Starting phenix.real_space_refine on Mon Aug 25 02:38:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j5o_35988/08_2025/8j5o_35988.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j5o_35988/08_2025/8j5o_35988.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8j5o_35988/08_2025/8j5o_35988.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j5o_35988/08_2025/8j5o_35988.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j5o_35988/08_2025/8j5o_35988.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j5o_35988/08_2025/8j5o_35988.map" } resolution = 2.9 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= 0.009 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: 7 Type Number sf(0) Gaussians Fe 5 7.16 5 P 4 5.49 5 Mg 48 5.21 5 S 75 5.16 5 C 16852 2.51 5 N 3297 2.21 5 O 3411 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s 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: 23692 Number of models: 1 Model: "" Number of chains: 69 Chain: "0" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "1" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 266 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "2" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "3" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 295 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "4" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "5" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "6" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "7" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 295 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "8" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "9" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 295 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "A" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "B" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "C" Number of atoms: 2404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2404 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 24, 'TRANS': 290} Chain: "D" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "E" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "F" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 295 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "H" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "I" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "J" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 295 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "K" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "L" Number of atoms: 2364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2364 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 16, 'TRANS': 282} Chain breaks: 1 Chain: "M" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2488 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 16, 'TRANS': 289} Chain: "N" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 295 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "O" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "P" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 295 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "Q" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "R" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "S" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "T" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "U" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "V" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 295 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "W" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "X" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 206 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 1, 'TRANS': 24} Chain: "Y" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 259 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 2, 'TRANS': 29} Chain: "Z" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 362 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 4, 'TRANS': 42} Chain: "0" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 214 Unusual residues: {'BCL': 2, 'KGD': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "1" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 148 Unusual residues: {'BCL': 1, 'KGD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "2" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'KGD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "3" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'KGD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "5" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "6" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'KGD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "7" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "8" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'KGD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "9" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'KGD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 299 Unusual residues: {'HEM': 4, 'KGD': 2, 'PGV': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "D" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 148 Unusual residues: {'BCL': 1, 'KGD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'KGD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'KGD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 148 Unusual residues: {'BCL': 1, 'KGD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'KGD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 438 Unusual residues: {' FE': 1, 'BCL': 2, 'BPH': 2, 'MQE': 1, 'PGV': 3} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'PGV:plan-3': 2} Unresolved non-hydrogen planarities: 7 Chain: "M" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 223 Unusual residues: {'BCL': 1, 'BPH': 1, 'MQE': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'MQE:plan-2': 1, 'MQE:plan-3': 1, 'MQE:plan-4': 1, 'MQE:plan-5': 1, 'MQE:plan-6': 1, 'MQE:plan-9': 1, 'MQE:plan-10': 1, 'MQE:plan-11': 1, 'MQE:plan-12': 1} Unresolved non-hydrogen planarities: 44 Chain: "N" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'KGD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "P" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'KGD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 214 Unusual residues: {'BCL': 2, 'KGD': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "T" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'KGD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "V" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.00, per 1000 atoms: 0.25 Number of scatterers: 23692 At special positions: 0 Unit cell: (142.88, 131.271, 126.806, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 5 26.01 S 75 16.00 P 4 15.00 Mg 48 11.99 O 3411 8.00 N 3297 7.00 C 16852 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=58, symmetry=0 Number of additional bonds: simple=58, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.62 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 953.7 nanoseconds 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4346 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 4 sheets defined 68.5% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain '0' and resid 19 through 51 removed outlier: 4.225A pdb=" N LEU 0 24 " --> pdb=" O ASN 0 20 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL 0 25 " --> pdb=" O ALA 0 21 " (cutoff:3.500A) Processing helix chain '1' and resid 8 through 34 removed outlier: 3.727A pdb=" N GLY 1 34 " --> pdb=" O VAL 1 30 " (cutoff:3.500A) Processing helix chain '2' and resid 19 through 51 removed outlier: 3.819A pdb=" N LEU 2 24 " --> pdb=" O ASN 2 20 " (cutoff:3.500A) Processing helix chain '3' and resid 7 through 34 removed outlier: 3.934A pdb=" N GLY 3 34 " --> pdb=" O VAL 3 30 " (cutoff:3.500A) Processing helix chain '4' and resid 19 through 51 removed outlier: 4.274A pdb=" N LEU 4 24 " --> pdb=" O ASN 4 20 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL 4 25 " --> pdb=" O ALA 4 21 " (cutoff:3.500A) Processing helix chain '5' and resid 7 through 34 removed outlier: 3.850A pdb=" N GLY 5 34 " --> pdb=" O VAL 5 30 " (cutoff:3.500A) Processing helix chain '6' and resid 19 through 51 removed outlier: 4.356A pdb=" N LEU 6 24 " --> pdb=" O ASN 6 20 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL 6 25 " --> pdb=" O ALA 6 21 " (cutoff:3.500A) Processing helix chain '7' and resid 7 through 34 removed outlier: 3.944A pdb=" N GLY 7 34 " --> pdb=" O VAL 7 30 " (cutoff:3.500A) Processing helix chain '8' and resid 19 through 51 removed outlier: 4.156A pdb=" N LEU 8 24 " --> pdb=" O ASN 8 20 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL 8 25 " --> pdb=" O ALA 8 21 " (cutoff:3.500A) Processing helix chain '9' and resid 7 through 34 removed outlier: 3.911A pdb=" N GLY 9 34 " --> pdb=" O VAL 9 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 34 removed outlier: 3.703A pdb=" N GLY A 34 " --> pdb=" O VAL A 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 18 removed outlier: 3.624A pdb=" N PHE B 18 " --> pdb=" O LYS B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 51 removed outlier: 3.733A pdb=" N TRP B 23 " --> pdb=" O ASN B 19 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LEU B 24 " --> pdb=" O ASN B 20 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 14 Processing helix chain 'C' and resid 15 through 46 removed outlier: 3.941A pdb=" N TYR C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ILE C 22 " --> pdb=" O GLY C 18 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 85 removed outlier: 3.664A pdb=" N ASN C 79 " --> pdb=" O LEU C 75 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA C 80 " --> pdb=" O ALA C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 109 Processing helix chain 'C' and resid 109 through 115 removed outlier: 3.562A pdb=" N LEU C 114 " --> pdb=" O VAL C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 121 removed outlier: 3.731A pdb=" N CYS C 121 " --> pdb=" O CYS C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 156 removed outlier: 3.530A pdb=" N LYS C 139 " --> pdb=" O ASN C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 160 Processing helix chain 'C' and resid 170 through 175 removed outlier: 4.100A pdb=" N CYS C 174 " --> pdb=" O THR C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 190 Processing helix chain 'C' and resid 218 through 235 Processing helix chain 'C' and resid 256 through 274 Processing helix chain 'C' and resid 284 through 288 removed outlier: 4.334A pdb=" N ALA C 287 " --> pdb=" O GLY C 284 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLY C 288 " --> pdb=" O ILE C 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 284 through 288' Processing helix chain 'C' and resid 292 through 298 removed outlier: 4.046A pdb=" N CYS C 296 " --> pdb=" O SER C 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 33 Processing helix chain 'E' and resid 19 through 51 removed outlier: 4.085A pdb=" N LEU E 24 " --> pdb=" O ASN E 20 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL E 25 " --> pdb=" O ALA E 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 34 removed outlier: 3.775A pdb=" N GLY F 34 " --> pdb=" O VAL F 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 51 removed outlier: 4.076A pdb=" N LEU G 24 " --> pdb=" O ASN G 20 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL G 25 " --> pdb=" O ALA G 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 33 removed outlier: 3.526A pdb=" N SER H 33 " --> pdb=" O VAL H 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 51 removed outlier: 4.225A pdb=" N LEU I 24 " --> pdb=" O ASN I 20 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL I 25 " --> pdb=" O ALA I 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 34 removed outlier: 3.853A pdb=" N GLY J 34 " --> pdb=" O VAL J 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 21 through 51 removed outlier: 4.055A pdb=" N VAL K 25 " --> pdb=" O ALA K 21 " (cutoff:3.500A) Processing helix chain 'L' and resid 35 through 43 removed outlier: 4.002A pdb=" N ILE L 39 " --> pdb=" O PRO L 35 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 56 removed outlier: 3.566A pdb=" N ARG L 53 " --> pdb=" O THR L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 93 removed outlier: 3.582A pdb=" N ALA L 74 " --> pdb=" O GLY L 70 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE L 75 " --> pdb=" O LEU L 71 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLY L 91 " --> pdb=" O TYR L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 109 through 113 Processing helix chain 'L' and resid 122 through 150 removed outlier: 3.541A pdb=" N PHE L 126 " --> pdb=" O GLY L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 154 through 172 Processing helix chain 'L' and resid 172 through 179 Processing helix chain 'L' and resid 191 through 203 removed outlier: 3.609A pdb=" N TRP L 195 " --> pdb=" O HIS L 191 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR L 203 " --> pdb=" O ILE L 199 " (cutoff:3.500A) Processing helix chain 'L' and resid 209 through 235 Processing helix chain 'L' and resid 244 through 253 Processing helix chain 'L' and resid 259 through 288 removed outlier: 3.844A pdb=" N ILE L 263 " --> pdb=" O GLY L 259 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N HIS L 264 " --> pdb=" O GLU L 260 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG L 265 " --> pdb=" O ILE L 261 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL L 275 " --> pdb=" O GLY L 271 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR L 287 " --> pdb=" O PHE L 283 " (cutoff:3.500A) Processing helix chain 'L' and resid 293 through 299 removed outlier: 4.332A pdb=" N PHE L 298 " --> pdb=" O PHE L 295 " (cutoff:3.500A) Processing helix chain 'L' and resid 310 through 314 Processing helix chain 'M' and resid 337 through 343 Processing helix chain 'M' and resid 359 through 366 Processing helix chain 'M' and resid 379 through 401 removed outlier: 3.580A pdb=" N VAL M 401 " --> pdb=" O TYR M 397 " (cutoff:3.500A) Processing helix chain 'M' and resid 404 through 411 Processing helix chain 'M' and resid 412 through 415 Processing helix chain 'M' and resid 431 through 434 Processing helix chain 'M' and resid 435 through 464 removed outlier: 3.630A pdb=" N LEU M 439 " --> pdb=" O GLY M 435 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA M 440 " --> pdb=" O GLY M 436 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY M 464 " --> pdb=" O ALA M 460 " (cutoff:3.500A) Processing helix chain 'M' and resid 467 through 485 removed outlier: 3.668A pdb=" N TRP M 471 " --> pdb=" O THR M 467 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU M 479 " --> pdb=" O SER M 475 " (cutoff:3.500A) Processing helix chain 'M' and resid 493 through 497 removed outlier: 4.118A pdb=" N ALA M 496 " --> pdb=" O ASN M 493 " (cutoff:3.500A) Processing helix chain 'M' and resid 503 through 516 Processing helix chain 'M' and resid 518 through 521 Processing helix chain 'M' and resid 522 through 549 Processing helix chain 'M' and resid 550 through 553 Processing helix chain 'M' and resid 556 through 561 Processing helix chain 'M' and resid 565 through 580 Processing helix chain 'M' and resid 586 through 613 removed outlier: 3.963A pdb=" N ILE M 590 " --> pdb=" O TYR M 586 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLY M 611 " --> pdb=" O LEU M 607 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N THR M 612 " --> pdb=" O PHE M 608 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU M 613 " --> pdb=" O LEU M 609 " (cutoff:3.500A) Processing helix chain 'M' and resid 616 through 624 Processing helix chain 'M' and resid 634 through 639 removed outlier: 4.112A pdb=" N GLN M 637 " --> pdb=" O ASP M 634 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL M 639 " --> pdb=" O ALA M 636 " (cutoff:3.500A) Processing helix chain 'N' and resid 7 through 34 removed outlier: 3.999A pdb=" N GLY N 34 " --> pdb=" O VAL N 30 " (cutoff:3.500A) Processing helix chain 'O' and resid 19 through 51 removed outlier: 3.704A pdb=" N TRP O 23 " --> pdb=" O ASN O 19 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LEU O 24 " --> pdb=" O ASN O 20 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL O 25 " --> pdb=" O ALA O 21 " (cutoff:3.500A) Processing helix chain 'P' and resid 7 through 34 removed outlier: 3.873A pdb=" N GLY P 34 " --> pdb=" O VAL P 30 " (cutoff:3.500A) Processing helix chain 'Q' and resid 14 through 18 Processing helix chain 'Q' and resid 19 through 51 removed outlier: 4.428A pdb=" N LEU Q 24 " --> pdb=" O ASN Q 20 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL Q 25 " --> pdb=" O ALA Q 21 " (cutoff:3.500A) Processing helix chain 'R' and resid 7 through 34 removed outlier: 3.826A pdb=" N GLY R 34 " --> pdb=" O VAL R 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 19 through 51 removed outlier: 4.447A pdb=" N LEU S 24 " --> pdb=" O ASN S 20 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 7 through 34 removed outlier: 3.666A pdb=" N GLY T 34 " --> pdb=" O VAL T 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 11 through 15 removed outlier: 3.620A pdb=" N LYS U 15 " --> pdb=" O ASP U 12 " (cutoff:3.500A) Processing helix chain 'U' and resid 19 through 51 removed outlier: 4.387A pdb=" N LEU U 24 " --> pdb=" O ASN U 20 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL U 25 " --> pdb=" O ALA U 21 " (cutoff:3.500A) Processing helix chain 'V' and resid 7 through 33 Processing helix chain 'W' and resid 19 through 51 removed outlier: 4.412A pdb=" N LEU W 24 " --> pdb=" O ASN W 20 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL W 25 " --> pdb=" O ALA W 21 " (cutoff:3.500A) Processing helix chain 'X' and resid 2 through 25 Processing helix chain 'Y' and resid 2 through 17 removed outlier: 3.542A pdb=" N ALA Y 6 " --> pdb=" O ASN Y 2 " (cutoff:3.500A) Processing helix chain 'Y' and resid 17 through 30 removed outlier: 3.878A pdb=" N VAL Y 21 " --> pdb=" O PHE Y 17 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 47 Proline residue: Z 26 - end of helix Processing sheet with id=AA1, first strand: chain 'L' and resid 8 through 9 Processing sheet with id=AA2, first strand: chain 'L' and resid 32 through 34 removed outlier: 4.104A pdb=" N TYR Z 49 " --> pdb=" O ILE L 34 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 62 through 64 removed outlier: 3.705A pdb=" N PHE L 62 " --> pdb=" O VAL L 69 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE L 67 " --> pdb=" O ILE L 64 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 349 through 351 1198 hydrogen bonds defined for protein. 3519 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: 3.51 Time building geometry restraints manager: 3.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.37: 6834 1.37 - 1.57: 17569 1.57 - 1.77: 8 1.77 - 1.98: 125 1.98 - 2.18: 208 Bond restraints: 24744 Sorted by residual: bond pdb=" NA BCL K 102 " pdb="MG BCL K 102 " ideal model delta sigma weight residual 2.170 1.997 0.173 2.40e-02 1.74e+03 5.19e+01 bond pdb=" NA BCL W 102 " pdb="MG BCL W 102 " ideal model delta sigma weight residual 2.170 2.000 0.170 2.40e-02 1.74e+03 5.00e+01 bond pdb=" CGD BCL W 102 " pdb=" O2D BCL W 102 " ideal model delta sigma weight residual 1.324 1.450 -0.126 2.10e-02 2.27e+03 3.60e+01 bond pdb=" CAY KGD J 103 " pdb=" CBD KGD J 103 " ideal model delta sigma weight residual 1.500 1.381 0.119 2.00e-02 2.50e+03 3.54e+01 bond pdb=" C1A BCL K 102 " pdb=" CHA BCL K 102 " ideal model delta sigma weight residual 1.368 1.487 -0.119 2.00e-02 2.50e+03 3.52e+01 ... (remaining 24739 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 33792 3.36 - 6.73: 618 6.73 - 10.09: 72 10.09 - 13.46: 8 13.46 - 16.82: 3 Bond angle restraints: 34493 Sorted by residual: angle pdb=" N PHE L 185 " pdb=" CA PHE L 185 " pdb=" C PHE L 185 " ideal model delta sigma weight residual 109.93 121.06 -11.13 1.24e+00 6.50e-01 8.06e+01 angle pdb=" C1D BCL K 102 " pdb=" C2D BCL K 102 " pdb=" CMD BCL K 102 " ideal model delta sigma weight residual 125.57 139.17 -13.59 1.83e+00 2.99e-01 5.53e+01 angle pdb=" C1D BCL W 102 " pdb=" C2D BCL W 102 " pdb=" CMD BCL W 102 " ideal model delta sigma weight residual 125.57 138.52 -12.94 1.83e+00 2.99e-01 5.01e+01 angle pdb=" NA BCL W 102 " pdb="MG BCL W 102 " pdb=" NC BCL W 102 " ideal model delta sigma weight residual 160.52 177.34 -16.82 2.84e+00 1.24e-01 3.51e+01 angle pdb=" N HIS L 183 " pdb=" CA HIS L 183 " pdb=" CB HIS L 183 " ideal model delta sigma weight residual 110.91 102.27 8.64 1.58e+00 4.01e-01 2.99e+01 ... (remaining 34488 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 12546 36.00 - 71.99: 364 71.99 - 107.99: 55 107.99 - 143.99: 11 143.99 - 179.98: 2 Dihedral angle restraints: 12978 sinusoidal: 6291 harmonic: 6687 Sorted by residual: dihedral pdb=" C1 BCL L1002 " pdb=" C2 BCL L1002 " pdb=" C3 BCL L1002 " pdb=" C5 BCL L1002 " ideal model delta sinusoidal sigma weight residual 180.00 0.02 179.98 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL W 102 " pdb=" CGA BCL W 102 " pdb=" O2A BCL W 102 " pdb=" CBA BCL W 102 " ideal model delta sinusoidal sigma weight residual 180.00 122.95 57.05 1 6.00e+00 2.78e-02 1.22e+02 dihedral pdb=" C2C HEM C 501 " pdb=" C3C HEM C 501 " pdb=" CAC HEM C 501 " pdb=" CBC HEM C 501 " ideal model delta sinusoidal sigma weight residual 0.00 89.17 -89.17 2 1.00e+01 1.00e-02 4.80e+01 ... (remaining 12975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 3377 0.121 - 0.241: 23 0.241 - 0.362: 4 0.362 - 0.483: 0 0.483 - 0.603: 1 Chirality restraints: 3405 Sorted by residual: chirality pdb=" CA PHE L 185 " pdb=" N PHE L 185 " pdb=" C PHE L 185 " pdb=" CB PHE L 185 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.10e+00 chirality pdb=" CA ALA L 315 " pdb=" N ALA L 315 " pdb=" C ALA L 315 " pdb=" CB ALA L 315 " both_signs ideal model delta sigma weight residual False 2.48 2.14 0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" CA TYR E 34 " pdb=" N TYR E 34 " pdb=" C TYR E 34 " pdb=" CB TYR E 34 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.29 2.00e-01 2.50e+01 2.03e+00 ... (remaining 3402 not shown) Planarity restraints: 4200 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL W 102 " 0.328 3.00e-02 1.11e+03 2.65e-01 3.90e+02 pdb=" CBA BCL W 102 " 0.192 3.00e-02 1.11e+03 pdb=" CGA BCL W 102 " -0.079 3.00e-02 1.11e+03 pdb=" O1A BCL W 102 " 0.006 3.00e-02 1.11e+03 pdb=" O2A BCL W 102 " -0.447 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1A BCL K 102 " 0.035 3.20e-02 9.77e+02 1.72e-01 1.45e+02 pdb=" C4A BCL K 102 " 0.094 3.20e-02 9.77e+02 pdb=" CHA BCL K 102 " -0.173 3.20e-02 9.77e+02 pdb=" CHB BCL K 102 " -0.210 3.20e-02 9.77e+02 pdb=" NA BCL K 102 " 0.254 3.20e-02 9.77e+02 delta sigma weight rms_deltas residual plane pdb=" C1A BCL W 102 " 0.032 3.20e-02 9.77e+02 1.55e-01 1.18e+02 pdb=" C4A BCL W 102 " 0.113 3.20e-02 9.77e+02 pdb=" CHA BCL W 102 " -0.154 3.20e-02 9.77e+02 pdb=" CHB BCL W 102 " -0.200 3.20e-02 9.77e+02 pdb=" NA BCL W 102 " 0.208 3.20e-02 9.77e+02 ... (remaining 4197 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 48 2.46 - 3.07: 14648 3.07 - 3.68: 32362 3.68 - 4.29: 53062 4.29 - 4.90: 89583 Nonbonded interactions: 189703 Sorted by model distance: nonbonded pdb=" CE1 HIS 3 27 " pdb="MG BCL 3 101 " model vdw 1.849 3.130 nonbonded pdb=" CE1 HIS P 27 " pdb="MG BCL P 101 " model vdw 2.084 3.130 nonbonded pdb=" OE2 GLU M 557 " pdb="FE FE L1004 " model vdw 2.086 2.260 nonbonded pdb=" SD MET C 229 " pdb="FE HEM C 503 " model vdw 2.127 3.360 nonbonded pdb=" SD MET C 145 " pdb="FE HEM C 502 " model vdw 2.132 3.360 ... (remaining 189698 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: 0.00 Found NCS groups: ncs_group { reference = (chain '0' and resid 7 through 101) selection = (chain '2' and resid 7 through 101) selection = (chain '4' and resid 7 through 101) selection = (chain '6' and resid 7 through 101) selection = (chain '8' and resid 7 through 101) selection = (chain 'B' and resid 7 through 101) selection = (chain 'E' and resid 7 through 101) selection = (chain 'G' and resid 7 through 101) selection = (chain 'I' and resid 7 through 101) selection = (chain 'K' and resid 7 through 101) selection = (chain 'O' and resid 7 through 101) selection = (chain 'Q' and resid 7 through 101) selection = (chain 'S' and resid 7 through 101) selection = (chain 'U' and resid 7 through 101) selection = (chain 'W' and resid 7 through 101) } ncs_group { reference = (chain '1' and resid 7 through 40) selection = (chain '3' and resid 7 through 40) selection = (chain '5' and resid 7 through 40) selection = (chain '7' and resid 7 through 40) selection = (chain '9' and resid 7 through 40) selection = (chain 'A' and resid 7 through 40) selection = (chain 'D' and resid 7 through 40) selection = (chain 'F' and resid 7 through 40) selection = (chain 'H' and resid 7 through 40) selection = (chain 'J' and resid 7 through 40) selection = (chain 'N' and resid 7 through 40) selection = (chain 'P' and resid 7 through 40) selection = (chain 'R' and resid 7 through 40) selection = (chain 'T' and resid 7 through 40) selection = (chain 'V' and resid 7 through 40) } 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: 0.010 Normalize map: mean=0, sd=1: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 21.670 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 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 : 0.010 0.403 24802 Z= 0.727 Angle : 0.980 16.821 34493 Z= 0.403 Chirality : 0.043 0.603 3405 Planarity : 0.008 0.265 4200 Dihedral : 17.270 179.983 8632 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % 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: 2.71 (0.18), residues: 2244 helix: 3.62 (0.13), residues: 1398 sheet: None (None), residues: 0 loop : -1.59 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 251 TYR 0.030 0.002 TYR L 204 PHE 0.040 0.002 PHE L 185 TRP 0.058 0.002 TRP L 305 HIS 0.022 0.001 HIS L 192 Details of bonding type rmsd covalent geometry : bond 0.00742 (24744) covalent geometry : angle 0.98010 (34493) hydrogen bonds : bond 0.12015 ( 1198) hydrogen bonds : angle 4.07481 ( 3519) Misc. bond : bond 0.13283 ( 58) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 0.791 Fit side-chains REVERT: 5 22 MET cc_start: 0.9206 (mmp) cc_final: 0.8989 (mmp) REVERT: 7 16 THR cc_start: 0.8956 (m) cc_final: 0.8693 (m) REVERT: N 14 VAL cc_start: 0.8349 (t) cc_final: 0.8131 (t) outliers start: 0 outliers final: 1 residues processed: 301 average time/residue: 0.5747 time to fit residues: 200.3577 Evaluate side-chains 236 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 235 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 240 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 20 ASN ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN C 61 ASN ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 ASN C 245 ASN C 301 ASN G 13 GLN H 37 ASN I 22 GLN L 183 HIS L 209 ASN L 252 ASN L 264 HIS M 637 GLN O 13 GLN Q 13 GLN U 13 GLN U 22 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.123987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.105083 restraints weight = 28430.326| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.10 r_work: 0.2826 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.156 24802 Z= 0.182 Angle : 0.812 12.232 34493 Z= 0.324 Chirality : 0.043 0.185 3405 Planarity : 0.005 0.060 4200 Dihedral : 17.453 179.907 4635 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.53 % Allowed : 6.61 % Favored : 91.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.52 (0.18), residues: 2244 helix: 3.37 (0.13), residues: 1423 sheet: None (None), residues: 0 loop : -1.64 (0.20), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 4 TYR 0.014 0.002 TYR C 205 PHE 0.024 0.002 PHE L 185 TRP 0.026 0.002 TRP L 305 HIS 0.013 0.001 HIS L 192 Details of bonding type rmsd covalent geometry : bond 0.00445 (24744) covalent geometry : angle 0.81241 (34493) hydrogen bonds : bond 0.07207 ( 1198) hydrogen bonds : angle 3.62074 ( 3519) Misc. bond : bond 0.02466 ( 58) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 233 time to evaluate : 0.807 Fit side-chains REVERT: 5 22 MET cc_start: 0.9208 (mmp) cc_final: 0.8982 (mmp) REVERT: 7 16 THR cc_start: 0.8987 (m) cc_final: 0.8733 (m) REVERT: C 78 MET cc_start: 0.5861 (tmm) cc_final: 0.5568 (ttm) REVERT: C 247 ARG cc_start: 0.8901 (OUTLIER) cc_final: 0.7971 (ptm160) REVERT: C 272 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.7894 (mt-10) REVERT: L 94 ASN cc_start: 0.7272 (m110) cc_final: 0.6907 (m-40) REVERT: N 14 VAL cc_start: 0.8401 (t) cc_final: 0.8197 (t) REVERT: Q 15 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7682 (mttt) REVERT: Z 42 ASP cc_start: 0.8492 (t70) cc_final: 0.8159 (t0) REVERT: Z 53 ASP cc_start: 0.7466 (t0) cc_final: 0.7252 (t0) outliers start: 30 outliers final: 15 residues processed: 247 average time/residue: 0.5487 time to fit residues: 157.2226 Evaluate side-chains 238 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 220 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 240 ASN Chi-restraints excluded: chain L residue 241 ILE Chi-restraints excluded: chain M residue 607 LEU Chi-restraints excluded: chain O residue 31 LYS Chi-restraints excluded: chain Q residue 15 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 3 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 167 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 chunk 172 optimal weight: 9.9990 chunk 151 optimal weight: 0.9990 chunk 154 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 186 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 20 ASN ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 ASN C 226 GLN G 13 GLN H 37 ASN I 22 GLN M 572 GLN M 637 GLN O 13 GLN U 13 GLN U 22 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.120117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.101076 restraints weight = 28508.079| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 1.07 r_work: 0.2752 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.120 24802 Z= 0.214 Angle : 0.859 13.744 34493 Z= 0.343 Chirality : 0.045 0.213 3405 Planarity : 0.005 0.059 4200 Dihedral : 17.093 179.877 4635 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.73 % Allowed : 9.41 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.14 (0.18), residues: 2244 helix: 3.15 (0.13), residues: 1408 sheet: None (None), residues: 0 loop : -1.85 (0.19), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 3 4 TYR 0.020 0.002 TYR C 205 PHE 0.028 0.002 PHE 9 36 TRP 0.025 0.002 TRP L 305 HIS 0.011 0.001 HIS L 192 Details of bonding type rmsd covalent geometry : bond 0.00537 (24744) covalent geometry : angle 0.85944 (34493) hydrogen bonds : bond 0.08274 ( 1198) hydrogen bonds : angle 3.68935 ( 3519) Misc. bond : bond 0.01724 ( 58) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 238 time to evaluate : 0.637 Fit side-chains REVERT: 7 17 LEU cc_start: 0.8533 (mm) cc_final: 0.8195 (tp) REVERT: C 78 MET cc_start: 0.6037 (tmm) cc_final: 0.5616 (ttm) REVERT: C 247 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.7958 (ptm160) REVERT: C 253 GLU cc_start: 0.7803 (pt0) cc_final: 0.7530 (pt0) REVERT: C 272 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.7936 (mt-10) REVERT: J 4 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.6913 (ptt90) REVERT: L 94 ASN cc_start: 0.7698 (m110) cc_final: 0.7333 (m-40) REVERT: L 106 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8061 (mm-30) REVERT: L 310 GLN cc_start: 0.6143 (OUTLIER) cc_final: 0.5932 (tp40) REVERT: M 343 TYR cc_start: 0.8270 (m-80) cc_final: 0.8063 (m-80) REVERT: M 367 GLU cc_start: 0.8529 (tp30) cc_final: 0.8152 (tm-30) REVERT: N 14 VAL cc_start: 0.8458 (t) cc_final: 0.8257 (t) REVERT: O 20 ASN cc_start: 0.8990 (t0) cc_final: 0.8767 (t0) REVERT: V 16 THR cc_start: 0.9013 (m) cc_final: 0.8777 (m) REVERT: Z 53 ASP cc_start: 0.7452 (t0) cc_final: 0.7227 (t0) outliers start: 34 outliers final: 18 residues processed: 257 average time/residue: 0.6209 time to fit residues: 184.4902 Evaluate side-chains 248 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 225 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 240 CYS Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain J residue 4 ARG Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 310 GLN Chi-restraints excluded: chain M residue 375 VAL Chi-restraints excluded: chain M residue 607 LEU Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain Q residue 37 LEU Chi-restraints excluded: chain W residue 12 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 84 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 75 optimal weight: 8.9990 chunk 76 optimal weight: 0.5980 chunk 72 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 104 optimal weight: 0.6980 chunk 49 optimal weight: 8.9990 chunk 89 optimal weight: 7.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 20 ASN 6 20 ASN ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN H 37 ASN I 22 GLN O 13 GLN P 37 ASN U 13 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.122607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.103508 restraints weight = 28467.845| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 1.09 r_work: 0.2812 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 24802 Z= 0.146 Angle : 0.730 12.199 34493 Z= 0.289 Chirality : 0.040 0.172 3405 Planarity : 0.005 0.053 4200 Dihedral : 16.254 179.966 4633 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.32 % Allowed : 10.63 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.42 (0.18), residues: 2244 helix: 3.42 (0.13), residues: 1410 sheet: None (None), residues: 0 loop : -1.86 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 4 TYR 0.016 0.001 TYR C 205 PHE 0.017 0.001 PHE M 387 TRP 0.012 0.001 TRP M 594 HIS 0.009 0.001 HIS L 192 Details of bonding type rmsd covalent geometry : bond 0.00346 (24744) covalent geometry : angle 0.72973 (34493) hydrogen bonds : bond 0.06560 ( 1198) hydrogen bonds : angle 3.45705 ( 3519) Misc. bond : bond 0.01530 ( 58) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 229 time to evaluate : 0.782 Fit side-chains REVERT: 7 17 LEU cc_start: 0.8459 (mm) cc_final: 0.8147 (tp) REVERT: C 78 MET cc_start: 0.6200 (tmm) cc_final: 0.5717 (ttm) REVERT: C 247 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.7721 (ptm160) REVERT: C 272 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.7901 (mt-10) REVERT: L 94 ASN cc_start: 0.7506 (m110) cc_final: 0.7150 (m-40) REVERT: M 341 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7233 (mp0) REVERT: M 367 GLU cc_start: 0.8480 (tp30) cc_final: 0.8144 (tm-30) REVERT: N 14 VAL cc_start: 0.8407 (t) cc_final: 0.8177 (t) REVERT: V 16 THR cc_start: 0.9008 (m) cc_final: 0.8795 (m) REVERT: Z 42 ASP cc_start: 0.8505 (t70) cc_final: 0.8258 (t0) REVERT: Z 53 ASP cc_start: 0.7580 (t0) cc_final: 0.7348 (t0) outliers start: 26 outliers final: 13 residues processed: 244 average time/residue: 0.6244 time to fit residues: 176.8377 Evaluate side-chains 240 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 224 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 240 ASN Chi-restraints excluded: chain M residue 341 GLU Chi-restraints excluded: chain M residue 630 TRP Chi-restraints excluded: chain Q residue 37 LEU Chi-restraints excluded: chain W residue 12 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 201 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 167 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 185 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 20 ASN ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 ASN E 22 GLN G 13 GLN H 37 ASN I 22 GLN L 205 ASN O 13 GLN U 13 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.119438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.100145 restraints weight = 28366.464| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.09 r_work: 0.2757 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 24802 Z= 0.197 Angle : 0.826 13.552 34493 Z= 0.328 Chirality : 0.043 0.210 3405 Planarity : 0.005 0.058 4200 Dihedral : 16.399 179.946 4633 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.29 % Allowed : 10.57 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.10 (0.18), residues: 2244 helix: 3.10 (0.13), residues: 1423 sheet: None (None), residues: 0 loop : -1.94 (0.20), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 4 TYR 0.019 0.002 TYR C 205 PHE 0.017 0.002 PHE L 185 TRP 0.013 0.002 TRP L 305 HIS 0.008 0.001 HIS L 192 Details of bonding type rmsd covalent geometry : bond 0.00488 (24744) covalent geometry : angle 0.82617 (34493) hydrogen bonds : bond 0.07896 ( 1198) hydrogen bonds : angle 3.61196 ( 3519) Misc. bond : bond 0.01629 ( 58) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 230 time to evaluate : 0.841 Fit side-chains REVERT: 7 17 LEU cc_start: 0.8528 (mm) cc_final: 0.8216 (tp) REVERT: A 4 ARG cc_start: 0.7441 (OUTLIER) cc_final: 0.5075 (ppt-90) REVERT: C 78 MET cc_start: 0.6275 (tmm) cc_final: 0.5774 (ttm) REVERT: C 247 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.7855 (ptm160) REVERT: C 272 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.7937 (mt-10) REVERT: I 7 ASN cc_start: 0.6821 (p0) cc_final: 0.6587 (p0) REVERT: J 4 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.6954 (ptt90) REVERT: L 94 ASN cc_start: 0.7673 (m110) cc_final: 0.7341 (m-40) REVERT: M 341 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7424 (mp0) REVERT: M 343 TYR cc_start: 0.8302 (m-80) cc_final: 0.8086 (m-80) REVERT: M 367 GLU cc_start: 0.8541 (tp30) cc_final: 0.8217 (tm-30) REVERT: N 14 VAL cc_start: 0.8433 (t) cc_final: 0.8220 (t) REVERT: V 16 THR cc_start: 0.9005 (m) cc_final: 0.8775 (m) REVERT: Z 42 ASP cc_start: 0.8561 (t70) cc_final: 0.8205 (t0) REVERT: Z 53 ASP cc_start: 0.7534 (t0) cc_final: 0.7306 (t0) outliers start: 45 outliers final: 22 residues processed: 258 average time/residue: 0.6512 time to fit residues: 194.6643 Evaluate side-chains 247 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 220 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain 6 residue 15 LYS Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 240 CYS Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain J residue 4 ARG Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 240 ASN Chi-restraints excluded: chain L residue 281 CYS Chi-restraints excluded: chain M residue 341 GLU Chi-restraints excluded: chain M residue 375 VAL Chi-restraints excluded: chain M residue 630 TRP Chi-restraints excluded: chain Q residue 37 LEU Chi-restraints excluded: chain U residue 31 LYS Chi-restraints excluded: chain W residue 12 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 141 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 177 optimal weight: 10.0000 chunk 163 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 152 optimal weight: 9.9990 chunk 73 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 182 optimal weight: 6.9990 chunk 7 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 37 ASN ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN H 37 ASN ** L 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 13 GLN U 13 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.118421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.099285 restraints weight = 28570.548| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.07 r_work: 0.2730 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 24802 Z= 0.216 Angle : 0.860 13.610 34493 Z= 0.342 Chirality : 0.045 0.231 3405 Planarity : 0.005 0.058 4200 Dihedral : 16.455 179.936 4633 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.29 % Allowed : 11.08 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.96 (0.18), residues: 2244 helix: 3.03 (0.13), residues: 1408 sheet: None (None), residues: 0 loop : -1.98 (0.19), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 4 TYR 0.021 0.002 TYR C 205 PHE 0.017 0.002 PHE L 185 TRP 0.015 0.002 TRP L 181 HIS 0.008 0.001 HIS L 192 Details of bonding type rmsd covalent geometry : bond 0.00543 (24744) covalent geometry : angle 0.85956 (34493) hydrogen bonds : bond 0.08271 ( 1198) hydrogen bonds : angle 3.67578 ( 3519) Misc. bond : bond 0.01375 ( 58) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 227 time to evaluate : 0.878 Fit side-chains REVERT: 7 17 LEU cc_start: 0.8557 (mm) cc_final: 0.8233 (tp) REVERT: C 78 MET cc_start: 0.6302 (tmm) cc_final: 0.5764 (ttm) REVERT: C 247 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.7988 (ptm160) REVERT: C 272 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.7939 (mt-10) REVERT: I 7 ASN cc_start: 0.6899 (p0) cc_final: 0.6663 (p0) REVERT: J 4 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.6939 (ptt90) REVERT: L 94 ASN cc_start: 0.7763 (m110) cc_final: 0.7394 (m-40) REVERT: L 145 ASP cc_start: 0.8205 (m-30) cc_final: 0.8002 (m-30) REVERT: M 341 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7471 (mp0) REVERT: M 343 TYR cc_start: 0.8329 (m-80) cc_final: 0.8069 (m-80) REVERT: M 367 GLU cc_start: 0.8606 (tp30) cc_final: 0.8285 (tm-30) REVERT: M 609 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7895 (mp) REVERT: N 14 VAL cc_start: 0.8449 (t) cc_final: 0.8240 (t) REVERT: V 16 THR cc_start: 0.9035 (m) cc_final: 0.8803 (m) REVERT: Z 42 ASP cc_start: 0.8607 (t70) cc_final: 0.8207 (t0) outliers start: 45 outliers final: 22 residues processed: 255 average time/residue: 0.6393 time to fit residues: 189.3012 Evaluate side-chains 251 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 224 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain 6 residue 15 LYS Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 240 CYS Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain J residue 4 ARG Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 281 CYS Chi-restraints excluded: chain M residue 341 GLU Chi-restraints excluded: chain M residue 375 VAL Chi-restraints excluded: chain M residue 607 LEU Chi-restraints excluded: chain M residue 609 LEU Chi-restraints excluded: chain M residue 630 TRP Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain Q residue 37 LEU Chi-restraints excluded: chain W residue 12 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 197 optimal weight: 5.9990 chunk 160 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 149 optimal weight: 3.9990 chunk 175 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 148 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 37 ASN ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN H 37 ASN I 22 GLN ** L 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 13 GLN U 13 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.119640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.100550 restraints weight = 28385.306| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.08 r_work: 0.2749 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 24802 Z= 0.191 Angle : 0.817 13.188 34493 Z= 0.326 Chirality : 0.043 0.224 3405 Planarity : 0.005 0.057 4200 Dihedral : 16.239 179.901 4633 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.14 % Allowed : 11.85 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.99 (0.18), residues: 2244 helix: 3.03 (0.13), residues: 1422 sheet: None (None), residues: 0 loop : -2.02 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 4 TYR 0.020 0.002 TYR M 424 PHE 0.016 0.002 PHE L 185 TRP 0.013 0.002 TRP C 40 HIS 0.008 0.001 HIS L 192 Details of bonding type rmsd covalent geometry : bond 0.00472 (24744) covalent geometry : angle 0.81707 (34493) hydrogen bonds : bond 0.07698 ( 1198) hydrogen bonds : angle 3.60419 ( 3519) Misc. bond : bond 0.01196 ( 58) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 224 time to evaluate : 0.683 Fit side-chains REVERT: 7 17 LEU cc_start: 0.8553 (mm) cc_final: 0.8231 (tp) REVERT: A 4 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.5242 (ppt-90) REVERT: C 78 MET cc_start: 0.6363 (tmm) cc_final: 0.5793 (ttm) REVERT: C 247 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.7807 (ptm160) REVERT: C 272 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.7892 (mt-10) REVERT: I 7 ASN cc_start: 0.7072 (p0) cc_final: 0.6864 (p0) REVERT: L 94 ASN cc_start: 0.7667 (m110) cc_final: 0.7319 (m-40) REVERT: L 145 ASP cc_start: 0.8130 (m-30) cc_final: 0.7868 (m-30) REVERT: M 341 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7408 (mp0) REVERT: M 343 TYR cc_start: 0.8329 (m-80) cc_final: 0.8085 (m-80) REVERT: M 367 GLU cc_start: 0.8613 (tp30) cc_final: 0.8294 (tm-30) REVERT: M 557 GLU cc_start: 0.9149 (OUTLIER) cc_final: 0.8220 (mm-30) REVERT: M 609 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7799 (mp) REVERT: N 14 VAL cc_start: 0.8435 (t) cc_final: 0.8219 (t) REVERT: V 16 THR cc_start: 0.9032 (m) cc_final: 0.8806 (m) REVERT: X 18 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.6974 (mm) REVERT: Z 42 ASP cc_start: 0.8595 (t70) cc_final: 0.8177 (t0) outliers start: 42 outliers final: 24 residues processed: 254 average time/residue: 0.5632 time to fit residues: 166.0579 Evaluate side-chains 253 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 222 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 37 ASN Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 240 CYS Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 281 CYS Chi-restraints excluded: chain M residue 341 GLU Chi-restraints excluded: chain M residue 375 VAL Chi-restraints excluded: chain M residue 557 GLU Chi-restraints excluded: chain M residue 609 LEU Chi-restraints excluded: chain M residue 630 TRP Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain Q residue 37 LEU Chi-restraints excluded: chain U residue 31 LYS Chi-restraints excluded: chain W residue 12 ASP Chi-restraints excluded: chain X residue 18 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 137 optimal weight: 1.9990 chunk 192 optimal weight: 7.9990 chunk 154 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 66 optimal weight: 0.7980 chunk 117 optimal weight: 0.9980 chunk 111 optimal weight: 0.5980 chunk 191 optimal weight: 6.9990 chunk 145 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 ASN G 13 GLN H 37 ASN I 22 GLN O 13 GLN U 13 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.126640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.107948 restraints weight = 28327.032| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.08 r_work: 0.2863 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24802 Z= 0.119 Angle : 0.669 12.605 34493 Z= 0.268 Chirality : 0.038 0.152 3405 Planarity : 0.005 0.050 4200 Dihedral : 15.419 179.981 4633 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.12 % Allowed : 13.07 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.59 (0.18), residues: 2244 helix: 3.58 (0.13), residues: 1411 sheet: None (None), residues: 0 loop : -1.87 (0.20), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 399 TYR 0.023 0.001 TYR M 424 PHE 0.015 0.001 PHE L 283 TRP 0.015 0.001 TRP M 594 HIS 0.006 0.000 HIS M 589 Details of bonding type rmsd covalent geometry : bond 0.00266 (24744) covalent geometry : angle 0.66923 (34493) hydrogen bonds : bond 0.05403 ( 1198) hydrogen bonds : angle 3.32688 ( 3519) Misc. bond : bond 0.01053 ( 58) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 226 time to evaluate : 0.832 Fit side-chains REVERT: 7 17 LEU cc_start: 0.8462 (mm) cc_final: 0.8129 (tp) REVERT: A 4 ARG cc_start: 0.7535 (OUTLIER) cc_final: 0.5262 (ppt-90) REVERT: C 78 MET cc_start: 0.6394 (tmm) cc_final: 0.5532 (ttm) REVERT: C 272 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7753 (mt-10) REVERT: L 94 ASN cc_start: 0.7226 (m110) cc_final: 0.6903 (m-40) REVERT: L 95 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7501 (mt-10) REVERT: M 341 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7138 (mp0) REVERT: M 367 GLU cc_start: 0.8492 (tp30) cc_final: 0.8181 (tm-30) REVERT: N 14 VAL cc_start: 0.8340 (t) cc_final: 0.8103 (t) REVERT: V 16 THR cc_start: 0.9016 (m) cc_final: 0.8807 (m) REVERT: X 18 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.6900 (mm) outliers start: 22 outliers final: 11 residues processed: 240 average time/residue: 0.5824 time to fit residues: 162.8802 Evaluate side-chains 232 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 217 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 240 CYS Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain H residue 37 ASN Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 281 CYS Chi-restraints excluded: chain M residue 341 GLU Chi-restraints excluded: chain M residue 375 VAL Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain X residue 18 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 63 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 56 optimal weight: 9.9990 chunk 172 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 162 optimal weight: 10.0000 chunk 152 optimal weight: 9.9990 chunk 111 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 37 ASN A 27 HIS C 220 HIS G 13 GLN H 37 ASN I 22 GLN ** L 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 13 GLN U 13 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.116890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.097790 restraints weight = 28511.769| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 1.08 r_work: 0.2705 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2581 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.204 24802 Z= 0.354 Angle : 1.037 15.848 34493 Z= 0.417 Chirality : 0.053 0.315 3405 Planarity : 0.006 0.080 4200 Dihedral : 16.928 179.729 4633 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.98 % Allowed : 13.07 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.60 (0.17), residues: 2244 helix: 2.73 (0.13), residues: 1408 sheet: None (None), residues: 0 loop : -2.09 (0.19), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 4 TYR 0.020 0.003 TYR C 205 PHE 0.023 0.003 PHE Z 40 TRP 0.030 0.003 TRP M 630 HIS 0.008 0.002 HIS L 192 Details of bonding type rmsd covalent geometry : bond 0.00851 (24744) covalent geometry : angle 1.03741 (34493) hydrogen bonds : bond 0.09990 ( 1198) hydrogen bonds : angle 3.86864 ( 3519) Misc. bond : bond 0.03108 ( 58) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 233 time to evaluate : 0.728 Fit side-chains REVERT: 6 37 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8087 (mm) REVERT: 7 17 LEU cc_start: 0.8593 (mm) cc_final: 0.8270 (tp) REVERT: A 4 ARG cc_start: 0.7470 (OUTLIER) cc_final: 0.5427 (ppt-90) REVERT: C 78 MET cc_start: 0.6258 (tmm) cc_final: 0.5609 (ttm) REVERT: C 272 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.7814 (mt-10) REVERT: J 4 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7027 (ptt90) REVERT: L 94 ASN cc_start: 0.7825 (m110) cc_final: 0.7508 (m-40) REVERT: M 341 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7533 (mp0) REVERT: M 367 GLU cc_start: 0.8609 (tp30) cc_final: 0.8285 (tm-30) REVERT: M 557 GLU cc_start: 0.9153 (OUTLIER) cc_final: 0.8265 (mm-30) REVERT: X 18 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.7003 (mm) REVERT: Z 43 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8238 (ttpt) outliers start: 39 outliers final: 24 residues processed: 258 average time/residue: 0.6144 time to fit residues: 184.6131 Evaluate side-chains 258 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 226 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain 6 residue 9 LEU Chi-restraints excluded: chain 6 residue 37 LEU Chi-restraints excluded: chain 7 residue 37 ASN Chi-restraints excluded: chain 8 residue 15 LYS Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 240 CYS Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 37 ASN Chi-restraints excluded: chain J residue 4 ARG Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain M residue 341 GLU Chi-restraints excluded: chain M residue 375 VAL Chi-restraints excluded: chain M residue 557 GLU Chi-restraints excluded: chain M residue 607 LEU Chi-restraints excluded: chain M residue 630 TRP Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain Q residue 37 LEU Chi-restraints excluded: chain W residue 12 ASP Chi-restraints excluded: chain X residue 18 LEU Chi-restraints excluded: chain Z residue 43 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 180 optimal weight: 3.9990 chunk 173 optimal weight: 0.9990 chunk 172 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 166 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 37 ASN G 13 GLN H 37 ASN L 183 HIS O 13 GLN U 13 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.122161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.103130 restraints weight = 28391.543| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.08 r_work: 0.2790 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 24802 Z= 0.143 Angle : 0.739 13.095 34493 Z= 0.298 Chirality : 0.040 0.198 3405 Planarity : 0.005 0.052 4200 Dihedral : 15.972 179.941 4633 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.12 % Allowed : 14.13 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.21 (0.18), residues: 2244 helix: 3.29 (0.13), residues: 1410 sheet: None (None), residues: 0 loop : -2.03 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 9 40 TYR 0.023 0.001 TYR M 424 PHE 0.016 0.001 PHE M 387 TRP 0.014 0.002 TRP M 594 HIS 0.008 0.001 HIS L 192 Details of bonding type rmsd covalent geometry : bond 0.00330 (24744) covalent geometry : angle 0.73856 (34493) hydrogen bonds : bond 0.06641 ( 1198) hydrogen bonds : angle 3.49974 ( 3519) Misc. bond : bond 0.01184 ( 58) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 224 time to evaluate : 0.590 Fit side-chains REVERT: 7 17 LEU cc_start: 0.8461 (mm) cc_final: 0.8142 (tp) REVERT: A 4 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.5313 (ppt-90) REVERT: C 78 MET cc_start: 0.6251 (tmm) cc_final: 0.5540 (ttm) REVERT: C 272 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7773 (mt-10) REVERT: L 94 ASN cc_start: 0.7588 (m110) cc_final: 0.7226 (m-40) REVERT: M 341 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7282 (mp0) REVERT: M 367 GLU cc_start: 0.8563 (tp30) cc_final: 0.8254 (tm-30) outliers start: 22 outliers final: 14 residues processed: 238 average time/residue: 0.5084 time to fit residues: 140.8934 Evaluate side-chains 237 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 220 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain 7 residue 37 ASN Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 240 CYS Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain H residue 37 ASN Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 240 ASN Chi-restraints excluded: chain M residue 341 GLU Chi-restraints excluded: chain M residue 375 VAL Chi-restraints excluded: chain M residue 630 TRP Chi-restraints excluded: chain P residue 24 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 137 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 116 optimal weight: 4.9990 chunk 71 optimal weight: 9.9990 chunk 140 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 176 optimal weight: 6.9990 chunk 172 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 37 ASN G 13 GLN H 37 ASN I 22 GLN O 13 GLN U 13 GLN Z 44 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.118991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.099811 restraints weight = 28461.499| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.09 r_work: 0.2734 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 24802 Z= 0.225 Angle : 0.876 13.950 34493 Z= 0.353 Chirality : 0.045 0.262 3405 Planarity : 0.006 0.060 4200 Dihedral : 16.332 179.783 4633 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.27 % Allowed : 14.29 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.96 (0.18), residues: 2244 helix: 3.05 (0.13), residues: 1408 sheet: None (None), residues: 0 loop : -2.01 (0.19), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 9 40 TYR 0.018 0.002 TYR C 205 PHE 0.018 0.002 PHE Z 40 TRP 0.024 0.002 TRP M 630 HIS 0.008 0.001 HIS L 192 Details of bonding type rmsd covalent geometry : bond 0.00568 (24744) covalent geometry : angle 0.87556 (34493) hydrogen bonds : bond 0.08264 ( 1198) hydrogen bonds : angle 3.66724 ( 3519) Misc. bond : bond 0.01435 ( 58) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6838.96 seconds wall clock time: 117 minutes 16.89 seconds (7036.89 seconds total)