Starting phenix.real_space_refine on Fri May 23 23:14:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j5p_35989/05_2025/8j5p_35989.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j5p_35989/05_2025/8j5p_35989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j5p_35989/05_2025/8j5p_35989.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j5p_35989/05_2025/8j5p_35989.map" model { file = "/net/cci-nas-00/data/ceres_data/8j5p_35989/05_2025/8j5p_35989.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j5p_35989/05_2025/8j5p_35989.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 3 5.49 5 Mg 48 5.21 5 S 75 5.16 5 C 16876 2.51 5 N 3316 2.21 5 O 3414 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 23737 Number of models: 1 Model: "" Number of chains: 70 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: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} 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: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} 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: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} 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: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} 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: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} 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: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} 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: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2375 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 16, 'TRANS': 283} 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: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} 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: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} 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: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} 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: 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: "1" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} 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: 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: "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: 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: "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: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 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: 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: "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: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 254 Unusual residues: {'HEM': 4, 'KGD': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "D" 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: "E" 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: "F" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "G" 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: "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: 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: "J" 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: "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: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 407 Unusual residues: {'BCL': 2, 'BPB': 2, 'MQE': 1, 'PGV': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 224 Unusual residues: {' FE': 1, 'BCL': 1, 'BPB': 1, 'MQE': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'MQE:plan-12': 1, 'MQE:plan-11': 1, 'MQE:plan-10': 1, 'MQE:plan-9': 1, 'MQE:plan-6': 1, 'MQE:plan-5': 1, 'MQE:plan-4': 1, 'MQE:plan-3': 1, 'MQE:plan-2': 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: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 183 Unusual residues: {'BCL': 1, 'KGD': 2, 'PGV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 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: 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: "T" 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: "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: 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: "X" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 15.81, per 1000 atoms: 0.67 Number of scatterers: 23737 At special positions: 0 Unit cell: (127.699, 137.522, 138.415, 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 3 15.00 Mg 48 11.99 O 3414 8.00 N 3316 7.00 C 16876 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=60, symmetry=0 Number of additional bonds: simple=60, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.52 Conformation dependent library (CDL) restraints added in 2.4 seconds 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4372 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 4 sheets defined 67.0% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain '0' and resid 20 through 51 removed outlier: 4.534A pdb=" N LEU 0 24 " --> pdb=" O ASN 0 20 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL 0 25 " --> pdb=" O ALA 0 21 " (cutoff:3.500A) Processing helix chain '1' and resid 6 through 34 removed outlier: 3.555A pdb=" N SER 1 11 " --> pdb=" O GLU 1 7 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL 1 14 " --> pdb=" O THR 1 10 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY 1 34 " --> pdb=" O VAL 1 30 " (cutoff:3.500A) Processing helix chain '2' and resid 21 through 51 removed outlier: 3.936A pdb=" N VAL 2 25 " --> pdb=" O ALA 2 21 " (cutoff:3.500A) Processing helix chain '3' and resid 7 through 34 removed outlier: 4.143A pdb=" N GLY 3 34 " --> pdb=" O VAL 3 30 " (cutoff:3.500A) Processing helix chain '4' and resid 21 through 51 removed outlier: 4.142A pdb=" N VAL 4 25 " --> pdb=" O ALA 4 21 " (cutoff:3.500A) Processing helix chain '5' and resid 7 through 33 Processing helix chain '6' and resid 21 through 51 removed outlier: 3.895A pdb=" N VAL 6 25 " --> pdb=" O ALA 6 21 " (cutoff:3.500A) Processing helix chain '7' and resid 7 through 34 removed outlier: 4.284A pdb=" N GLY 7 34 " --> pdb=" O VAL 7 30 " (cutoff:3.500A) Processing helix chain '8' and resid 21 through 51 removed outlier: 3.844A pdb=" N VAL 8 25 " --> pdb=" O ALA 8 21 " (cutoff:3.500A) Processing helix chain '9' and resid 7 through 33 Processing helix chain 'A' and resid 7 through 34 removed outlier: 4.058A pdb=" N GLY A 34 " --> pdb=" O VAL A 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 51 removed outlier: 3.668A pdb=" N TRP B 23 " --> pdb=" O ASN B 19 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU B 24 " --> pdb=" O ASN B 20 " (cutoff:3.500A) removed outlier: 4.002A 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 47 removed outlier: 3.554A pdb=" N TYR C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ILE C 22 " --> pdb=" O GLY C 18 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N VAL C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 85 removed outlier: 3.596A pdb=" N ALA C 77 " --> pdb=" O GLU C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 109 Processing helix chain 'C' and resid 109 through 115 Processing helix chain 'C' and resid 117 through 121 Processing helix chain 'C' and resid 135 through 156 removed outlier: 3.937A pdb=" N LYS C 139 " --> pdb=" O ASN C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 176 removed outlier: 4.396A pdb=" N CYS C 174 " --> pdb=" O THR C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 237 Processing helix chain 'C' and resid 255 through 274 removed outlier: 4.222A pdb=" N HIS C 259 " --> pdb=" O ALA C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 289 removed outlier: 4.390A pdb=" N GLY C 288 " --> pdb=" O ILE C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 297 removed outlier: 4.264A 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: 4.367A pdb=" N LEU E 24 " --> pdb=" O ASN E 20 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL E 25 " --> pdb=" O ALA E 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 33 Processing helix chain 'G' and resid 21 through 51 removed outlier: 3.953A pdb=" N VAL G 25 " --> pdb=" O ALA G 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 34 removed outlier: 4.185A pdb=" N GLY H 34 " --> pdb=" O VAL H 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 51 removed outlier: 3.749A pdb=" N TRP I 23 " --> pdb=" O ASN I 19 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU I 24 " --> pdb=" O ASN I 20 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL I 25 " --> pdb=" O ALA I 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 34 removed outlier: 4.123A pdb=" N GLY J 34 " --> pdb=" O VAL J 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 51 removed outlier: 3.514A pdb=" N TRP K 23 " --> pdb=" O ASN K 19 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU K 24 " --> pdb=" O ASN K 20 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL K 25 " --> pdb=" O ALA K 21 " (cutoff:3.500A) Processing helix chain 'L' and resid 35 through 44 removed outlier: 4.395A pdb=" N ILE L 39 " --> pdb=" O PRO L 35 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 55 removed outlier: 3.655A pdb=" N ARG L 53 " --> pdb=" O THR L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 93 removed outlier: 3.742A pdb=" N ALA L 74 " --> pdb=" O GLY L 70 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE L 75 " --> pdb=" O LEU L 71 " (cutoff:3.500A) removed outlier: 4.258A 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: 3.703A pdb=" N PHE L 126 " --> pdb=" O GLY L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 154 through 172 removed outlier: 3.623A pdb=" N LEU L 170 " --> pdb=" O SER L 166 " (cutoff:3.500A) Processing helix chain 'L' and resid 172 through 179 Processing helix chain 'L' and resid 191 through 203 removed outlier: 3.614A pdb=" N TYR L 203 " --> pdb=" O ILE L 199 " (cutoff:3.500A) Processing helix chain 'L' and resid 205 through 208 Processing helix chain 'L' and resid 209 through 236 removed outlier: 3.818A pdb=" N GLU L 236 " --> pdb=" O ALA L 232 " (cutoff:3.500A) Processing helix chain 'L' and resid 244 through 253 Processing helix chain 'L' and resid 261 through 288 removed outlier: 3.647A pdb=" N ARG L 265 " --> pdb=" O ILE L 261 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL L 275 " --> pdb=" O GLY L 271 " (cutoff:3.500A) Processing helix chain 'L' and resid 291 through 296 removed outlier: 4.119A pdb=" N TRP L 296 " --> pdb=" O TRP L 292 " (cutoff:3.500A) Processing helix chain 'L' and resid 297 through 302 removed outlier: 4.252A pdb=" N ASP L 300 " --> pdb=" O GLY L 297 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET L 302 " --> pdb=" O TRP L 299 " (cutoff:3.500A) Processing helix chain 'L' and resid 310 through 314 Processing helix chain 'M' and resid 337 through 344 removed outlier: 3.526A pdb=" N GLU M 341 " --> pdb=" O ASP M 337 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU M 342 " --> pdb=" O LEU M 338 " (cutoff:3.500A) Processing helix chain 'M' and resid 359 through 366 Processing helix chain 'M' and resid 380 through 400 removed outlier: 3.555A pdb=" N GLN M 400 " --> pdb=" O ASP M 396 " (cutoff:3.500A) Processing helix chain 'M' and resid 404 through 411 Processing helix chain 'M' and resid 412 through 415 removed outlier: 3.801A pdb=" N LEU M 415 " --> pdb=" O PHE M 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 412 through 415' Processing helix chain 'M' and resid 435 through 464 removed outlier: 3.735A pdb=" N LEU M 439 " --> pdb=" O GLY M 435 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA M 440 " --> pdb=" O GLY M 436 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA M 441 " --> pdb=" O ALA M 437 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR M 463 " --> pdb=" O ARG M 459 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY M 464 " --> pdb=" O ALA M 460 " (cutoff:3.500A) Processing helix chain 'M' and resid 467 through 485 removed outlier: 3.678A pdb=" N TRP M 471 " --> pdb=" O THR M 467 " (cutoff:3.500A) Processing helix chain 'M' and resid 493 through 497 removed outlier: 3.796A pdb=" N ALA M 496 " --> pdb=" O ASN M 493 " (cutoff:3.500A) Processing helix chain 'M' and resid 503 through 516 removed outlier: 3.665A pdb=" N TRP M 516 " --> pdb=" O VAL M 512 " (cutoff:3.500A) 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 removed outlier: 3.508A pdb=" N MET M 579 " --> pdb=" O TRP M 575 " (cutoff:3.500A) Processing helix chain 'M' and resid 586 through 613 removed outlier: 4.045A pdb=" N ILE M 590 " --> pdb=" O TYR M 586 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY M 611 " --> pdb=" O LEU M 607 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR M 612 " --> pdb=" O PHE M 608 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU M 613 " --> pdb=" O LEU M 609 " (cutoff:3.500A) Processing helix chain 'M' and resid 616 through 624 removed outlier: 3.648A pdb=" N THR M 623 " --> pdb=" O ALA M 619 " (cutoff:3.500A) Processing helix chain 'M' and resid 634 through 639 removed outlier: 4.056A pdb=" N GLN M 637 " --> pdb=" O ASP M 634 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL M 639 " --> pdb=" O ALA M 636 " (cutoff:3.500A) Processing helix chain 'N' and resid 7 through 33 Processing helix chain 'O' and resid 21 through 51 removed outlier: 3.914A pdb=" N VAL O 25 " --> pdb=" O ALA O 21 " (cutoff:3.500A) Processing helix chain 'P' and resid 7 through 34 removed outlier: 4.105A pdb=" N GLY P 34 " --> pdb=" O VAL P 30 " (cutoff:3.500A) Processing helix chain 'Q' and resid 20 through 51 removed outlier: 4.408A pdb=" N LEU Q 24 " --> pdb=" O ASN Q 20 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL Q 25 " --> pdb=" O ALA Q 21 " (cutoff:3.500A) Processing helix chain 'R' and resid 7 through 33 Processing helix chain 'S' and resid 19 through 51 removed outlier: 3.674A pdb=" N TRP S 23 " --> pdb=" O ASN S 19 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU S 24 " --> pdb=" O ASN S 20 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 7 through 34 removed outlier: 4.008A pdb=" N GLY T 34 " --> pdb=" O VAL T 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 21 through 51 removed outlier: 4.075A 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: 3.601A pdb=" N TRP W 23 " --> pdb=" O ASN W 19 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LEU W 24 " --> pdb=" O ASN W 20 " (cutoff:3.500A) removed outlier: 4.136A 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 31 removed outlier: 4.007A pdb=" N ALA Y 6 " --> pdb=" O ASN Y 2 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE Y 17 " --> pdb=" O VAL Y 13 " (cutoff:3.500A) Proline residue: Y 19 - end of helix removed outlier: 3.963A pdb=" N ASN Y 31 " --> pdb=" O THR Y 27 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 47 removed outlier: 3.645A pdb=" N CYS Z 23 " --> pdb=" O GLY Z 19 " (cutoff:3.500A) Proline residue: Z 26 - end of helix Processing helix chain 'Z' and resid 53 through 58 removed outlier: 4.325A pdb=" N ASN Z 58 " --> pdb=" O PRO Z 54 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 7 through 9 removed outlier: 3.736A pdb=" N LEU L 16 " --> pdb=" O LEU L 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 33 through 34 removed outlier: 3.607A pdb=" N ILE L 34 " --> pdb=" O TYR Z 49 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TYR Z 49 " --> pdb=" O ILE L 34 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'L' and resid 62 through 64 removed outlier: 3.841A pdb=" N PHE L 62 " --> pdb=" O VAL L 69 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 350 through 351 1174 hydrogen bonds defined for protein. 3477 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.31 Time building geometry restraints manager: 8.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.41: 10209 1.41 - 1.66: 14250 1.66 - 1.90: 126 1.90 - 2.14: 146 2.14 - 2.38: 61 Bond restraints: 24792 Sorted by residual: bond pdb=" C3C BPB M 704 " pdb=" CAC BPB M 704 " ideal model delta sigma weight residual 1.334 1.537 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C3C BPB L1003 " pdb=" CAC BPB L1003 " ideal model delta sigma weight residual 1.334 1.534 -0.200 2.00e-02 2.50e+03 1.00e+02 bond pdb=" C3C BPB L1005 " pdb=" CAC BPB L1005 " ideal model delta sigma weight residual 1.334 1.531 -0.197 2.00e-02 2.50e+03 9.68e+01 bond pdb=" CAE KGD C 406 " pdb=" CAI KGD C 406 " ideal model delta sigma weight residual 1.502 1.387 0.115 2.00e-02 2.50e+03 3.28e+01 bond pdb=" CAB KGD C 406 " pdb=" CAD KGD C 406 " ideal model delta sigma weight residual 1.528 1.435 0.093 2.00e-02 2.50e+03 2.18e+01 ... (remaining 24787 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.11: 34079 4.11 - 8.21: 456 8.21 - 12.32: 22 12.32 - 16.43: 7 16.43 - 20.53: 3 Bond angle restraints: 34567 Sorted by residual: angle pdb=" N VAL L 314 " pdb=" CA VAL L 314 " pdb=" C VAL L 314 " ideal model delta sigma weight residual 108.11 116.41 -8.30 1.40e+00 5.10e-01 3.52e+01 angle pdb=" C2C BPB L1003 " pdb=" C3C BPB L1003 " pdb=" CAC BPB L1003 " ideal model delta sigma weight residual 127.33 110.95 16.38 3.00e+00 1.11e-01 2.98e+01 angle pdb=" C2C BPB L1005 " pdb=" C3C BPB L1005 " pdb=" CAC BPB L1005 " ideal model delta sigma weight residual 127.33 111.22 16.11 3.00e+00 1.11e-01 2.88e+01 angle pdb=" N GLU 1 7 " pdb=" CA GLU 1 7 " pdb=" C GLU 1 7 " ideal model delta sigma weight residual 111.28 117.12 -5.84 1.09e+00 8.42e-01 2.87e+01 angle pdb=" C2C BPB M 704 " pdb=" C3C BPB M 704 " pdb=" CAC BPB M 704 " ideal model delta sigma weight residual 127.33 111.31 16.02 3.00e+00 1.11e-01 2.85e+01 ... (remaining 34562 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 12497 35.97 - 71.95: 393 71.95 - 107.92: 62 107.92 - 143.90: 14 143.90 - 179.87: 5 Dihedral angle restraints: 12971 sinusoidal: 6245 harmonic: 6726 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 0.13 179.87 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C2C HEM C 402 " pdb=" C3C HEM C 402 " pdb=" CAC HEM C 402 " pdb=" CBC HEM C 402 " ideal model delta sinusoidal sigma weight residual 180.00 91.94 88.06 2 1.00e+01 1.00e-02 4.79e+01 dihedral pdb=" C2B HEM C 403 " pdb=" C3B HEM C 403 " pdb=" CAB HEM C 403 " pdb=" CBB HEM C 403 " ideal model delta sinusoidal sigma weight residual 180.00 94.17 85.83 2 1.00e+01 1.00e-02 4.77e+01 ... (remaining 12968 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 3012 0.063 - 0.126: 384 0.126 - 0.189: 12 0.189 - 0.252: 1 0.252 - 0.315: 4 Chirality restraints: 3413 Sorted by residual: chirality pdb=" CA ASP 4 8 " pdb=" N ASP 4 8 " pdb=" C ASP 4 8 " pdb=" CB ASP 4 8 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CA GLU 1 7 " pdb=" N GLU 1 7 " pdb=" C GLU 1 7 " pdb=" CB GLU 1 7 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA ASP L 243 " pdb=" N ASP L 243 " pdb=" C ASP L 243 " pdb=" CB ASP L 243 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.89e+00 ... (remaining 3410 not shown) Planarity restraints: 4217 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2C BPB M 704 " -0.472 2.00e-02 2.50e+03 4.10e-01 2.10e+03 pdb=" C3C BPB M 704 " 0.491 2.00e-02 2.50e+03 pdb=" C4C BPB M 704 " -0.009 2.00e-02 2.50e+03 pdb=" CAC BPB M 704 " 0.428 2.00e-02 2.50e+03 pdb=" CBC BPB M 704 " -0.438 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2C BPB L1003 " 0.024 2.00e-02 2.50e+03 2.89e-01 1.04e+03 pdb=" C3C BPB L1003 " 0.323 2.00e-02 2.50e+03 pdb=" C4C BPB L1003 " -0.081 2.00e-02 2.50e+03 pdb=" CAC BPB L1003 " -0.501 2.00e-02 2.50e+03 pdb=" CBC BPB L1003 " 0.235 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2C BPB L1005 " 0.049 2.00e-02 2.50e+03 2.59e-01 8.37e+02 pdb=" C3C BPB L1005 " -0.446 2.00e-02 2.50e+03 pdb=" C4C BPB L1005 " 0.299 2.00e-02 2.50e+03 pdb=" CAC BPB L1005 " -0.091 2.00e-02 2.50e+03 pdb=" CBC BPB L1005 " 0.190 2.00e-02 2.50e+03 ... (remaining 4214 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 268 2.67 - 3.22: 20365 3.22 - 3.78: 35211 3.78 - 4.34: 49130 4.34 - 4.90: 82599 Nonbonded interactions: 187573 Sorted by model distance: nonbonded pdb=" SD MET C 229 " pdb="FE HEM C 404 " model vdw 2.107 3.360 nonbonded pdb=" O ILE L 189 " pdb=" OG1 THR L 190 " model vdw 2.208 3.040 nonbonded pdb=" SD MET C 106 " pdb="FE HEM C 402 " model vdw 2.226 3.360 nonbonded pdb=" OH TYR S 34 " pdb=" OBD BCL S 102 " model vdw 2.226 3.040 nonbonded pdb=" N GLU C 11 " pdb=" OE1 GLU C 11 " model vdw 2.276 3.120 ... (remaining 187568 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 55 or resid 101)) selection = (chain '2' and (resid 7 through 55 or resid 101)) selection = (chain '4' and (resid 7 through 55 or resid 101)) selection = (chain '6' and (resid 7 through 55 or resid 101)) selection = (chain '8' and (resid 7 through 55 or resid 101)) selection = (chain 'B' and (resid 7 through 55 or resid 101)) selection = (chain 'E' and (resid 7 through 55 or resid 101)) selection = (chain 'G' and (resid 7 through 55 or resid 101)) selection = (chain 'I' and (resid 7 through 55 or resid 101)) selection = (chain 'K' and (resid 7 through 55 or resid 101)) selection = (chain 'O' and (resid 7 through 55 or resid 101)) selection = (chain 'Q' and (resid 7 through 55 or resid 101)) selection = (chain 'S' and (resid 7 through 55 or resid 101)) selection = (chain 'U' and (resid 7 through 55 or resid 101)) selection = (chain 'W' and (resid 7 through 55 or resid 101)) } ncs_group { reference = (chain '1' and resid 4 through 41) selection = (chain '3' and resid 4 through 41) selection = (chain '5' and resid 4 through 41) selection = (chain '7' and resid 4 through 41) selection = (chain '9' and resid 4 through 41) selection = (chain 'A' and resid 4 through 41) selection = (chain 'D' and resid 4 through 41) selection = (chain 'F' and resid 4 through 41) selection = (chain 'H' and resid 4 through 41) selection = (chain 'J' and resid 4 through 41) selection = (chain 'N' and resid 4 through 41) selection = (chain 'P' and resid 4 through 41) selection = (chain 'R' and resid 4 through 41) selection = (chain 'T' and resid 4 through 41) selection = (chain 'V' and resid 4 through 41) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.110 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: 0.000 Extract box with map and model: 0.740 Check model and map are aligned: 0.190 Set scattering table: 0.220 Process input model: 52.870 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 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 24852 Z= 0.716 Angle : 1.019 20.533 34567 Z= 0.402 Chirality : 0.041 0.315 3413 Planarity : 0.011 0.410 4217 Dihedral : 18.338 179.869 8599 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.46 % Favored : 96.50 % Rotamer: Outliers : 0.30 % Allowed : 0.30 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.18), residues: 2257 helix: 3.22 (0.13), residues: 1403 sheet: 1.12 (1.93), residues: 8 loop : -1.99 (0.19), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP M 594 HIS 0.010 0.001 HIS 1 27 PHE 0.028 0.001 PHE M 391 TYR 0.036 0.001 TYR C 21 ARG 0.009 0.000 ARG 2 55 Details of bonding type rmsd hydrogen bonds : bond 0.13531 ( 1174) hydrogen bonds : angle 4.23777 ( 3477) covalent geometry : bond 0.00689 (24792) covalent geometry : angle 1.01922 (34567) Misc. bond : bond 0.13345 ( 60) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 369 time to evaluate : 2.148 Fit side-chains revert: symmetry clash REVERT: B 22 GLN cc_start: 0.7256 (mt0) cc_final: 0.6936 (mt0) REVERT: C 73 GLU cc_start: 0.6342 (pp20) cc_final: 0.5406 (pm20) REVERT: H 16 THR cc_start: 0.8886 (m) cc_final: 0.8678 (m) REVERT: L 308 VAL cc_start: 0.7548 (m) cc_final: 0.7343 (t) REVERT: T 32 SER cc_start: 0.9023 (p) cc_final: 0.8649 (m) REVERT: U 31 LYS cc_start: 0.8129 (mtpt) cc_final: 0.7833 (mtmt) REVERT: W 24 LEU cc_start: 0.8260 (mp) cc_final: 0.8012 (mt) REVERT: X 1 MET cc_start: 0.5758 (mtp) cc_final: 0.4852 (mmp) REVERT: Z 46 THR cc_start: 0.7838 (m) cc_final: 0.7615 (m) outliers start: 6 outliers final: 3 residues processed: 372 average time/residue: 0.3216 time to fit residues: 189.9481 Evaluate side-chains 278 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 275 time to evaluate : 2.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 7 ASN Chi-restraints excluded: chain 6 residue 8 ASP Chi-restraints excluded: chain C residue 145 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 8.9990 chunk 155 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 53 optimal weight: 20.0000 chunk 104 optimal weight: 30.0000 chunk 83 optimal weight: 0.0370 chunk 160 optimal weight: 20.0000 chunk 62 optimal weight: 0.1980 chunk 97 optimal weight: 9.9990 chunk 119 optimal weight: 0.8980 chunk 186 optimal weight: 4.9990 overall best weight: 2.4262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 ASN B 20 ASN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 205 ASN L 264 HIS L 293 ASN O 20 ASN Q 20 ASN U 7 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.109582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.092811 restraints weight = 37561.718| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.25 r_work: 0.2900 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.237 24852 Z= 0.157 Angle : 0.765 12.277 34567 Z= 0.307 Chirality : 0.041 0.199 3413 Planarity : 0.005 0.066 4217 Dihedral : 18.622 179.885 4594 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.72 % Favored : 96.23 % Rotamer: Outliers : 1.98 % Allowed : 6.85 % Favored : 91.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.18), residues: 2257 helix: 3.30 (0.13), residues: 1411 sheet: 0.37 (1.56), residues: 8 loop : -1.87 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP O 50 HIS 0.010 0.001 HIS L 192 PHE 0.015 0.001 PHE C 9 TYR 0.017 0.001 TYR C 21 ARG 0.004 0.000 ARG 2 55 Details of bonding type rmsd hydrogen bonds : bond 0.06187 ( 1174) hydrogen bonds : angle 3.46705 ( 3477) covalent geometry : bond 0.00383 (24792) covalent geometry : angle 0.76514 (34567) Misc. bond : bond 0.04246 ( 60) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 272 time to evaluate : 2.482 Fit side-chains revert: symmetry clash REVERT: A 17 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.7730 (tt) REVERT: C 106 MET cc_start: 0.8792 (mmt) cc_final: 0.7827 (mmt) REVERT: K 27 ASP cc_start: 0.7933 (t0) cc_final: 0.7702 (t0) REVERT: M 553 LYS cc_start: 0.7664 (mmmt) cc_final: 0.7377 (mttm) REVERT: T 32 SER cc_start: 0.8940 (p) cc_final: 0.8610 (m) REVERT: U 31 LYS cc_start: 0.8180 (mtpt) cc_final: 0.7934 (mtmt) REVERT: X 6 MET cc_start: 0.6812 (mtm) cc_final: 0.6463 (mmm) REVERT: X 21 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7514 (mp) outliers start: 39 outliers final: 27 residues processed: 295 average time/residue: 0.3264 time to fit residues: 155.7805 Evaluate side-chains 287 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 258 time to evaluate : 2.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 45 VAL Chi-restraints excluded: chain 4 residue 32 THR Chi-restraints excluded: chain 5 residue 15 SER Chi-restraints excluded: chain 5 residue 24 LEU Chi-restraints excluded: chain 6 residue 41 VAL Chi-restraints excluded: chain 6 residue 45 VAL Chi-restraints excluded: chain 9 residue 21 VAL Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain B residue 8 ASP Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain D residue 6 PHE Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain M residue 539 LEU Chi-restraints excluded: chain R residue 32 SER Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain Y residue 21 VAL Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain Z residue 22 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 21 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 192 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 140 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 165 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 7 ASN 4 13 GLN B 20 ASN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 7 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.108613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.092229 restraints weight = 37723.992| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.34 r_work: 0.2860 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 24852 Z= 0.151 Angle : 0.722 12.858 34567 Z= 0.287 Chirality : 0.040 0.185 3413 Planarity : 0.005 0.056 4217 Dihedral : 17.352 179.860 4590 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.90 % Favored : 96.06 % Rotamer: Outliers : 2.59 % Allowed : 8.73 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.18), residues: 2257 helix: 3.40 (0.13), residues: 1416 sheet: -0.15 (1.20), residues: 8 loop : -1.76 (0.20), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 38 HIS 0.005 0.001 HIS M 487 PHE 0.015 0.001 PHE L 185 TYR 0.009 0.001 TYR C 230 ARG 0.002 0.000 ARG C 247 Details of bonding type rmsd hydrogen bonds : bond 0.06133 ( 1174) hydrogen bonds : angle 3.31518 ( 3477) covalent geometry : bond 0.00368 (24792) covalent geometry : angle 0.72209 (34567) Misc. bond : bond 0.02385 ( 60) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 271 time to evaluate : 2.273 Fit side-chains REVERT: B 51 THR cc_start: 0.8779 (t) cc_final: 0.8447 (p) REVERT: C 89 GLN cc_start: 0.7857 (mt0) cc_final: 0.7425 (mp10) REVERT: C 106 MET cc_start: 0.8855 (mmt) cc_final: 0.7886 (mmt) REVERT: M 553 LYS cc_start: 0.7708 (mmmt) cc_final: 0.7329 (mttm) REVERT: S 9 LEU cc_start: 0.7501 (mt) cc_final: 0.7287 (mt) REVERT: U 31 LYS cc_start: 0.8176 (mtpt) cc_final: 0.7956 (mtmt) REVERT: W 50 TRP cc_start: 0.7983 (t60) cc_final: 0.7683 (t60) REVERT: X 6 MET cc_start: 0.6777 (mtm) cc_final: 0.6568 (mmm) REVERT: X 17 THR cc_start: 0.8147 (OUTLIER) cc_final: 0.7828 (t) REVERT: X 21 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7562 (mp) REVERT: Z 22 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.7056 (mp) outliers start: 51 outliers final: 40 residues processed: 303 average time/residue: 0.3229 time to fit residues: 158.2728 Evaluate side-chains 300 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 257 time to evaluate : 2.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 45 VAL Chi-restraints excluded: chain 2 residue 10 VAL Chi-restraints excluded: chain 4 residue 7 ASN Chi-restraints excluded: chain 4 residue 32 THR Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain 5 residue 15 SER Chi-restraints excluded: chain 5 residue 24 LEU Chi-restraints excluded: chain 6 residue 41 VAL Chi-restraints excluded: chain 6 residue 45 VAL Chi-restraints excluded: chain 7 residue 29 VAL Chi-restraints excluded: chain 8 residue 27 ASP Chi-restraints excluded: chain 9 residue 21 VAL Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain B residue 8 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain D residue 6 PHE Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain M residue 539 LEU Chi-restraints excluded: chain M residue 561 MET Chi-restraints excluded: chain M residue 609 LEU Chi-restraints excluded: chain N residue 17 LEU Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain R residue 32 SER Chi-restraints excluded: chain U residue 7 ASN Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain X residue 17 THR Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain Y residue 21 VAL Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain Z residue 22 LEU Chi-restraints excluded: chain Z residue 50 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 71 optimal weight: 0.8980 chunk 5 optimal weight: 10.0000 chunk 192 optimal weight: 20.0000 chunk 99 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 116 optimal weight: 3.9990 chunk 104 optimal weight: 0.5980 chunk 34 optimal weight: 9.9990 chunk 158 optimal weight: 2.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 13 GLN B 19 ASN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 198 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.107826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.091498 restraints weight = 37787.961| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 1.34 r_work: 0.2842 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 24852 Z= 0.157 Angle : 0.730 12.687 34567 Z= 0.290 Chirality : 0.040 0.183 3413 Planarity : 0.005 0.052 4217 Dihedral : 17.171 179.870 4590 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.77 % Favored : 96.19 % Rotamer: Outliers : 2.54 % Allowed : 10.40 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.18), residues: 2257 helix: 3.38 (0.13), residues: 1415 sheet: -0.22 (1.21), residues: 8 loop : -1.74 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 594 HIS 0.005 0.001 HIS C 122 PHE 0.015 0.001 PHE L 185 TYR 0.011 0.001 TYR M 424 ARG 0.005 0.000 ARG V 40 Details of bonding type rmsd hydrogen bonds : bond 0.06275 ( 1174) hydrogen bonds : angle 3.32581 ( 3477) covalent geometry : bond 0.00389 (24792) covalent geometry : angle 0.72986 (34567) Misc. bond : bond 0.02032 ( 60) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 264 time to evaluate : 2.189 Fit side-chains REVERT: C 89 GLN cc_start: 0.7973 (mt0) cc_final: 0.7471 (mp10) REVERT: C 106 MET cc_start: 0.8827 (mmt) cc_final: 0.7900 (mmt) REVERT: M 553 LYS cc_start: 0.7721 (mmmt) cc_final: 0.7409 (mttm) REVERT: S 9 LEU cc_start: 0.7449 (mt) cc_final: 0.7246 (mt) REVERT: U 31 LYS cc_start: 0.8187 (mtpt) cc_final: 0.7969 (mtmt) REVERT: X 6 MET cc_start: 0.6790 (mtm) cc_final: 0.6587 (mmm) REVERT: X 17 THR cc_start: 0.8212 (t) cc_final: 0.7911 (t) REVERT: X 21 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7528 (mp) REVERT: Z 22 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.7196 (mp) outliers start: 50 outliers final: 40 residues processed: 292 average time/residue: 0.3178 time to fit residues: 149.5950 Evaluate side-chains 298 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 256 time to evaluate : 2.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 45 VAL Chi-restraints excluded: chain 2 residue 10 VAL Chi-restraints excluded: chain 4 residue 32 THR Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain 5 residue 15 SER Chi-restraints excluded: chain 5 residue 24 LEU Chi-restraints excluded: chain 6 residue 41 VAL Chi-restraints excluded: chain 6 residue 45 VAL Chi-restraints excluded: chain 9 residue 21 VAL Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain B residue 8 ASP Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain L residue 14 GLU Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain M residue 423 GLU Chi-restraints excluded: chain M residue 539 LEU Chi-restraints excluded: chain M residue 561 MET Chi-restraints excluded: chain M residue 609 LEU Chi-restraints excluded: chain N residue 17 LEU Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain R residue 32 SER Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain Y residue 21 VAL Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain Z residue 22 LEU Chi-restraints excluded: chain Z residue 50 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 45 optimal weight: 8.9990 chunk 159 optimal weight: 8.9990 chunk 151 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 154 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 chunk 126 optimal weight: 7.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 13 GLN B 20 ASN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 414 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.107295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.091110 restraints weight = 37492.052| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.34 r_work: 0.2840 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.127 24852 Z= 0.159 Angle : 0.727 12.656 34567 Z= 0.289 Chirality : 0.040 0.183 3413 Planarity : 0.005 0.052 4217 Dihedral : 16.966 179.882 4590 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.79 % Allowed : 10.96 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.18), residues: 2257 helix: 3.37 (0.13), residues: 1417 sheet: 0.10 (1.38), residues: 8 loop : -1.70 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP V 38 HIS 0.005 0.001 HIS C 122 PHE 0.015 0.001 PHE L 185 TYR 0.011 0.001 TYR M 521 ARG 0.002 0.000 ARG 1 40 Details of bonding type rmsd hydrogen bonds : bond 0.06352 ( 1174) hydrogen bonds : angle 3.33700 ( 3477) covalent geometry : bond 0.00393 (24792) covalent geometry : angle 0.72676 (34567) Misc. bond : bond 0.01969 ( 60) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 263 time to evaluate : 2.307 Fit side-chains REVERT: C 106 MET cc_start: 0.8829 (mmt) cc_final: 0.7876 (mmt) REVERT: E 13 GLN cc_start: 0.6992 (tp40) cc_final: 0.6667 (tp40) REVERT: M 360 TRP cc_start: 0.8441 (p-90) cc_final: 0.8108 (p-90) REVERT: M 519 PHE cc_start: 0.9145 (OUTLIER) cc_final: 0.8935 (t80) REVERT: M 553 LYS cc_start: 0.7688 (mmmt) cc_final: 0.7378 (mttm) REVERT: U 15 LYS cc_start: 0.8247 (tppt) cc_final: 0.7894 (mmtp) REVERT: U 31 LYS cc_start: 0.8193 (mtpt) cc_final: 0.7980 (mtmt) REVERT: X 17 THR cc_start: 0.8261 (t) cc_final: 0.7982 (t) REVERT: X 21 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7569 (mp) REVERT: Z 22 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7266 (mp) outliers start: 55 outliers final: 42 residues processed: 294 average time/residue: 0.3303 time to fit residues: 156.1675 Evaluate side-chains 301 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 256 time to evaluate : 2.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 45 VAL Chi-restraints excluded: chain 2 residue 10 VAL Chi-restraints excluded: chain 4 residue 32 THR Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain 5 residue 15 SER Chi-restraints excluded: chain 5 residue 24 LEU Chi-restraints excluded: chain 6 residue 41 VAL Chi-restraints excluded: chain 6 residue 45 VAL Chi-restraints excluded: chain 8 residue 27 ASP Chi-restraints excluded: chain 9 residue 21 VAL Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain B residue 8 ASP Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain L residue 14 GLU Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain M residue 423 GLU Chi-restraints excluded: chain M residue 519 PHE Chi-restraints excluded: chain M residue 539 LEU Chi-restraints excluded: chain M residue 561 MET Chi-restraints excluded: chain M residue 609 LEU Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain Q residue 10 VAL Chi-restraints excluded: chain R residue 32 SER Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain Y residue 21 VAL Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain Z residue 22 LEU Chi-restraints excluded: chain Z residue 46 THR Chi-restraints excluded: chain Z residue 50 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 13 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 161 optimal weight: 1.9990 chunk 102 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 119 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 187 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 13 GLN C 56 ASN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 20 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.107784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.091532 restraints weight = 37395.079| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.38 r_work: 0.2843 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 24852 Z= 0.146 Angle : 0.703 12.149 34567 Z= 0.280 Chirality : 0.040 0.177 3413 Planarity : 0.005 0.051 4217 Dihedral : 16.743 179.874 4590 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.44 % Allowed : 12.02 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.18), residues: 2257 helix: 3.42 (0.13), residues: 1416 sheet: 0.20 (1.48), residues: 8 loop : -1.69 (0.20), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 594 HIS 0.004 0.001 HIS C 122 PHE 0.014 0.001 PHE L 185 TYR 0.010 0.001 TYR M 424 ARG 0.002 0.000 ARG 1 40 Details of bonding type rmsd hydrogen bonds : bond 0.06047 ( 1174) hydrogen bonds : angle 3.29716 ( 3477) covalent geometry : bond 0.00354 (24792) covalent geometry : angle 0.70314 (34567) Misc. bond : bond 0.01775 ( 60) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 257 time to evaluate : 2.312 Fit side-chains REVERT: C 106 MET cc_start: 0.8818 (mmt) cc_final: 0.7870 (mmt) REVERT: E 13 GLN cc_start: 0.7085 (tp40) cc_final: 0.6791 (tp40) REVERT: M 519 PHE cc_start: 0.9136 (OUTLIER) cc_final: 0.8919 (t80) REVERT: M 553 LYS cc_start: 0.7692 (mmmt) cc_final: 0.7400 (mttm) REVERT: U 31 LYS cc_start: 0.8213 (mtpt) cc_final: 0.8000 (mtmt) REVERT: X 17 THR cc_start: 0.8216 (t) cc_final: 0.7945 (t) REVERT: X 21 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7534 (mp) outliers start: 48 outliers final: 42 residues processed: 284 average time/residue: 0.3287 time to fit residues: 150.7312 Evaluate side-chains 301 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 257 time to evaluate : 2.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 45 VAL Chi-restraints excluded: chain 4 residue 32 THR Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain 5 residue 15 SER Chi-restraints excluded: chain 5 residue 24 LEU Chi-restraints excluded: chain 6 residue 41 VAL Chi-restraints excluded: chain 6 residue 45 VAL Chi-restraints excluded: chain 9 residue 21 VAL Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain B residue 8 ASP Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain L residue 14 GLU Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain M residue 423 GLU Chi-restraints excluded: chain M residue 519 PHE Chi-restraints excluded: chain M residue 539 LEU Chi-restraints excluded: chain M residue 561 MET Chi-restraints excluded: chain M residue 609 LEU Chi-restraints excluded: chain N residue 17 LEU Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain Q residue 10 VAL Chi-restraints excluded: chain R residue 32 SER Chi-restraints excluded: chain S residue 20 ASN Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain Y residue 21 VAL Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain Z residue 46 THR Chi-restraints excluded: chain Z residue 50 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 197 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 70 optimal weight: 20.0000 chunk 125 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 109 optimal weight: 8.9990 chunk 151 optimal weight: 0.9990 chunk 160 optimal weight: 3.9990 chunk 137 optimal weight: 8.9990 chunk 130 optimal weight: 0.0370 overall best weight: 3.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 13 GLN B 20 ASN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.106839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.090468 restraints weight = 37716.533| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.40 r_work: 0.2822 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 24852 Z= 0.165 Angle : 0.733 12.843 34567 Z= 0.293 Chirality : 0.041 0.184 3413 Planarity : 0.005 0.049 4217 Dihedral : 16.746 179.847 4590 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.38 % Allowed : 12.38 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.18), residues: 2257 helix: 3.33 (0.13), residues: 1417 sheet: 0.28 (1.52), residues: 8 loop : -1.71 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP V 38 HIS 0.005 0.001 HIS C 122 PHE 0.015 0.001 PHE L 185 TYR 0.014 0.001 TYR M 424 ARG 0.003 0.000 ARG V 40 Details of bonding type rmsd hydrogen bonds : bond 0.06472 ( 1174) hydrogen bonds : angle 3.35658 ( 3477) covalent geometry : bond 0.00408 (24792) covalent geometry : angle 0.73260 (34567) Misc. bond : bond 0.01768 ( 60) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 260 time to evaluate : 2.161 Fit side-chains REVERT: C 89 GLN cc_start: 0.8065 (mt0) cc_final: 0.7640 (mp10) REVERT: C 106 MET cc_start: 0.8829 (mmt) cc_final: 0.7847 (mmt) REVERT: C 145 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.7643 (mmt) REVERT: E 13 GLN cc_start: 0.7208 (tp40) cc_final: 0.6920 (tp40) REVERT: G 7 ASN cc_start: 0.6129 (p0) cc_final: 0.5713 (p0) REVERT: M 360 TRP cc_start: 0.8427 (p-90) cc_final: 0.8028 (p-90) REVERT: M 519 PHE cc_start: 0.9148 (OUTLIER) cc_final: 0.8941 (t80) REVERT: M 553 LYS cc_start: 0.7727 (mmmt) cc_final: 0.7402 (mttm) REVERT: U 31 LYS cc_start: 0.8211 (mtpt) cc_final: 0.8001 (mtmt) REVERT: X 6 MET cc_start: 0.7165 (mmm) cc_final: 0.6952 (mmt) REVERT: X 17 THR cc_start: 0.8182 (t) cc_final: 0.7914 (t) REVERT: X 21 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7575 (mp) outliers start: 47 outliers final: 41 residues processed: 285 average time/residue: 0.3176 time to fit residues: 146.6845 Evaluate side-chains 298 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 254 time to evaluate : 2.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 45 VAL Chi-restraints excluded: chain 4 residue 32 THR Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain 5 residue 15 SER Chi-restraints excluded: chain 5 residue 24 LEU Chi-restraints excluded: chain 6 residue 41 VAL Chi-restraints excluded: chain 6 residue 45 VAL Chi-restraints excluded: chain 8 residue 27 ASP Chi-restraints excluded: chain 9 residue 21 VAL Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain B residue 8 ASP Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain L residue 14 GLU Chi-restraints excluded: chain M residue 423 GLU Chi-restraints excluded: chain M residue 519 PHE Chi-restraints excluded: chain M residue 539 LEU Chi-restraints excluded: chain M residue 561 MET Chi-restraints excluded: chain M residue 609 LEU Chi-restraints excluded: chain N residue 17 LEU Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain Q residue 10 VAL Chi-restraints excluded: chain R residue 32 SER Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain Y residue 21 VAL Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain Z residue 46 THR Chi-restraints excluded: chain Z residue 50 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 110 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 127 optimal weight: 5.9990 chunk 163 optimal weight: 10.0000 chunk 169 optimal weight: 3.9990 chunk 154 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 40 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: 4 13 GLN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 GLN S 20 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.105199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.088794 restraints weight = 37615.230| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 1.40 r_work: 0.2794 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.123 24852 Z= 0.193 Angle : 0.783 13.891 34567 Z= 0.313 Chirality : 0.043 0.222 3413 Planarity : 0.005 0.051 4217 Dihedral : 16.966 179.831 4590 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.23 % Allowed : 13.29 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.18), residues: 2257 helix: 3.18 (0.13), residues: 1416 sheet: 0.39 (1.64), residues: 8 loop : -1.78 (0.21), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP V 38 HIS 0.006 0.001 HIS L 183 PHE 0.016 0.002 PHE L 185 TYR 0.018 0.002 TYR M 424 ARG 0.002 0.000 ARG B 55 Details of bonding type rmsd hydrogen bonds : bond 0.07225 ( 1174) hydrogen bonds : angle 3.47665 ( 3477) covalent geometry : bond 0.00478 (24792) covalent geometry : angle 0.78278 (34567) Misc. bond : bond 0.01857 ( 60) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 265 time to evaluate : 2.371 Fit side-chains REVERT: C 73 GLU cc_start: 0.6760 (pp20) cc_final: 0.6309 (pt0) REVERT: C 89 GLN cc_start: 0.8047 (mt0) cc_final: 0.7643 (mp10) REVERT: C 106 MET cc_start: 0.8827 (mmt) cc_final: 0.7827 (mmt) REVERT: G 7 ASN cc_start: 0.6478 (p0) cc_final: 0.6049 (p0) REVERT: L 8 LEU cc_start: 0.7869 (mt) cc_final: 0.7666 (mt) REVERT: M 553 LYS cc_start: 0.7760 (mmmt) cc_final: 0.7435 (mttm) REVERT: U 31 LYS cc_start: 0.8204 (mtpt) cc_final: 0.8001 (mtmt) outliers start: 44 outliers final: 33 residues processed: 293 average time/residue: 0.3163 time to fit residues: 150.7336 Evaluate side-chains 291 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 258 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 45 VAL Chi-restraints excluded: chain 4 residue 32 THR Chi-restraints excluded: chain 5 residue 15 SER Chi-restraints excluded: chain 6 residue 41 VAL Chi-restraints excluded: chain 6 residue 45 VAL Chi-restraints excluded: chain 9 residue 21 VAL Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain B residue 8 ASP Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain L residue 14 GLU Chi-restraints excluded: chain M residue 423 GLU Chi-restraints excluded: chain M residue 539 LEU Chi-restraints excluded: chain M residue 561 MET Chi-restraints excluded: chain M residue 609 LEU Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain Q residue 10 VAL Chi-restraints excluded: chain R residue 32 SER Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain Y residue 21 VAL Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain Z residue 46 THR Chi-restraints excluded: chain Z residue 50 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 15 optimal weight: 1.9990 chunk 160 optimal weight: 0.1980 chunk 142 optimal weight: 9.9990 chunk 189 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 178 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 120 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 196 optimal weight: 0.1980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 13 GLN B 13 GLN B 20 ASN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.109752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.093829 restraints weight = 37451.817| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.37 r_work: 0.2880 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 24852 Z= 0.116 Angle : 0.656 10.917 34567 Z= 0.264 Chirality : 0.038 0.146 3413 Planarity : 0.004 0.047 4217 Dihedral : 16.297 179.970 4587 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.22 % Allowed : 14.56 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.18), residues: 2257 helix: 3.61 (0.13), residues: 1414 sheet: 0.20 (1.52), residues: 8 loop : -1.68 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 594 HIS 0.003 0.001 HIS L 183 PHE 0.011 0.001 PHE Y 17 TYR 0.009 0.001 TYR C 230 ARG 0.002 0.000 ARG L 53 Details of bonding type rmsd hydrogen bonds : bond 0.05206 ( 1174) hydrogen bonds : angle 3.20638 ( 3477) covalent geometry : bond 0.00267 (24792) covalent geometry : angle 0.65555 (34567) Misc. bond : bond 0.01487 ( 60) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 261 time to evaluate : 2.279 Fit side-chains REVERT: 1 20 LEU cc_start: 0.8343 (tp) cc_final: 0.7721 (mt) REVERT: C 73 GLU cc_start: 0.6713 (pp20) cc_final: 0.6308 (pm20) REVERT: C 89 GLN cc_start: 0.8028 (mt0) cc_final: 0.7628 (mp10) REVERT: C 106 MET cc_start: 0.8754 (mmt) cc_final: 0.7887 (mmt) REVERT: C 247 ARG cc_start: 0.9094 (OUTLIER) cc_final: 0.7128 (ptm160) REVERT: G 7 ASN cc_start: 0.6342 (p0) cc_final: 0.5998 (p0) REVERT: L 243 ASP cc_start: 0.7649 (t0) cc_final: 0.7271 (t70) REVERT: M 553 LYS cc_start: 0.7608 (mmmt) cc_final: 0.7345 (mttm) REVERT: U 31 LYS cc_start: 0.8189 (mtpt) cc_final: 0.7971 (mtmt) outliers start: 24 outliers final: 22 residues processed: 274 average time/residue: 0.3279 time to fit residues: 146.5186 Evaluate side-chains 274 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 251 time to evaluate : 2.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 45 VAL Chi-restraints excluded: chain 4 residue 32 THR Chi-restraints excluded: chain 5 residue 24 LEU Chi-restraints excluded: chain 6 residue 41 VAL Chi-restraints excluded: chain 8 residue 27 ASP Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain B residue 8 ASP Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain L residue 14 GLU Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain M residue 539 LEU Chi-restraints excluded: chain M residue 561 MET Chi-restraints excluded: chain N residue 17 LEU Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain R residue 32 SER Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain Z residue 46 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 73 optimal weight: 7.9990 chunk 154 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 164 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 195 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 13 GLN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 19 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.106573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.090231 restraints weight = 37806.207| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.40 r_work: 0.2818 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 24852 Z= 0.175 Angle : 0.739 12.931 34567 Z= 0.297 Chirality : 0.041 0.187 3413 Planarity : 0.005 0.052 4217 Dihedral : 16.499 179.822 4587 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.27 % Allowed : 14.71 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.18), residues: 2257 helix: 3.34 (0.13), residues: 1418 sheet: 0.31 (1.57), residues: 8 loop : -1.72 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP V 38 HIS 0.005 0.001 HIS C 122 PHE 0.016 0.001 PHE L 185 TYR 0.016 0.001 TYR M 424 ARG 0.002 0.000 ARG J 9 Details of bonding type rmsd hydrogen bonds : bond 0.06498 ( 1174) hydrogen bonds : angle 3.35764 ( 3477) covalent geometry : bond 0.00438 (24792) covalent geometry : angle 0.73860 (34567) Misc. bond : bond 0.01619 ( 60) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 252 time to evaluate : 2.405 Fit side-chains REVERT: 7 22 MET cc_start: 0.8588 (tpp) cc_final: 0.8161 (tpp) REVERT: C 73 GLU cc_start: 0.6772 (pp20) cc_final: 0.6363 (pm20) REVERT: C 106 MET cc_start: 0.8794 (mmt) cc_final: 0.7834 (mmt) REVERT: C 247 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.7320 (ptm160) REVERT: G 7 ASN cc_start: 0.6352 (p0) cc_final: 0.5999 (p0) REVERT: L 8 LEU cc_start: 0.7860 (mt) cc_final: 0.7649 (mt) REVERT: L 243 ASP cc_start: 0.7698 (t0) cc_final: 0.7326 (t70) REVERT: M 553 LYS cc_start: 0.7670 (mmmt) cc_final: 0.7372 (mttm) REVERT: U 31 LYS cc_start: 0.8207 (mtpt) cc_final: 0.7998 (mtmt) outliers start: 25 outliers final: 23 residues processed: 266 average time/residue: 0.3219 time to fit residues: 138.3536 Evaluate side-chains 275 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 251 time to evaluate : 2.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 45 VAL Chi-restraints excluded: chain 4 residue 32 THR Chi-restraints excluded: chain 5 residue 15 SER Chi-restraints excluded: chain 5 residue 24 LEU Chi-restraints excluded: chain 6 residue 41 VAL Chi-restraints excluded: chain 8 residue 27 ASP Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain B residue 8 ASP Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain L residue 14 GLU Chi-restraints excluded: chain M residue 539 LEU Chi-restraints excluded: chain M residue 561 MET Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain R residue 32 SER Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain Z residue 46 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 185 optimal weight: 10.0000 chunk 84 optimal weight: 0.0870 chunk 146 optimal weight: 0.0470 chunk 65 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 202 optimal weight: 0.3980 chunk 51 optimal weight: 30.0000 chunk 177 optimal weight: 10.0000 chunk 196 optimal weight: 1.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 13 GLN B 20 ASN C 154 GLN U 19 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.111973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.095828 restraints weight = 37358.124| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.44 r_work: 0.2909 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 24852 Z= 0.106 Angle : 0.629 10.542 34567 Z= 0.253 Chirality : 0.037 0.146 3413 Planarity : 0.004 0.047 4217 Dihedral : 15.925 179.962 4587 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.07 % Allowed : 14.76 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.86 (0.18), residues: 2257 helix: 3.76 (0.13), residues: 1409 sheet: 0.28 (1.44), residues: 8 loop : -1.64 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 594 HIS 0.003 0.001 HIS M 589 PHE 0.011 0.001 PHE Y 17 TYR 0.011 0.001 TYR C 230 ARG 0.002 0.000 ARG M 344 Details of bonding type rmsd hydrogen bonds : bond 0.04463 ( 1174) hydrogen bonds : angle 3.11052 ( 3477) covalent geometry : bond 0.00244 (24792) covalent geometry : angle 0.62889 (34567) Misc. bond : bond 0.01542 ( 60) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11807.58 seconds wall clock time: 204 minutes 33.96 seconds (12273.96 seconds total)