Starting phenix.real_space_refine on Fri Jun 27 14:18:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xge_38319/06_2025/8xge_38319.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xge_38319/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8xge_38319/06_2025/8xge_38319.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xge_38319/06_2025/8xge_38319.map" model { file = "/net/cci-nas-00/data/ceres_data/8xge_38319/06_2025/8xge_38319.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xge_38319/06_2025/8xge_38319.cif" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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-2': 4, 'MC3:plan-1': 4} Unresolved non-hydrogen planarities: 29 Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, L Time building chain proxies: 8.86, per 1000 atoms: 0.27 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 E 55 " - pdb=" SG CYS E 242 " distance=2.04 Simple disulfide: pdb=" SG CYS D 55 " - pdb=" SG CYS D 242 " distance=2.03 Simple disulfide: pdb=" SG CYS G 55 " - pdb=" SG CYS G 242 " distance=2.03 Simple disulfide: pdb=" SG CYS F 55 " - pdb=" SG CYS F 242 " distance=2.03 Simple disulfide: pdb=" SG CYS I 55 " - pdb=" SG CYS I 242 " distance=2.04 Simple disulfide: pdb=" SG CYS H 55 " - pdb=" SG CYS H 242 " distance=2.03 Simple disulfide: pdb=" SG CYS K 55 " - pdb=" SG CYS K 242 " distance=2.03 Simple disulfide: pdb=" SG CYS J 55 " - pdb=" SG CYS J 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 E 62 " - pdb=" SG CYS E 236 " distance=2.03 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 236 " distance=2.03 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 236 " distance=2.03 Simple disulfide: pdb=" SG CYS F 62 " - pdb=" SG CYS F 236 " distance=2.03 Simple disulfide: pdb=" SG CYS I 62 " - pdb=" SG CYS I 236 " distance=2.03 Simple disulfide: pdb=" SG CYS H 62 " - pdb=" SG CYS H 236 " distance=2.03 Simple disulfide: pdb=" SG CYS K 62 " - pdb=" SG CYS K 236 " distance=2.03 Simple disulfide: pdb=" SG CYS J 62 " - pdb=" SG CYS J 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 E 66 " - pdb=" SG CYS E 231 " distance=2.04 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 231 " distance=2.04 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 231 " distance=2.04 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 231 " distance=2.03 Simple disulfide: pdb=" SG CYS I 66 " - pdb=" SG CYS I 231 " distance=2.03 Simple disulfide: pdb=" SG CYS H 66 " - pdb=" SG CYS H 231 " distance=2.04 Simple disulfide: pdb=" SG CYS K 66 " - pdb=" SG CYS K 231 " distance=2.04 Simple disulfide: pdb=" SG CYS J 66 " - pdb=" SG CYS J 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: 7.96 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 2.16 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: 11.08 Time building geometry restraints manager: 9.66 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: 0.18 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' 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: 12.470 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: 0.520 Extract box with map and model: 1.250 Check model and map are aligned: 0.240 Set scattering table: 0.330 Process input model: 56.980 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.140 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:11.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.150 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.005 0.002 TRP H 79 HIS 0.005 0.001 HIS G 75 PHE 0.006 0.001 PHE D 256 TYR 0.008 0.001 TYR I 67 ARG 0.003 0.000 ARG F 233 Details of bonding type rmsd hydrogen bonds : bond 0.12318 ( 1164) hydrogen bonds : angle 3.85611 ( 3456) SS BOND : bond 0.00337 ( 36) SS BOND : angle 1.01550 ( 72) covalent geometry : bond 0.00255 (16716) covalent geometry : angle 0.60884 (22548) 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 : 2.714 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: 0.7583 (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: 0.7567 (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: 3.4068 time to fit residues: 911.1058 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 : 2.499 ------------------------------------------------------------------------------- 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 162 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 112 optimal weight: 10.0000 chunk 174 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.4496 r_free = 0.4496 target = 0.216118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.168623 restraints weight = 44814.133| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 1.59 r_work: 0.3843 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3726 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 16764 Z= 0.233 Angle : 0.732 8.432 22620 Z= 0.375 Chirality : 0.045 0.165 2604 Planarity : 0.005 0.063 2748 Dihedral : 8.542 57.974 2464 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.61 % Allowed : 18.00 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.27 (0.18), residues: 1944 helix: 3.06 (0.13), residues: 1356 sheet: 2.10 (0.47), residues: 120 loop : -0.68 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP A 79 HIS 0.002 0.001 HIS C 99 PHE 0.019 0.002 PHE D 81 TYR 0.012 0.002 TYR E 234 ARG 0.006 0.001 ARG A 69 Details of bonding type rmsd hydrogen bonds : bond 0.07366 ( 1164) hydrogen bonds : angle 3.48367 ( 3456) SS BOND : bond 0.00558 ( 36) SS BOND : angle 1.47179 ( 72) covalent geometry : bond 0.00551 (16716) covalent geometry : angle 0.72799 (22548) Misc. bond : bond 0.00113 ( 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 352 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 305 time to evaluate : 2.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 VAL cc_start: 0.8995 (OUTLIER) cc_final: 0.8757 (p) REVERT: C 85 MET cc_start: 0.7504 (OUTLIER) cc_final: 0.7174 (mmt) REVERT: C 239 GLU cc_start: 0.8009 (tt0) cc_final: 0.7758 (tt0) REVERT: D 54 VAL cc_start: 0.8981 (OUTLIER) cc_final: 0.8743 (p) REVERT: F 239 GLU cc_start: 0.8020 (tt0) cc_final: 0.7750 (tt0) REVERT: G 54 VAL cc_start: 0.8993 (OUTLIER) cc_final: 0.8756 (p) REVERT: J 54 VAL cc_start: 0.8994 (OUTLIER) cc_final: 0.8753 (p) REVERT: K 230 GLU cc_start: 0.8139 (mp0) cc_final: 0.7921 (mm-30) outliers start: 47 outliers final: 12 residues processed: 348 average time/residue: 2.3296 time to fit residues: 913.5041 Evaluate side-chains 287 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 270 time to evaluate : 2.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL 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 D residue 54 VAL Chi-restraints excluded: chain E residue 83 ILE Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain I residue 83 ILE Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 275 LEU Chi-restraints excluded: chain L residue 83 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 94 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 179 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.4452 r_free = 0.4452 target = 0.209420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.162280 restraints weight = 44490.981| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 1.57 r_work: 0.3735 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3622 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.5000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16764 Z= 0.173 Angle : 0.629 7.695 22620 Z= 0.311 Chirality : 0.043 0.141 2604 Planarity : 0.004 0.056 2748 Dihedral : 6.844 56.661 2460 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.11 % Allowed : 24.44 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.60 (0.18), residues: 1944 helix: 3.39 (0.12), residues: 1356 sheet: 1.88 (0.45), residues: 120 loop : -0.76 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP A 79 HIS 0.006 0.002 HIS F 75 PHE 0.008 0.001 PHE A 71 TYR 0.010 0.002 TYR E 243 ARG 0.004 0.001 ARG F 206 Details of bonding type rmsd hydrogen bonds : bond 0.06955 ( 1164) hydrogen bonds : angle 3.30721 ( 3456) SS BOND : bond 0.00410 ( 36) SS BOND : angle 0.97449 ( 72) covalent geometry : bond 0.00418 (16716) covalent geometry : angle 0.62740 (22548) Misc. bond : bond 0.00607 ( 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 317 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 279 time to evaluate : 3.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8521 (t70) cc_final: 0.8292 (t0) REVERT: A 201 ILE cc_start: 0.8326 (mt) cc_final: 0.7864 (pp) REVERT: A 268 ASN cc_start: 0.7294 (m-40) cc_final: 0.6974 (m-40) REVERT: C 239 GLU cc_start: 0.7927 (tt0) cc_final: 0.7670 (tt0) REVERT: B 47 ASP cc_start: 0.8535 (t70) cc_final: 0.8309 (t0) REVERT: D 47 ASP cc_start: 0.8478 (t70) cc_final: 0.8244 (t0) REVERT: D 201 ILE cc_start: 0.8250 (mt) cc_final: 0.7800 (pp) REVERT: D 268 ASN cc_start: 0.7146 (m-40) cc_final: 0.6825 (m-40) REVERT: E 47 ASP cc_start: 0.8558 (t70) cc_final: 0.8338 (t0) REVERT: F 239 GLU cc_start: 0.7909 (tt0) cc_final: 0.7620 (tt0) REVERT: G 47 ASP cc_start: 0.8476 (t70) cc_final: 0.8261 (t0) REVERT: G 201 ILE cc_start: 0.8274 (mt) cc_final: 0.7826 (pp) REVERT: G 268 ASN cc_start: 0.7168 (m-40) cc_final: 0.6849 (m-40) REVERT: H 47 ASP cc_start: 0.8534 (t70) cc_final: 0.8313 (t0) REVERT: J 47 ASP cc_start: 0.8492 (t70) cc_final: 0.8278 (t0) REVERT: J 201 ILE cc_start: 0.8303 (mt) cc_final: 0.7840 (pp) REVERT: J 268 ASN cc_start: 0.7201 (m-40) cc_final: 0.6888 (m-40) REVERT: K 47 ASP cc_start: 0.8542 (t70) cc_final: 0.8316 (t0) outliers start: 38 outliers final: 9 residues processed: 295 average time/residue: 2.5685 time to fit residues: 870.0550 Evaluate side-chains 281 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 272 time to evaluate : 2.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain K residue 28 THR 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 141 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 56 optimal weight: 0.3980 chunk 112 optimal weight: 10.0000 chunk 152 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN D 232 ASN G 232 ASN J 232 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.201254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.154150 restraints weight = 44592.143| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 1.55 r_work: 0.3693 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3580 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.5871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 16764 Z= 0.147 Angle : 0.556 5.233 22620 Z= 0.282 Chirality : 0.041 0.142 2604 Planarity : 0.003 0.027 2748 Dihedral : 6.683 59.210 2460 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.39 % Allowed : 25.56 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.86 (0.18), residues: 1944 helix: 3.56 (0.12), residues: 1356 sheet: 1.97 (0.44), residues: 120 loop : -0.58 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 79 HIS 0.005 0.002 HIS A 75 PHE 0.010 0.001 PHE H 71 TYR 0.008 0.002 TYR E 67 ARG 0.002 0.000 ARG C 206 Details of bonding type rmsd hydrogen bonds : bond 0.05950 ( 1164) hydrogen bonds : angle 3.21103 ( 3456) SS BOND : bond 0.00359 ( 36) SS BOND : angle 0.87857 ( 72) covalent geometry : bond 0.00353 (16716) covalent geometry : angle 0.55446 (22548) Misc. bond : bond 0.00040 ( 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 293 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 268 time to evaluate : 2.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 ILE cc_start: 0.8335 (mt) cc_final: 0.8017 (pp) REVERT: A 206 ARG cc_start: 0.7222 (OUTLIER) cc_final: 0.6346 (ttp80) REVERT: B 47 ASP cc_start: 0.8527 (t70) cc_final: 0.8285 (t0) REVERT: D 201 ILE cc_start: 0.8328 (mt) cc_final: 0.8013 (pp) REVERT: D 206 ARG cc_start: 0.7212 (OUTLIER) cc_final: 0.6329 (ttp80) REVERT: E 47 ASP cc_start: 0.8518 (t70) cc_final: 0.8276 (t0) REVERT: G 201 ILE cc_start: 0.8327 (mt) cc_final: 0.8011 (pp) REVERT: G 206 ARG cc_start: 0.7219 (OUTLIER) cc_final: 0.6334 (ttp80) REVERT: H 47 ASP cc_start: 0.8531 (t70) cc_final: 0.8291 (t0) REVERT: J 201 ILE cc_start: 0.8313 (mt) cc_final: 0.7990 (pp) REVERT: J 206 ARG cc_start: 0.7193 (OUTLIER) cc_final: 0.6311 (ttp80) REVERT: K 47 ASP cc_start: 0.8547 (t70) cc_final: 0.8304 (t0) outliers start: 25 outliers final: 2 residues processed: 280 average time/residue: 2.1928 time to fit residues: 700.4197 Evaluate side-chains 262 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 256 time to evaluate : 2.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain D residue 206 ARG Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 206 ARG Chi-restraints excluded: chain J residue 206 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 18 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 99 optimal weight: 0.9980 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 B 232 ASN D 232 ASN E 232 ASN G 232 ASN H 232 ASN J 232 ASN K 232 ASN L 232 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.195953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.148467 restraints weight = 44485.543| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 1.53 r_work: 0.3636 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3524 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.6453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16764 Z= 0.170 Angle : 0.583 4.897 22620 Z= 0.295 Chirality : 0.043 0.140 2604 Planarity : 0.004 0.032 2748 Dihedral : 6.205 42.327 2460 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.56 % Allowed : 26.28 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.85 (0.18), residues: 1944 helix: 3.55 (0.12), residues: 1356 sheet: 1.95 (0.45), residues: 120 loop : -0.57 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP A 79 HIS 0.005 0.001 HIS A 75 PHE 0.009 0.001 PHE C 71 TYR 0.011 0.002 TYR E 243 ARG 0.003 0.000 ARG H 206 Details of bonding type rmsd hydrogen bonds : bond 0.06177 ( 1164) hydrogen bonds : angle 3.21617 ( 3456) SS BOND : bond 0.00429 ( 36) SS BOND : angle 1.00282 ( 72) covalent geometry : bond 0.00418 (16716) covalent geometry : angle 0.58120 (22548) Misc. bond : bond 0.00322 ( 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 332 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 304 time to evaluate : 2.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.7664 (tp30) cc_final: 0.7409 (tp30) REVERT: A 201 ILE cc_start: 0.8462 (mt) cc_final: 0.8142 (pp) REVERT: A 206 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.6363 (ttp80) REVERT: D 43 GLU cc_start: 0.7695 (tp30) cc_final: 0.7444 (tp30) REVERT: D 49 GLU cc_start: 0.8456 (pt0) cc_final: 0.8238 (pt0) REVERT: D 201 ILE cc_start: 0.8479 (mt) cc_final: 0.8172 (pp) REVERT: D 206 ARG cc_start: 0.7275 (OUTLIER) cc_final: 0.6349 (ttp80) REVERT: E 201 ILE cc_start: 0.8393 (mt) cc_final: 0.8080 (pp) REVERT: G 43 GLU cc_start: 0.7656 (tp30) cc_final: 0.7404 (tp30) REVERT: G 201 ILE cc_start: 0.8480 (mt) cc_final: 0.8174 (pp) REVERT: G 206 ARG cc_start: 0.7286 (OUTLIER) cc_final: 0.6353 (ttp80) REVERT: J 43 GLU cc_start: 0.7658 (tp30) cc_final: 0.7406 (tp30) REVERT: J 201 ILE cc_start: 0.8447 (mt) cc_final: 0.8125 (pp) REVERT: J 206 ARG cc_start: 0.7275 (OUTLIER) cc_final: 0.6341 (ttp80) REVERT: K 201 ILE cc_start: 0.8396 (mt) cc_final: 0.8061 (pp) outliers start: 28 outliers final: 8 residues processed: 322 average time/residue: 1.7861 time to fit residues: 672.3540 Evaluate side-chains 283 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 271 time to evaluate : 2.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain D residue 206 ARG Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain G residue 206 ARG Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain J residue 206 ARG Chi-restraints excluded: chain L residue 28 THR 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 182 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 185 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 232 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.184556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.135902 restraints weight = 45104.248| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.56 r_work: 0.3434 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.7161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16764 Z= 0.190 Angle : 0.598 5.403 22620 Z= 0.305 Chirality : 0.044 0.153 2604 Planarity : 0.004 0.035 2748 Dihedral : 6.808 39.363 2460 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.22 % Allowed : 26.83 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.54 (0.18), residues: 1944 helix: 3.32 (0.12), residues: 1356 sheet: 1.71 (0.44), residues: 120 loop : -0.65 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 79 HIS 0.012 0.003 HIS F 75 PHE 0.011 0.002 PHE K 71 TYR 0.011 0.002 TYR G 67 ARG 0.003 0.000 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.06353 ( 1164) hydrogen bonds : angle 3.31140 ( 3456) SS BOND : bond 0.00540 ( 36) SS BOND : angle 1.15276 ( 72) covalent geometry : bond 0.00466 (16716) covalent geometry : angle 0.59503 (22548) Misc. bond : bond 0.00154 ( 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 337 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 297 time to evaluate : 2.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.7666 (tp30) cc_final: 0.7371 (tp30) REVERT: A 206 ARG cc_start: 0.7167 (OUTLIER) cc_final: 0.6148 (ttp80) REVERT: D 43 GLU cc_start: 0.7681 (tp30) cc_final: 0.7392 (tp30) REVERT: D 206 ARG cc_start: 0.7160 (OUTLIER) cc_final: 0.6136 (ttp80) REVERT: G 43 GLU cc_start: 0.7674 (tp30) cc_final: 0.7377 (tp30) REVERT: G 206 ARG cc_start: 0.7155 (OUTLIER) cc_final: 0.6139 (ttp80) REVERT: J 43 GLU cc_start: 0.7686 (tp30) cc_final: 0.7403 (tp30) REVERT: J 206 ARG cc_start: 0.7157 (OUTLIER) cc_final: 0.6140 (ttp80) outliers start: 40 outliers final: 13 residues processed: 315 average time/residue: 1.8277 time to fit residues: 675.0943 Evaluate side-chains 290 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 273 time to evaluate : 3.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain D residue 206 ARG Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 87 CYS 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 H residue 87 CYS Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain J residue 206 ARG Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 87 CYS Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 201 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 18 optimal weight: 0.9990 chunk 139 optimal weight: 3.9990 chunk 156 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 186 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 188 optimal weight: 0.5980 chunk 117 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.4128 r_free = 0.4128 target = 0.187523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.139510 restraints weight = 45442.219| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.56 r_work: 0.3482 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.7412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 16764 Z= 0.110 Angle : 0.500 4.570 22620 Z= 0.254 Chirality : 0.040 0.129 2604 Planarity : 0.003 0.028 2748 Dihedral : 5.750 35.064 2460 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.56 % Allowed : 29.06 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.06 (0.18), residues: 1944 helix: 3.73 (0.12), residues: 1356 sheet: 1.98 (0.44), residues: 120 loop : -0.58 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 79 HIS 0.002 0.001 HIS G 75 PHE 0.007 0.001 PHE A 71 TYR 0.009 0.001 TYR E 243 ARG 0.001 0.000 ARG L 206 Details of bonding type rmsd hydrogen bonds : bond 0.05240 ( 1164) hydrogen bonds : angle 3.09123 ( 3456) SS BOND : bond 0.00213 ( 36) SS BOND : angle 0.74007 ( 72) covalent geometry : bond 0.00233 (16716) covalent geometry : angle 0.49927 (22548) Misc. bond : bond 0.00110 ( 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 315 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 287 time to evaluate : 2.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.7636 (tp30) cc_final: 0.7351 (tp30) REVERT: A 206 ARG cc_start: 0.7133 (OUTLIER) cc_final: 0.6101 (ttp80) REVERT: D 43 GLU cc_start: 0.7684 (tp30) cc_final: 0.7418 (tp30) REVERT: D 49 GLU cc_start: 0.8537 (pt0) cc_final: 0.8221 (pt0) REVERT: D 206 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.6128 (ttp80) REVERT: G 43 GLU cc_start: 0.7646 (tp30) cc_final: 0.7368 (tp30) REVERT: G 206 ARG cc_start: 0.7139 (OUTLIER) cc_final: 0.6128 (ttp80) REVERT: J 43 GLU cc_start: 0.7673 (tp30) cc_final: 0.7393 (tp30) REVERT: J 206 ARG cc_start: 0.7119 (OUTLIER) cc_final: 0.6093 (ttp80) outliers start: 28 outliers final: 14 residues processed: 298 average time/residue: 2.0243 time to fit residues: 720.4388 Evaluate side-chains 297 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 279 time to evaluate : 3.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 206 ARG Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 206 ARG Chi-restraints excluded: chain I residue 83 ILE Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 206 ARG Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 83 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 33 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 188 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 190 optimal weight: 0.9980 chunk 176 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 = 0.4118 r_free = 0.4118 target = 0.186611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.138412 restraints weight = 45298.881| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.57 r_work: 0.3466 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.7565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16764 Z= 0.125 Angle : 0.521 4.710 22620 Z= 0.262 Chirality : 0.041 0.224 2604 Planarity : 0.003 0.028 2748 Dihedral : 5.782 35.590 2460 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.61 % Allowed : 29.33 % Favored : 69.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.14 (0.18), residues: 1944 helix: 3.80 (0.12), residues: 1356 sheet: 2.02 (0.44), residues: 120 loop : -0.56 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 79 HIS 0.005 0.001 HIS A 75 PHE 0.007 0.001 PHE A 81 TYR 0.008 0.002 TYR B 243 ARG 0.002 0.000 ARG E 24 Details of bonding type rmsd hydrogen bonds : bond 0.05181 ( 1164) hydrogen bonds : angle 3.10936 ( 3456) SS BOND : bond 0.00283 ( 36) SS BOND : angle 0.79778 ( 72) covalent geometry : bond 0.00296 (16716) covalent geometry : angle 0.52005 (22548) Misc. bond : bond 0.00135 ( 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 312 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 283 time to evaluate : 2.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.7663 (tp30) cc_final: 0.7380 (tp30) REVERT: A 206 ARG cc_start: 0.7136 (OUTLIER) cc_final: 0.6106 (ttp80) REVERT: D 43 GLU cc_start: 0.7697 (tp30) cc_final: 0.7433 (tp30) REVERT: D 49 GLU cc_start: 0.8529 (pt0) cc_final: 0.8197 (pt0) REVERT: D 206 ARG cc_start: 0.7138 (OUTLIER) cc_final: 0.6087 (ttp80) REVERT: G 43 GLU cc_start: 0.7683 (tp30) cc_final: 0.7407 (tp30) REVERT: G 206 ARG cc_start: 0.7134 (OUTLIER) cc_final: 0.6089 (ttp80) REVERT: J 43 GLU cc_start: 0.7695 (tp30) cc_final: 0.7416 (tp30) REVERT: J 206 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.6114 (ttp80) REVERT: K 43 GLU cc_start: 0.7608 (pp20) cc_final: 0.7178 (pp20) REVERT: K 44 THR cc_start: 0.8300 (t) cc_final: 0.7923 (m) outliers start: 29 outliers final: 11 residues processed: 298 average time/residue: 1.8138 time to fit residues: 628.2349 Evaluate side-chains 297 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 282 time to evaluate : 2.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 206 ARG Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 206 ARG Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 206 ARG 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 81 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 chunk 170 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 131 optimal weight: 0.0570 chunk 58 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN D 232 ASN G 232 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.183786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.135157 restraints weight = 45256.217| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.56 r_work: 0.3413 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.7848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16764 Z= 0.170 Angle : 0.582 8.379 22620 Z= 0.293 Chirality : 0.043 0.298 2604 Planarity : 0.004 0.034 2748 Dihedral : 6.616 41.592 2460 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.78 % Allowed : 29.72 % Favored : 69.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.92 (0.18), residues: 1944 helix: 3.64 (0.12), residues: 1356 sheet: 1.85 (0.45), residues: 120 loop : -0.63 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP D 79 HIS 0.010 0.002 HIS D 75 PHE 0.010 0.001 PHE E 205 TYR 0.010 0.002 TYR D 67 ARG 0.003 0.000 ARG H 24 Details of bonding type rmsd hydrogen bonds : bond 0.05720 ( 1164) hydrogen bonds : angle 3.24028 ( 3456) SS BOND : bond 0.00510 ( 36) SS BOND : angle 1.05305 ( 72) covalent geometry : bond 0.00421 (16716) covalent geometry : angle 0.57989 (22548) Misc. bond : bond 0.00194 ( 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 308 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 294 time to evaluate : 2.384 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: A 43 GLU cc_start: 0.7688 (tp30) cc_final: 0.7406 (tp30) REVERT: A 206 ARG cc_start: 0.7123 (OUTLIER) cc_final: 0.6030 (ttp80) REVERT: C 272 LEU cc_start: 0.6049 (tt) cc_final: 0.5688 (tp) REVERT: D 43 GLU cc_start: 0.7704 (tp30) cc_final: 0.7429 (tp30) REVERT: D 206 ARG cc_start: 0.7108 (OUTLIER) cc_final: 0.6019 (ttp80) REVERT: F 272 LEU cc_start: 0.6114 (tt) cc_final: 0.5729 (tp) REVERT: G 43 GLU cc_start: 0.7710 (tp30) cc_final: 0.7435 (tp30) REVERT: G 206 ARG cc_start: 0.7110 (OUTLIER) cc_final: 0.6043 (ttp80) REVERT: I 272 LEU cc_start: 0.6089 (tt) cc_final: 0.5710 (tp) REVERT: J 43 GLU cc_start: 0.7721 (tp30) cc_final: 0.7446 (tp30) REVERT: J 206 ARG cc_start: 0.7124 (OUTLIER) cc_final: 0.6045 (ttp80) REVERT: L 272 LEU cc_start: 0.6049 (tt) cc_final: 0.5689 (tp) outliers start: 14 outliers final: 5 residues processed: 302 average time/residue: 1.7459 time to fit residues: 614.4826 Evaluate side-chains 295 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 286 time to evaluate : 2.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain D residue 206 ARG 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 J residue 206 ARG Chi-restraints excluded: chain L residue 32 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 101 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 141 optimal weight: 0.7980 chunk 146 optimal weight: 0.5980 chunk 135 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS F 75 HIS I 75 HIS J 75 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.185919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.137979 restraints weight = 45063.820| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.56 r_work: 0.3445 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.7936 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= 0.110 Angle : 0.508 5.067 22620 Z= 0.255 Chirality : 0.040 0.129 2604 Planarity : 0.003 0.030 2748 Dihedral : 5.890 38.376 2460 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.89 % Allowed : 29.72 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.21 (0.18), residues: 1944 helix: 3.88 (0.12), residues: 1356 sheet: 2.05 (0.44), residues: 120 loop : -0.65 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 79 HIS 0.002 0.001 HIS C 75 PHE 0.011 0.001 PHE E 205 TYR 0.008 0.001 TYR H 243 ARG 0.002 0.000 ARG I 206 Details of bonding type rmsd hydrogen bonds : bond 0.04909 ( 1164) hydrogen bonds : angle 3.12254 ( 3456) SS BOND : bond 0.00253 ( 36) SS BOND : angle 0.69500 ( 72) covalent geometry : bond 0.00250 (16716) covalent geometry : angle 0.50777 (22548) Misc. bond : bond 0.00113 ( 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: 16 poor density : 300 time to evaluate : 2.757 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 GLU cc_start: 0.7667 (tp30) cc_final: 0.7382 (tp30) REVERT: A 206 ARG cc_start: 0.7111 (OUTLIER) cc_final: 0.6018 (ttp80) REVERT: D 43 GLU cc_start: 0.7677 (tp30) cc_final: 0.7399 (tp30) REVERT: D 206 ARG cc_start: 0.7096 (OUTLIER) cc_final: 0.6010 (ttp80) REVERT: F 272 LEU cc_start: 0.6086 (tt) cc_final: 0.5705 (tp) REVERT: G 43 GLU cc_start: 0.7675 (tp30) cc_final: 0.7397 (tp30) REVERT: G 206 ARG cc_start: 0.7090 (OUTLIER) cc_final: 0.6023 (ttp80) REVERT: I 272 LEU cc_start: 0.6074 (tt) cc_final: 0.5706 (tp) REVERT: J 43 GLU cc_start: 0.7682 (tp30) cc_final: 0.7410 (tp30) REVERT: J 206 ARG cc_start: 0.7104 (OUTLIER) cc_final: 0.6019 (ttp80) REVERT: K 43 GLU cc_start: 0.7597 (pp20) cc_final: 0.7376 (pp20) REVERT: L 272 LEU cc_start: 0.5993 (tt) cc_final: 0.5645 (tp) outliers start: 16 outliers final: 13 residues processed: 308 average time/residue: 1.9052 time to fit residues: 691.8489 Evaluate side-chains 307 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 290 time to evaluate : 2.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain D residue 206 ARG Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain G residue 206 ARG Chi-restraints excluded: chain I residue 75 HIS 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 206 ARG 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 66 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 190 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS G 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 = 0.4109 r_free = 0.4109 target = 0.185342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.136901 restraints weight = 45181.814| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.58 r_work: 0.3436 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.7995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16764 Z= 0.150 Angle : 0.546 4.933 22620 Z= 0.277 Chirality : 0.041 0.149 2604 Planarity : 0.004 0.032 2748 Dihedral : 6.116 39.742 2460 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.00 % Allowed : 29.67 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.06 (0.18), residues: 1944 helix: 3.77 (0.12), residues: 1356 sheet: 2.04 (0.45), residues: 120 loop : -0.73 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 79 HIS 0.014 0.002 HIS F 75 PHE 0.013 0.001 PHE H 205 TYR 0.009 0.002 TYR D 67 ARG 0.002 0.000 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.05171 ( 1164) hydrogen bonds : angle 3.18660 ( 3456) SS BOND : bond 0.00380 ( 36) SS BOND : angle 0.87219 ( 72) covalent geometry : bond 0.00357 (16716) covalent geometry : angle 0.54418 (22548) Misc. bond : bond 0.00145 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22707.96 seconds wall clock time: 391 minutes 52.30 seconds (23512.30 seconds total)