Processing helix chain 'G' and resid 61 through 71 Processing helix chain 'G' and resid 74 through 86 Processing helix chain 'G' and resid 87 through 101 removed outlier: 3.631A pdb=" N LEU G 91 " --> pdb=" O CYS G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 222 Processing helix chain 'G' and resid 246 through 276 Processing helix chain 'H' and resid 20 through 41 removed outlier: 4.095A pdb=" N ARG H 24 " --> pdb=" O THR H 20 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE H 25 " --> pdb=" O MET H 21 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL H 41 " --> pdb=" O ILE H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 46 removed outlier: 3.869A pdb=" N VAL H 45 " --> pdb=" O VAL H 41 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR H 46 " --> pdb=" O GLY H 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 41 through 46' Processing helix chain 'H' and resid 61 through 71 Processing helix chain 'H' and resid 74 through 86 Processing helix chain 'H' and resid 87 through 101 removed outlier: 3.631A pdb=" N LEU H 91 " --> pdb=" O CYS H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 222 Processing helix chain 'H' and resid 246 through 276 Processing helix chain 'I' and resid 20 through 41 removed outlier: 4.095A pdb=" N ARG I 24 " --> pdb=" O THR I 20 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE I 25 " --> pdb=" O MET I 21 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL I 41 " --> pdb=" O ILE I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 46 removed outlier: 3.870A pdb=" N VAL I 45 " --> pdb=" O VAL I 41 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR I 46 " --> pdb=" O GLY I 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 41 through 46' Processing helix chain 'I' and resid 61 through 71 Processing helix chain 'I' and resid 74 through 86 Processing helix chain 'I' and resid 87 through 101 removed outlier: 3.631A pdb=" N LEU I 91 " --> pdb=" O CYS I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 222 Processing helix chain 'I' and resid 246 through 276 Processing helix chain 'J' and resid 20 through 41 removed outlier: 4.096A pdb=" N ARG J 24 " --> pdb=" O THR J 20 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE J 25 " --> pdb=" O MET J 21 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL J 41 " --> pdb=" O ILE J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 41 through 46 removed outlier: 3.870A pdb=" N VAL J 45 " --> pdb=" O VAL J 41 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR J 46 " --> pdb=" O GLY J 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 41 through 46' Processing helix chain 'J' and resid 61 through 71 Processing helix chain 'J' and resid 74 through 86 Processing helix chain 'J' and resid 87 through 101 removed outlier: 3.631A pdb=" N LEU J 91 " --> pdb=" O CYS J 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 222 Processing helix chain 'J' and resid 246 through 276 Processing helix chain 'K' and resid 20 through 41 removed outlier: 4.097A pdb=" N ARG K 24 " --> pdb=" O THR K 20 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE K 25 " --> pdb=" O MET K 21 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL K 41 " --> pdb=" O ILE K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 46 removed outlier: 3.870A pdb=" N VAL K 45 " --> pdb=" O VAL K 41 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR K 46 " --> pdb=" O GLY K 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 41 through 46' Processing helix chain 'K' and resid 61 through 71 Processing helix chain 'K' and resid 74 through 86 Processing helix chain 'K' and resid 87 through 101 removed outlier: 3.631A pdb=" N LEU K 91 " --> pdb=" O CYS K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 222 Processing helix chain 'K' and resid 246 through 276 Processing helix chain 'L' and resid 20 through 41 removed outlier: 4.096A pdb=" N ARG L 24 " --> pdb=" O THR L 20 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE L 25 " --> pdb=" O MET L 21 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL L 41 " --> pdb=" O ILE L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 46 removed outlier: 3.870A pdb=" N VAL L 45 " --> pdb=" O VAL L 41 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR L 46 " --> pdb=" O GLY L 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 41 through 46' Processing helix chain 'L' and resid 61 through 71 Processing helix chain 'L' and resid 74 through 86 Processing helix chain 'L' and resid 87 through 101 removed outlier: 3.631A pdb=" N LEU L 91 " --> pdb=" O CYS L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 195 through 222 Processing helix chain 'L' and resid 246 through 276 Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 55 removed outlier: 3.742A pdb=" N VAL A 54 " --> pdb=" O TYR A 243 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 54 through 55 removed outlier: 3.742A pdb=" N VAL C 54 " --> pdb=" O TYR C 243 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 54 through 55 removed outlier: 3.742A pdb=" N VAL B 54 " --> pdb=" O TYR B 243 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 54 through 55 removed outlier: 3.742A pdb=" N VAL D 54 " --> pdb=" O TYR D 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 54 through 55 removed outlier: 3.742A pdb=" N VAL E 54 " --> pdb=" O TYR E 243 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 54 through 55 removed outlier: 3.742A pdb=" N VAL F 54 " --> pdb=" O TYR F 243 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 54 through 55 removed outlier: 3.742A pdb=" N VAL G 54 " --> pdb=" O TYR G 243 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 54 through 55 removed outlier: 3.742A pdb=" N VAL H 54 " --> pdb=" O TYR H 243 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 54 through 55 removed outlier: 3.742A pdb=" N VAL I 54 " --> pdb=" O TYR I 243 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 54 through 55 removed outlier: 3.742A pdb=" N VAL J 54 " --> pdb=" O TYR J 243 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 54 through 55 removed outlier: 3.741A pdb=" N VAL K 54 " --> pdb=" O TYR K 243 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 54 through 55 removed outlier: 3.742A pdb=" N VAL L 54 " --> pdb=" O TYR L 243 " (cutoff:3.500A) 1164 hydrogen bonds defined for protein. 3456 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: 6.32 Time building geometry restraints manager: 3.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 15972 1.04 - 1.23: 301 1.23 - 1.43: 6731 1.43 - 1.63: 9516 1.63 - 1.82: 204 Bond restraints: 32724 Sorted by residual: bond pdb=" C43 MC3 J 403 " pdb=" C44 MC3 J 403 " ideal model delta sigma weight residual 1.523 1.509 0.014 2.00e-02 2.50e+03 4.77e-01 bond pdb=" CG PRO L 247 " pdb=" CD PRO L 247 " ideal model delta sigma weight residual 1.503 1.480 0.023 3.40e-02 8.65e+02 4.58e-01 bond pdb=" C43 MC3 A 403 " pdb=" C44 MC3 A 403 " ideal model delta sigma weight residual 1.523 1.510 0.013 2.00e-02 2.50e+03 4.49e-01 bond pdb=" C43 MC3 B 403 " pdb=" C44 MC3 B 403 " ideal model delta sigma weight residual 1.523 1.510 0.013 2.00e-02 2.50e+03 4.48e-01 bond pdb=" C43 MC3 L 403 " pdb=" C44 MC3 L 403 " ideal model delta sigma weight residual 1.523 1.510 0.013 2.00e-02 2.50e+03 4.46e-01 ... (remaining 32719 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 54724 1.13 - 2.25: 3556 2.25 - 3.38: 243 3.38 - 4.50: 73 4.50 - 5.63: 36 Bond angle restraints: 58632 Sorted by residual: angle pdb=" C31 MC3 I 402 " pdb=" C32 MC3 I 402 " pdb=" C33 MC3 I 402 " ideal model delta sigma weight residual 114.22 108.59 5.63 3.00e+00 1.11e-01 3.52e+00 angle pdb=" C31 MC3 F 402 " pdb=" C32 MC3 F 402 " pdb=" C33 MC3 F 402 " ideal model delta sigma weight residual 114.22 108.59 5.63 3.00e+00 1.11e-01 3.52e+00 angle pdb=" C31 MC3 L 402 " pdb=" C32 MC3 L 402 " pdb=" C33 MC3 L 402 " ideal model delta sigma weight residual 114.22 108.59 5.63 3.00e+00 1.11e-01 3.52e+00 angle pdb=" C31 MC3 E 402 " pdb=" C32 MC3 E 402 " pdb=" C33 MC3 E 402 " ideal model delta sigma weight residual 114.22 108.59 5.63 3.00e+00 1.11e-01 3.52e+00 angle pdb=" C31 MC3 C 402 " pdb=" C32 MC3 C 402 " pdb=" C33 MC3 C 402 " ideal model delta sigma weight residual 114.22 108.60 5.62 3.00e+00 1.11e-01 3.50e+00 ... (remaining 58627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.36: 13712 16.36 - 32.72: 1385 32.72 - 49.08: 407 49.08 - 65.44: 156 65.44 - 81.80: 24 Dihedral angle restraints: 15684 sinusoidal: 8412 harmonic: 7272 Sorted by residual: dihedral pdb=" CB CYS E 62 " pdb=" SG CYS E 62 " pdb=" SG CYS E 236 " pdb=" CB CYS E 236 " ideal model delta sinusoidal sigma weight residual 93.00 121.35 -28.35 1 1.00e+01 1.00e-02 1.15e+01 dihedral pdb=" CB CYS F 62 " pdb=" SG CYS F 62 " pdb=" SG CYS F 236 " pdb=" CB CYS F 236 " ideal model delta sinusoidal sigma weight residual 93.00 121.32 -28.32 1 1.00e+01 1.00e-02 1.15e+01 dihedral pdb=" CB CYS L 62 " pdb=" SG CYS L 62 " pdb=" SG CYS L 236 " pdb=" CB CYS L 236 " ideal model delta sinusoidal sigma weight residual 93.00 121.31 -28.31 1 1.00e+01 1.00e-02 1.15e+01 ... (remaining 15681 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1490 0.025 - 0.050: 547 0.050 - 0.075: 379 0.075 - 0.101: 150 0.101 - 0.126: 38 Chirality restraints: 2604 Sorted by residual: chirality pdb=" CA VAL B 225 " pdb=" N VAL B 225 " pdb=" C VAL B 225 " pdb=" CB VAL B 225 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.95e-01 chirality pdb=" CA VAL C 225 " pdb=" N VAL C 225 " pdb=" C VAL C 225 " pdb=" CB VAL C 225 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.93e-01 chirality pdb=" CA VAL J 225 " pdb=" N VAL J 225 " pdb=" C VAL J 225 " pdb=" CB VAL J 225 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.92e-01 ... (remaining 2601 not shown) Planarity restraints: 4644 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG I 246 " 0.028 5.00e-02 4.00e+02 4.24e-02 2.88e+00 pdb=" N PRO I 247 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO I 247 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO I 247 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 246 " -0.028 5.00e-02 4.00e+02 4.24e-02 2.88e+00 pdb=" N PRO E 247 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO E 247 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 247 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG K 246 " -0.028 5.00e-02 4.00e+02 4.24e-02 2.88e+00 pdb=" N PRO K 247 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO K 247 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO K 247 " -0.024 5.00e-02 4.00e+02 ... (remaining 4641 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.29: 4742 2.29 - 2.87: 69388 2.87 - 3.44: 75694 3.44 - 4.02: 104329 4.02 - 4.60: 159469 Nonbonded interactions: 413622 Sorted by model distance: nonbonded pdb=" O SER D 245 " pdb=" HZ1 LYS D 250 " model vdw 1.709 2.450 nonbonded pdb=" O SER G 245 " pdb=" HZ1 LYS G 250 " model vdw 1.709 2.450 nonbonded pdb=" O SER B 245 " pdb=" HZ1 LYS B 250 " model vdw 1.709 2.450 nonbonded pdb=" O SER J 245 " pdb=" HZ1 LYS J 250 " model vdw 1.710 2.450 nonbonded pdb=" O SER A 245 " pdb=" HZ1 LYS A 250 " model vdw 1.710 2.450 ... (remaining 413617 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 1.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.200 Extract box with map and model: 0.390 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 24.500 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 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 : 0.016 0.588 16764 Z= 1.577 Angle : 0.611 5.630 22620 Z= 0.303 Chirality : 0.039 0.126 2604 Planarity : 0.005 0.042 2748 Dihedral : 15.352 81.802 6024 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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 aren not related in a simple way. whole: 3.36 (0.19), residues: 1944 helix: 3.40 (0.13), residues: 1344 sheet: 1.86 (0.43), residues: 120 loop : -1.40 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 233 TYR 0.008 0.001 TYR I 67 PHE 0.006 0.001 PHE D 256 TRP 0.005 0.002 TRP H 79 HIS 0.005 0.001 HIS G 75 Details of bonding type rmsd covalent geometry : bond 0.00255 (16716) covalent geometry : angle 0.60884 (22548) SS BOND : bond 0.00337 ( 36) SS BOND : angle 1.01550 ( 72) hydrogen bonds : bond 0.12318 ( 1164) hydrogen bonds : angle 3.85611 ( 3456) Misc. bond : bond 0.58732 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 ASN cc_start: 0.7755 (p0) cc_final: 0.7503 (p0) REVERT: A 239 GLU cc_start: 0.8055 (tt0) cc_final: 0.7770 (tt0) REVERT: C 239 GLU cc_start: 0.8028 (tt0) cc_final: 0.7604 (tt0) REVERT: D 232 ASN cc_start: 0.7749 (p0) cc_final: 0.7495 (p0) REVERT: D 239 GLU cc_start: 0.8072 (tt0) cc_final: 0.7769 (tt0) REVERT: F 239 GLU cc_start: 0.8014 (tt0) cc_final: 0.7589 (tt0) REVERT: G 232 ASN cc_start: 0.7745 (p0) cc_final: 0.7498 (p0) REVERT: G 239 GLU cc_start: 0.8077 (tt0) cc_final: 0.7782 (tt0) REVERT: J 232 ASN cc_start: 0.7744 (p0) cc_final: 0.7487 (p0) outliers start: 0 outliers final: 2 residues processed: 244 average time/residue: 1.5453 time to fit residues: 409.7736 Evaluate side-chains 179 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 177 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 213 PHE Chi-restraints excluded: chain H residue 213 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.224366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.179833 restraints weight = 45448.457| |-----------------------------------------------------------------------------| r_work (start): 0.4108 rms_B_bonded: 1.55 r_work: 0.3953 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3841 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16764 Z= 0.192 Angle : 0.659 7.456 22620 Z= 0.334 Chirality : 0.042 0.145 2604 Planarity : 0.005 0.054 2748 Dihedral : 8.205 50.811 2464 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.39 % Allowed : 19.44 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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 aren not related in a simple way. whole: 3.55 (0.18), residues: 1944 helix: 3.33 (0.12), residues: 1356 sheet: 2.30 (0.47), residues: 120 loop : -0.83 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 69 TYR 0.010 0.002 TYR F 67 PHE 0.018 0.001 PHE A 81 TRP 0.007 0.002 TRP D 79 HIS 0.002 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00431 (16716) covalent geometry : angle 0.65766 (22548) SS BOND : bond 0.00392 ( 36) SS BOND : angle 1.07429 ( 72) hydrogen bonds : bond 0.06791 ( 1164) hydrogen bonds : angle 3.32742 ( 3456) Misc. bond : bond 0.00586 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 270 time to evaluate : 0.794 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: C 85 MET cc_start: 0.7492 (OUTLIER) cc_final: 0.7121 (mmt) REVERT: C 239 GLU cc_start: 0.8076 (tt0) cc_final: 0.7772 (tt0) REVERT: F 239 GLU cc_start: 0.8072 (tt0) cc_final: 0.7774 (tt0) REVERT: H 230 GLU cc_start: 0.8022 (mp0) cc_final: 0.7799 (mm-30) REVERT: H 239 GLU cc_start: 0.8263 (tt0) cc_final: 0.7978 (tt0) REVERT: K 230 GLU cc_start: 0.8040 (mp0) cc_final: 0.7817 (mm-30) REVERT: K 239 GLU cc_start: 0.8264 (tt0) cc_final: 0.7950 (tt0) outliers start: 25 outliers final: 9 residues processed: 294 average time/residue: 1.3248 time to fit residues: 434.1808 Evaluate side-chains 252 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 242 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain E residue 83 ILE Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 275 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 187 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 116 optimal weight: 0.0980 chunk 72 optimal weight: 6.9990 chunk 184 optimal weight: 9.9990 chunk 69 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN C 232 ASN D 232 ASN F 232 ASN G 232 ASN I 232 ASN J 232 ASN L 232 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.208343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.160717 restraints weight = 44189.502| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 1.57 r_work: 0.3758 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3649 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 16764 Z= 0.173 Angle : 0.638 9.866 22620 Z= 0.315 Chirality : 0.043 0.140 2604 Planarity : 0.004 0.031 2748 Dihedral : 6.826 59.180 2460 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.33 % Allowed : 22.17 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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 aren not related in a simple way. whole: 3.83 (0.18), residues: 1944 helix: 3.52 (0.12), residues: 1356 sheet: 2.29 (0.46), residues: 120 loop : -0.64 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 34 TYR 0.011 0.002 TYR E 243 PHE 0.013 0.002 PHE A 81 TRP 0.006 0.002 TRP H 79 HIS 0.006 0.002 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00407 (16716) covalent geometry : angle 0.63712 (22548) SS BOND : bond 0.00364 ( 36) SS BOND : angle 0.92876 ( 72) hydrogen bonds : bond 0.06579 ( 1164) hydrogen bonds : angle 3.26006 ( 3456) Misc. bond : bond 0.00527 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 279 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8482 (t70) cc_final: 0.8267 (t0) REVERT: A 201 ILE cc_start: 0.8307 (mt) cc_final: 0.7841 (pp) REVERT: C 200 ILE cc_start: 0.8114 (mm) cc_final: 0.7879 (mp) REVERT: C 239 GLU cc_start: 0.7957 (tt0) cc_final: 0.7602 (tt0) REVERT: B 47 ASP cc_start: 0.8535 (t70) cc_final: 0.8320 (t0) REVERT: D 47 ASP cc_start: 0.8449 (t70) cc_final: 0.8218 (t0) REVERT: D 201 ILE cc_start: 0.8294 (mt) cc_final: 0.7829 (pp) REVERT: E 47 ASP cc_start: 0.8568 (t70) cc_final: 0.8354 (t0) REVERT: F 239 GLU cc_start: 0.7963 (tt0) cc_final: 0.7621 (tt0) REVERT: G 47 ASP cc_start: 0.8476 (t70) cc_final: 0.8254 (t0) REVERT: G 201 ILE cc_start: 0.8313 (mt) cc_final: 0.7838 (pp) REVERT: H 47 ASP cc_start: 0.8588 (t70) cc_final: 0.8374 (t0) REVERT: J 47 ASP cc_start: 0.8459 (t70) cc_final: 0.8236 (t0) REVERT: J 201 ILE cc_start: 0.8290 (mt) cc_final: 0.7823 (pp) REVERT: K 47 ASP cc_start: 0.8580 (t70) cc_final: 0.8362 (t0) REVERT: L 200 ILE cc_start: 0.8107 (mm) cc_final: 0.7884 (mp) outliers start: 42 outliers final: 8 residues processed: 307 average time/residue: 1.1261 time to fit residues: 391.6937 Evaluate side-chains 283 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 275 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain E residue 85 MET Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain K residue 85 MET Chi-restraints excluded: chain K residue 275 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 31 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 182 optimal weight: 5.9990 chunk 161 optimal weight: 0.7980 chunk 142 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 178 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN B 268 ASN D 232 ASN E 268 ASN G 232 ASN H 268 ASN J 232 ASN K 268 ASN L 232 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.201949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.154931 restraints weight = 44035.781| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 1.53 r_work: 0.3707 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3594 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.5625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16764 Z= 0.153 Angle : 0.558 5.310 22620 Z= 0.284 Chirality : 0.042 0.139 2604 Planarity : 0.004 0.028 2748 Dihedral : 7.118 52.820 2460 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.39 % Allowed : 24.94 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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 aren not related in a simple way. whole: 3.89 (0.18), residues: 1944 helix: 3.60 (0.12), residues: 1356 sheet: 2.14 (0.44), residues: 120 loop : -0.66 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 34 TYR 0.009 0.002 TYR A 67 PHE 0.010 0.001 PHE K 71 TRP 0.007 0.002 TRP A 79 HIS 0.005 0.002 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00370 (16716) covalent geometry : angle 0.55638 (22548) SS BOND : bond 0.00387 ( 36) SS BOND : angle 0.88997 ( 72) hydrogen bonds : bond 0.06085 ( 1164) hydrogen bonds : angle 3.25896 ( 3456) Misc. bond : bond 0.00159 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 280 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 ILE cc_start: 0.8355 (mt) cc_final: 0.8016 (pp) REVERT: B 47 ASP cc_start: 0.8539 (t70) cc_final: 0.8294 (t0) REVERT: D 201 ILE cc_start: 0.8301 (mt) cc_final: 0.7981 (pp) REVERT: E 47 ASP cc_start: 0.8522 (t70) cc_final: 0.8278 (t0) REVERT: G 201 ILE cc_start: 0.8303 (mt) cc_final: 0.7978 (pp) REVERT: H 47 ASP cc_start: 0.8538 (t70) cc_final: 0.8296 (t0) REVERT: I 27 LEU cc_start: 0.7472 (tm) cc_final: 0.7271 (tp) REVERT: J 201 ILE cc_start: 0.8329 (mt) cc_final: 0.7985 (pp) REVERT: K 47 ASP cc_start: 0.8549 (t70) cc_final: 0.8309 (t0) REVERT: L 27 LEU cc_start: 0.7455 (tm) cc_final: 0.7253 (tp) outliers start: 25 outliers final: 8 residues processed: 292 average time/residue: 1.0771 time to fit residues: 359.9990 Evaluate side-chains 276 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 268 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain I residue 83 ILE Chi-restraints excluded: chain K residue 85 MET Chi-restraints excluded: chain L residue 83 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 189 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 190 optimal weight: 0.9980 chunk 185 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN B 232 ASN B 268 ASN D 232 ASN E 232 ASN E 268 ASN G 232 ASN H 232 ASN H 268 ASN I 232 ASN J 232 ASN K 232 ASN K 268 ASN L 232 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.198847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.151702 restraints weight = 44260.147| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 1.53 r_work: 0.3672 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3558 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.6232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16764 Z= 0.139 Angle : 0.550 4.996 22620 Z= 0.277 Chirality : 0.041 0.137 2604 Planarity : 0.004 0.029 2748 Dihedral : 5.612 40.365 2460 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.00 % Allowed : 26.78 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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 aren not related in a simple way. whole: 4.09 (0.18), residues: 1944 helix: 3.72 (0.12), residues: 1356 sheet: 2.32 (0.45), residues: 120 loop : -0.56 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 34 TYR 0.010 0.002 TYR B 243 PHE 0.008 0.001 PHE D 71 TRP 0.005 0.002 TRP H 79 HIS 0.009 0.002 HIS J 75 Details of bonding type rmsd covalent geometry : bond 0.00326 (16716) covalent geometry : angle 0.54846 (22548) SS BOND : bond 0.00343 ( 36) SS BOND : angle 0.84344 ( 72) hydrogen bonds : bond 0.05660 ( 1164) hydrogen bonds : angle 3.11658 ( 3456) Misc. bond : bond 0.00327 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 285 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 ILE cc_start: 0.8435 (mt) cc_final: 0.8104 (pp) REVERT: D 201 ILE cc_start: 0.8429 (mt) cc_final: 0.8103 (pp) REVERT: E 201 ILE cc_start: 0.8343 (mt) cc_final: 0.8048 (pp) REVERT: G 201 ILE cc_start: 0.8431 (mt) cc_final: 0.8105 (pp) REVERT: G 206 ARG cc_start: 0.7227 (OUTLIER) cc_final: 0.6333 (ttp80) REVERT: J 201 ILE cc_start: 0.8431 (mt) cc_final: 0.8098 (pp) REVERT: K 201 ILE cc_start: 0.8350 (mt) cc_final: 0.8050 (pp) outliers start: 18 outliers final: 4 residues processed: 296 average time/residue: 1.0719 time to fit residues: 363.0680 Evaluate side-chains 257 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 252 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain G residue 206 ARG Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain L residue 201 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 126 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 189 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 20 optimal weight: 0.4980 chunk 47 optimal weight: 2.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN A 268 ASN D 232 ASN D 268 ASN G 232 ASN J 232 ASN J 268 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.184436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.136369 restraints weight = 45312.521| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.60 r_work: 0.3413 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.6814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16764 Z= 0.184 Angle : 0.585 5.407 22620 Z= 0.300 Chirality : 0.044 0.148 2604 Planarity : 0.004 0.032 2748 Dihedral : 6.973 40.805 2460 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.78 % Allowed : 25.61 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.82 (0.18), residues: 1944 helix: 3.53 (0.12), residues: 1356 sheet: 1.93 (0.44), residues: 120 loop : -0.57 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 24 TYR 0.009 0.002 TYR G 67 PHE 0.011 0.001 PHE F 71 TRP 0.007 0.002 TRP E 79 HIS 0.013 0.003 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00457 (16716) covalent geometry : angle 0.58284 (22548) SS BOND : bond 0.00482 ( 36) SS BOND : angle 1.09666 ( 72) hydrogen bonds : bond 0.06141 ( 1164) hydrogen bonds : angle 3.31132 ( 3456) Misc. bond : bond 0.00188 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 288 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.7715 (tp30) cc_final: 0.7416 (tp30) REVERT: B 201 ILE cc_start: 0.8267 (mt) cc_final: 0.7945 (pp) REVERT: D 43 GLU cc_start: 0.7705 (tp30) cc_final: 0.7406 (tp30) REVERT: E 201 ILE cc_start: 0.8199 (mt) cc_final: 0.7915 (pp) REVERT: G 43 GLU cc_start: 0.7679 (tp30) cc_final: 0.7383 (tp30) REVERT: G 206 ARG cc_start: 0.7059 (OUTLIER) cc_final: 0.6123 (ttp80) REVERT: H 201 ILE cc_start: 0.8255 (mt) cc_final: 0.7936 (pp) REVERT: J 43 GLU cc_start: 0.7737 (tp30) cc_final: 0.7443 (tp30) REVERT: K 201 ILE cc_start: 0.8211 (mt) cc_final: 0.7923 (pp) outliers start: 32 outliers final: 9 residues processed: 297 average time/residue: 0.9255 time to fit residues: 320.7689 Evaluate side-chains 269 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 259 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain G residue 206 ARG Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain L residue 28 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 52 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 72 optimal weight: 20.0000 chunk 87 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 168 optimal weight: 20.0000 chunk 161 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 232 ASN K 232 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.186619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.138667 restraints weight = 45089.488| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.56 r_work: 0.3465 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.7288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16764 Z= 0.134 Angle : 0.526 4.460 22620 Z= 0.265 Chirality : 0.041 0.135 2604 Planarity : 0.004 0.029 2748 Dihedral : 5.947 37.712 2460 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.11 % Allowed : 26.83 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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 aren not related in a simple way. whole: 4.02 (0.18), residues: 1944 helix: 3.69 (0.12), residues: 1356 sheet: 2.04 (0.44), residues: 120 loop : -0.57 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 24 TYR 0.010 0.002 TYR G 67 PHE 0.008 0.001 PHE D 71 TRP 0.004 0.002 TRP J 79 HIS 0.006 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00312 (16716) covalent geometry : angle 0.52499 (22548) SS BOND : bond 0.00333 ( 36) SS BOND : angle 0.82585 ( 72) hydrogen bonds : bond 0.05484 ( 1164) hydrogen bonds : angle 3.12790 ( 3456) Misc. bond : bond 0.00164 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 274 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.7650 (tp30) cc_final: 0.7362 (tp30) REVERT: D 43 GLU cc_start: 0.7669 (tp30) cc_final: 0.7392 (tp30) REVERT: G 43 GLU cc_start: 0.7665 (tp30) cc_final: 0.7376 (tp30) REVERT: J 43 GLU cc_start: 0.7683 (tp30) cc_final: 0.7398 (tp30) outliers start: 38 outliers final: 7 residues processed: 291 average time/residue: 0.8625 time to fit residues: 294.6127 Evaluate side-chains 276 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 269 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain D residue 207 ASN Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain L residue 201 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 133 optimal weight: 2.9990 chunk 93 optimal weight: 0.3980 chunk 124 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.187192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.138936 restraints weight = 45018.912| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.57 r_work: 0.3476 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.7443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 16764 Z= 0.117 Angle : 0.512 4.532 22620 Z= 0.258 Chirality : 0.040 0.194 2604 Planarity : 0.003 0.027 2748 Dihedral : 5.742 36.637 2460 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.94 % Allowed : 28.67 % Favored : 70.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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 aren not related in a simple way. whole: 4.16 (0.18), residues: 1944 helix: 3.80 (0.12), residues: 1356 sheet: 2.11 (0.43), residues: 120 loop : -0.54 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 206 TYR 0.008 0.001 TYR B 243 PHE 0.007 0.001 PHE E 71 TRP 0.004 0.001 TRP H 79 HIS 0.004 0.001 HIS L 75 Details of bonding type rmsd covalent geometry : bond 0.00271 (16716) covalent geometry : angle 0.51095 (22548) SS BOND : bond 0.00267 ( 36) SS BOND : angle 0.75799 ( 72) hydrogen bonds : bond 0.05116 ( 1164) hydrogen bonds : angle 3.12164 ( 3456) Misc. bond : bond 0.00129 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 277 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.7671 (tp30) cc_final: 0.7401 (tp30) REVERT: C 36 LEU cc_start: 0.7635 (tp) cc_final: 0.7387 (tp) REVERT: D 43 GLU cc_start: 0.7672 (tp30) cc_final: 0.7409 (tp30) REVERT: G 43 GLU cc_start: 0.7682 (tp30) cc_final: 0.7413 (tp30) REVERT: I 36 LEU cc_start: 0.7599 (tp) cc_final: 0.7354 (tp) REVERT: J 43 GLU cc_start: 0.7698 (tp30) cc_final: 0.7433 (tp30) REVERT: L 36 LEU cc_start: 0.7603 (tp) cc_final: 0.7359 (tp) outliers start: 17 outliers final: 8 residues processed: 286 average time/residue: 0.8520 time to fit residues: 285.8975 Evaluate side-chains 281 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 273 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 201 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 147 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 170 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.185004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.136492 restraints weight = 45001.593| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.57 r_work: 0.3439 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.7694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16764 Z= 0.153 Angle : 0.558 7.123 22620 Z= 0.279 Chirality : 0.042 0.205 2604 Planarity : 0.004 0.031 2748 Dihedral : 6.239 39.645 2460 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.61 % Allowed : 29.06 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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 aren not related in a simple way. whole: 4.02 (0.18), residues: 1944 helix: 3.71 (0.12), residues: 1356 sheet: 1.96 (0.44), residues: 120 loop : -0.60 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 24 TYR 0.009 0.002 TYR G 67 PHE 0.009 0.001 PHE B 71 TRP 0.005 0.002 TRP J 79 HIS 0.008 0.002 HIS D 75 Details of bonding type rmsd covalent geometry : bond 0.00380 (16716) covalent geometry : angle 0.55677 (22548) SS BOND : bond 0.00415 ( 36) SS BOND : angle 0.94442 ( 72) hydrogen bonds : bond 0.05408 ( 1164) hydrogen bonds : angle 3.18027 ( 3456) Misc. bond : bond 0.00172 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 287 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.7708 (tp30) cc_final: 0.7433 (tp30) REVERT: C 36 LEU cc_start: 0.7767 (tp) cc_final: 0.7524 (tp) REVERT: C 272 LEU cc_start: 0.6066 (tt) cc_final: 0.5675 (tp) REVERT: D 43 GLU cc_start: 0.7682 (tp30) cc_final: 0.7422 (tp30) REVERT: F 272 LEU cc_start: 0.6038 (tt) cc_final: 0.5669 (tp) REVERT: G 43 GLU cc_start: 0.7693 (tp30) cc_final: 0.7424 (tp30) REVERT: I 36 LEU cc_start: 0.7748 (tp) cc_final: 0.7505 (tp) REVERT: I 272 LEU cc_start: 0.6055 (tt) cc_final: 0.5675 (tp) REVERT: J 43 GLU cc_start: 0.7738 (tp30) cc_final: 0.7476 (tp30) REVERT: L 36 LEU cc_start: 0.7743 (tp) cc_final: 0.7495 (tp) REVERT: L 272 LEU cc_start: 0.5997 (tt) cc_final: 0.5642 (tp) outliers start: 11 outliers final: 4 residues processed: 289 average time/residue: 0.7941 time to fit residues: 269.9631 Evaluate side-chains 281 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 277 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain L residue 201 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 177 optimal weight: 4.9990 chunk 165 optimal weight: 0.6980 chunk 160 optimal weight: 10.0000 chunk 125 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 127 optimal weight: 0.7980 chunk 155 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS A 232 ASN J 75 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.186857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.138806 restraints weight = 45023.992| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.58 r_work: 0.3519 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.7815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 16764 Z= 0.111 Angle : 0.501 4.532 22620 Z= 0.252 Chirality : 0.040 0.128 2604 Planarity : 0.003 0.029 2748 Dihedral : 5.671 37.240 2460 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.06 % Allowed : 29.39 % Favored : 69.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.29 (0.18), residues: 1944 helix: 3.92 (0.12), residues: 1356 sheet: 2.16 (0.44), residues: 120 loop : -0.58 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 206 TYR 0.008 0.001 TYR H 243 PHE 0.011 0.001 PHE E 205 TRP 0.003 0.001 TRP E 79 HIS 0.002 0.001 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00252 (16716) covalent geometry : angle 0.50037 (22548) SS BOND : bond 0.00243 ( 36) SS BOND : angle 0.70146 ( 72) hydrogen bonds : bond 0.04766 ( 1164) hydrogen bonds : angle 3.09626 ( 3456) Misc. bond : bond 0.00120 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 297 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.7655 (tp30) cc_final: 0.7424 (tp30) REVERT: C 36 LEU cc_start: 0.7802 (tp) cc_final: 0.7545 (tp) REVERT: C 272 LEU cc_start: 0.6227 (tt) cc_final: 0.5816 (tp) REVERT: B 44 THR cc_start: 0.8373 (t) cc_final: 0.8081 (m) REVERT: D 43 GLU cc_start: 0.7603 (tp30) cc_final: 0.7371 (tp30) REVERT: E 44 THR cc_start: 0.8422 (t) cc_final: 0.8139 (m) REVERT: F 21 MET cc_start: 0.5889 (ptt) cc_final: 0.5665 (ptt) REVERT: G 43 GLU cc_start: 0.7623 (tp30) cc_final: 0.7385 (tp30) REVERT: H 44 THR cc_start: 0.8440 (t) cc_final: 0.8158 (m) REVERT: I 21 MET cc_start: 0.5807 (ptt) cc_final: 0.5552 (ptt) REVERT: I 36 LEU cc_start: 0.7803 (tp) cc_final: 0.7549 (tp) REVERT: I 272 LEU cc_start: 0.6230 (tt) cc_final: 0.5820 (tp) REVERT: J 43 GLU cc_start: 0.7657 (tp30) cc_final: 0.7425 (tp30) REVERT: K 44 THR cc_start: 0.8422 (t) cc_final: 0.8140 (m) REVERT: K 205 PHE cc_start: 0.7556 (m-80) cc_final: 0.7316 (m-80) REVERT: L 36 LEU cc_start: 0.7814 (tp) cc_final: 0.7557 (tp) outliers start: 19 outliers final: 14 residues processed: 304 average time/residue: 0.7707 time to fit residues: 276.8509 Evaluate side-chains 304 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 290 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain I residue 87 CYS Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain J residue 75 HIS Chi-restraints excluded: chain J residue 85 MET Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 87 CYS Chi-restraints excluded: chain L residue 201 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 114 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 159 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 145 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS J 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.186765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.138855 restraints weight = 45353.880| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.57 r_work: 0.3467 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.7910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16764 Z= 0.144 Angle : 0.865 53.856 22620 Z= 0.571 Chirality : 0.040 0.197 2604 Planarity : 0.003 0.028 2748 Dihedral : 5.660 37.169 2460 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.61 % Allowed : 29.78 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.28 (0.18), residues: 1944 helix: 3.91 (0.12), residues: 1356 sheet: 2.16 (0.44), residues: 120 loop : -0.59 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 206 TYR 0.008 0.001 TYR F 199 PHE 0.010 0.001 PHE E 205 TRP 0.003 0.001 TRP E 79 HIS 0.020 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00272 (16716) covalent geometry : angle 0.86525 (22548) SS BOND : bond 0.00221 ( 36) SS BOND : angle 0.69338 ( 72) hydrogen bonds : bond 0.04742 ( 1164) hydrogen bonds : angle 3.12212 ( 3456) Misc. bond : bond 0.00118 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10594.62 seconds wall clock time: 179 minutes 56.67 seconds (10796.67 seconds total)