Starting phenix.real_space_refine on Thu Apr 11 20:13:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5p_35989/04_2024/8j5p_35989_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5p_35989/04_2024/8j5p_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5p_35989/04_2024/8j5p_35989.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5p_35989/04_2024/8j5p_35989.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5p_35989/04_2024/8j5p_35989_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5p_35989/04_2024/8j5p_35989_updated.pdb" } 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 Residue "1 ARG 4": "NH1" <-> "NH2" Residue "1 GLU 7": "OE1" <-> "OE2" Residue "3 GLU 7": "OE1" <-> "OE2" Residue "5 GLU 7": "OE1" <-> "OE2" Residue "7 GLU 7": "OE1" <-> "OE2" Residue "9 GLU 7": "OE1" <-> "OE2" Residue "C GLU 11": "OE1" <-> "OE2" Residue "C GLU 183": "OE1" <-> "OE2" Residue "D GLU 7": "OE1" <-> "OE2" Residue "J GLU 7": "OE1" <-> "OE2" Residue "L ARG 6": "NH1" <-> "NH2" Residue "L GLU 95": "OE1" <-> "OE2" Residue "L GLU 260": "OE1" <-> "OE2" Residue "M GLU 341": "OE1" <-> "OE2" Residue "M GLU 348": "OE1" <-> "OE2" Residue "M GLU 411": "OE1" <-> "OE2" Residue "M TYR 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 557": "OE1" <-> "OE2" Residue "M GLU 560": "OE1" <-> "OE2" Residue "M GLU 622": "OE1" <-> "OE2" Residue "T GLU 7": "OE1" <-> "OE2" Residue "V GLU 7": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 12.36, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 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: 10.44 Conformation dependent library (CDL) restraints added in 3.4 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... running ksdssp... Secondary structure from input PDB file: 77 helices and 2 sheets defined 60.8% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.72 Creating SS restraints... Processing helix chain '0' and resid 21 through 50 removed outlier: 3.902A pdb=" N VAL 0 25 " --> pdb=" O ALA 0 21 " (cutoff:3.500A) Processing helix chain '1' and resid 7 through 33 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) Processing helix chain '2' and resid 22 through 50 Processing helix chain '3' and resid 8 through 33 Processing helix chain '4' and resid 22 through 50 Processing helix chain '5' and resid 8 through 33 Processing helix chain '6' and resid 22 through 50 Processing helix chain '7' and resid 8 through 33 Processing helix chain '8' and resid 22 through 50 Processing helix chain '9' and resid 8 through 32 Processing helix chain 'A' and resid 8 through 33 Processing helix chain 'B' and resid 20 through 50 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 10 through 13 No H-bonds generated for 'chain 'C' and resid 10 through 13' Processing helix chain 'C' and resid 16 through 46 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 74 through 84 Processing helix chain 'C' and resid 99 through 108 Processing helix chain 'C' and resid 110 through 114 Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 136 through 155 Processing helix chain 'C' and resid 171 through 174 No H-bonds generated for 'chain 'C' and resid 171 through 174' Processing helix chain 'C' and resid 219 through 236 Processing helix chain 'C' and resid 256 through 273 Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 293 through 296 No H-bonds generated for 'chain 'C' and resid 293 through 296' Processing helix chain 'D' and resid 8 through 32 Processing helix chain 'E' and resid 20 through 50 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 8 through 32 Processing helix chain 'G' and resid 22 through 50 Processing helix chain 'H' and resid 8 through 33 Processing helix chain 'I' and resid 20 through 50 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 8 through 33 Processing helix chain 'K' and resid 20 through 50 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 36 through 43 Processing helix chain 'L' and resid 50 through 54 Processing helix chain 'L' and resid 71 through 92 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 110 through 112 No H-bonds generated for 'chain 'L' and resid 110 through 112' Processing helix chain 'L' and resid 123 through 150 Processing helix chain 'L' and resid 155 through 171 removed outlier: 3.623A pdb=" N LEU L 170 " --> pdb=" O SER L 166 " (cutoff:3.500A) Processing helix chain 'L' and resid 173 through 178 Processing helix chain 'L' and resid 192 through 202 Processing helix chain 'L' and resid 206 through 208 No H-bonds generated for 'chain 'L' and resid 206 through 208' Processing helix chain 'L' and resid 210 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 245 through 252 Processing helix chain 'L' and resid 262 through 287 removed outlier: 4.030A pdb=" N VAL L 275 " --> pdb=" O GLY L 271 " (cutoff:3.500A) Processing helix chain 'L' and resid 292 through 301 removed outlier: 4.119A pdb=" N TRP L 296 " --> pdb=" O TRP L 292 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLY L 297 " --> pdb=" O ASN L 293 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N PHE L 298 " --> pdb=" O ALA L 294 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N TRP L 299 " --> pdb=" O PHE L 295 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ASP L 300 " --> pdb=" O TRP L 296 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LYS L 301 " --> pdb=" O GLY L 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 292 through 301' Processing helix chain 'L' and resid 311 through 313 No H-bonds generated for 'chain 'L' and resid 311 through 313' Processing helix chain 'M' and resid 338 through 343 removed outlier: 3.531A pdb=" N GLU M 342 " --> pdb=" O LEU M 338 " (cutoff:3.500A) Processing helix chain 'M' and resid 360 through 365 Processing helix chain 'M' and resid 381 through 401 removed outlier: 3.555A pdb=" N GLN M 400 " --> pdb=" O ASP M 396 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL M 401 " --> pdb=" O TYR M 397 " (cutoff:3.500A) Processing helix chain 'M' and resid 405 through 410 Processing helix chain 'M' and resid 412 through 414 No H-bonds generated for 'chain 'M' and resid 412 through 414' Processing helix chain 'M' and resid 436 through 463 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) Processing helix chain 'M' and resid 468 through 484 Processing helix chain 'M' and resid 494 through 496 No H-bonds generated for 'chain 'M' and resid 494 through 496' Processing helix chain 'M' and resid 504 through 515 Processing helix chain 'M' and resid 519 through 521 No H-bonds generated for 'chain 'M' and resid 519 through 521' Processing helix chain 'M' and resid 523 through 548 Processing helix chain 'M' and resid 550 through 552 No H-bonds generated for 'chain 'M' and resid 550 through 552' Processing helix chain 'M' and resid 557 through 560 No H-bonds generated for 'chain 'M' and resid 557 through 560' Processing helix chain 'M' and resid 566 through 579 removed outlier: 3.508A pdb=" N MET M 579 " --> pdb=" O TRP M 575 " (cutoff:3.500A) Processing helix chain 'M' and resid 587 through 612 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) Processing helix chain 'M' and resid 617 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 635 through 638 Processing helix chain 'N' and resid 8 through 32 Processing helix chain 'O' and resid 22 through 50 Processing helix chain 'P' and resid 8 through 33 Processing helix chain 'Q' and resid 21 through 50 removed outlier: 4.009A pdb=" N VAL Q 25 " --> pdb=" O ALA Q 21 " (cutoff:3.500A) Processing helix chain 'R' and resid 8 through 32 Processing helix chain 'S' and resid 20 through 50 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 8 through 33 Processing helix chain 'U' and resid 22 through 50 Processing helix chain 'V' and resid 8 through 32 Processing helix chain 'W' and resid 20 through 50 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 24 Processing helix chain 'Y' and resid 2 through 30 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 Processing helix chain 'Z' and resid 17 through 46 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 54 through 57 No H-bonds generated for 'chain 'Z' and resid 54 through 57' Processing sheet with id= A, 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= B, 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) 1075 hydrogen bonds defined for protein. 3219 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: 5.93 Time building geometry restraints manager: 11.30 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: 80.29 - 100.02: 211 100.02 - 119.75: 21396 119.75 - 139.48: 12805 139.48 - 159.22: 114 159.22 - 178.95: 41 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: 270 2.67 - 3.22: 20420 3.22 - 3.78: 35308 3.78 - 4.34: 49325 4.34 - 4.90: 82646 Nonbonded interactions: 187969 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 2.440 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 2.440 nonbonded pdb=" N GLU C 11 " pdb=" OE1 GLU C 11 " model vdw 2.276 2.520 ... (remaining 187964 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 0.010 Normalize map: mean=0, sd=1: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.420 Check model and map are aligned: 0.350 Set scattering table: 0.250 Process input model: 61.520 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.480 ------------------------------------------------------------------------------- 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 : 0.007 0.303 24792 Z= 0.345 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 *********************** 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 fitting. rotamer outliers: 6 poor density : 369 time to evaluate : 2.297 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: 0.3449 time to fit residues: 203.9687 Evaluate side-chains 278 residues out of total 1971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 275 time to evaluate : 2.324 ------------------------------------------------------------------------------- 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: 4.9990 chunk 155 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 104 optimal weight: 20.0000 chunk 83 optimal weight: 0.3980 chunk 160 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 119 optimal weight: 7.9990 chunk 186 optimal weight: 6.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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** K 7 ASN L 198 ASN L 205 ASN L 264 HIS L 293 ASN M 493 ASN O 20 ASN Q 20 ASN R 37 ASN U 7 ASN W 7 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 24792 Z= 0.214 Angle : 0.754 12.022 34567 Z= 0.300 Chirality : 0.040 0.200 3413 Planarity : 0.005 0.065 4217 Dihedral : 18.606 179.887 4594 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.72 % Favored : 96.23 % Rotamer: Outliers : 2.38 % Allowed : 7.36 % Favored : 90.26 % 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: 2.20 (0.18), residues: 2257 helix: 3.25 (0.13), residues: 1403 sheet: 0.32 (1.57), residues: 8 loop : -1.87 (0.19), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP O 50 HIS 0.007 0.001 HIS L 192 PHE 0.014 0.001 PHE L 185 TYR 0.016 0.001 TYR C 21 ARG 0.004 0.000 ARG 2 55 *********************** 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 314 residues out of total 1971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 267 time to evaluate : 2.464 Fit side-chains revert: symmetry clash REVERT: A 7 GLU cc_start: 0.7446 (mt-10) cc_final: 0.7168 (mt-10) REVERT: A 17 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.7829 (tt) REVERT: C 106 MET cc_start: 0.8745 (mmt) cc_final: 0.8011 (mmt) REVERT: T 32 SER cc_start: 0.8919 (p) cc_final: 0.8620 (m) REVERT: U 31 LYS cc_start: 0.8165 (mtpt) cc_final: 0.7873 (mtmt) REVERT: W 24 LEU cc_start: 0.8247 (mp) cc_final: 0.8010 (mt) REVERT: X 6 MET cc_start: 0.6888 (mtm) cc_final: 0.6563 (mmm) REVERT: X 21 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7722 (mp) outliers start: 47 outliers final: 30 residues processed: 298 average time/residue: 0.3340 time to fit residues: 162.0832 Evaluate side-chains 286 residues out of total 1971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 254 time to evaluate : 2.333 ------------------------------------------------------------------------------- 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 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 G residue 24 LEU Chi-restraints excluded: chain H residue 32 SER 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 493 ASN 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 16 THR 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 103 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 154 optimal weight: 8.9990 chunk 126 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 186 optimal weight: 9.9990 chunk 201 optimal weight: 0.9990 chunk 166 optimal weight: 10.0000 chunk 184 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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** ** M 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 7 ASN W 7 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 24792 Z= 0.219 Angle : 0.728 12.968 34567 Z= 0.288 Chirality : 0.040 0.184 3413 Planarity : 0.005 0.055 4217 Dihedral : 17.544 179.910 4590 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.85 % Favored : 96.10 % Rotamer: Outliers : 2.74 % Allowed : 9.13 % Favored : 88.13 % 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: 2.30 (0.18), residues: 2257 helix: 3.33 (0.13), residues: 1402 sheet: 0.08 (1.33), residues: 8 loop : -1.82 (0.20), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP O 50 HIS 0.006 0.001 HIS L 192 PHE 0.015 0.001 PHE L 185 TYR 0.009 0.001 TYR C 230 ARG 0.003 0.000 ARG 2 55 *********************** 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 317 residues out of total 1971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 263 time to evaluate : 2.443 Fit side-chains REVERT: C 21 TYR cc_start: 0.6635 (m-80) cc_final: 0.6276 (m-80) REVERT: C 106 MET cc_start: 0.8824 (mmt) cc_final: 0.8056 (mmt) REVERT: S 9 LEU cc_start: 0.7521 (mt) cc_final: 0.7295 (mt) REVERT: U 31 LYS cc_start: 0.8189 (mtpt) cc_final: 0.7912 (mtmt) REVERT: X 17 THR cc_start: 0.8325 (OUTLIER) cc_final: 0.8030 (t) REVERT: X 21 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7752 (mp) REVERT: Z 22 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.6985 (mp) outliers start: 54 outliers final: 41 residues processed: 299 average time/residue: 0.3381 time to fit residues: 164.0106 Evaluate side-chains 300 residues out of total 1971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 256 time to evaluate : 2.312 ------------------------------------------------------------------------------- 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 9 residue 21 VAL 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 47 THR Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 32 SER 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 493 ASN 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 16 THR 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 184 optimal weight: 10.0000 chunk 140 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 chunk 125 optimal weight: 0.8980 chunk 187 optimal weight: 9.9990 chunk 198 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 177 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** M 493 ASN W 7 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 24792 Z= 0.145 Angle : 0.648 10.059 34567 Z= 0.254 Chirality : 0.037 0.150 3413 Planarity : 0.004 0.046 4217 Dihedral : 16.880 179.993 4590 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.59 % Favored : 96.37 % Rotamer: Outliers : 2.03 % Allowed : 11.11 % Favored : 86.86 % 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: 2.64 (0.18), residues: 2257 helix: 3.60 (0.13), residues: 1405 sheet: 0.04 (1.23), residues: 8 loop : -1.71 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 594 HIS 0.005 0.001 HIS L 192 PHE 0.010 0.001 PHE M 383 TYR 0.009 0.001 TYR C 230 ARG 0.002 0.000 ARG 7 40 *********************** 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 303 residues out of total 1971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 263 time to evaluate : 2.489 Fit side-chains REVERT: 9 22 MET cc_start: 0.8873 (mmm) cc_final: 0.8486 (mmm) REVERT: B 51 THR cc_start: 0.8766 (t) cc_final: 0.8549 (p) REVERT: C 106 MET cc_start: 0.8754 (mmt) cc_final: 0.8142 (mmt) REVERT: U 31 LYS cc_start: 0.8166 (mtpt) cc_final: 0.7885 (mtmt) REVERT: W 50 TRP cc_start: 0.8085 (t60) cc_final: 0.7727 (t60) REVERT: X 17 THR cc_start: 0.8316 (t) cc_final: 0.8050 (t) REVERT: X 21 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7732 (mp) outliers start: 40 outliers final: 29 residues processed: 287 average time/residue: 0.3286 time to fit residues: 155.0672 Evaluate side-chains 281 residues out of total 1971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 251 time to evaluate : 2.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 45 VAL 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 A residue 32 SER Chi-restraints excluded: chain B residue 8 ASP Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 37 LEU 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 E residue 45 VAL Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain L residue 14 GLU Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain M residue 385 THR Chi-restraints excluded: chain M residue 493 ASN Chi-restraints excluded: chain M residue 539 LEU Chi-restraints excluded: chain M residue 561 MET Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain R residue 32 SER Chi-restraints excluded: chain V residue 16 THR Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain Z residue 46 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 165 optimal weight: 9.9990 chunk 112 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 147 optimal weight: 10.0000 chunk 81 optimal weight: 8.9990 chunk 169 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 20.0000 chunk 177 optimal weight: 8.9990 chunk 50 optimal weight: 0.2980 overall best weight: 4.0588 ------------------------------------------------------------------------------- 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 C 231 HIS M 414 ASN M 493 ASN S 20 ASN W 7 ASN Z 58 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 24792 Z= 0.297 Angle : 0.798 14.238 34567 Z= 0.316 Chirality : 0.042 0.206 3413 Planarity : 0.005 0.052 4217 Dihedral : 17.173 179.774 4590 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.34 % Favored : 95.61 % Rotamer: Outliers : 2.94 % Allowed : 11.31 % Favored : 85.74 % 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: 2.17 (0.18), residues: 2257 helix: 3.17 (0.13), residues: 1404 sheet: 0.49 (1.45), residues: 8 loop : -1.78 (0.20), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP V 38 HIS 0.007 0.001 HIS C 122 PHE 0.016 0.002 PHE L 185 TYR 0.014 0.002 TYR M 424 ARG 0.003 0.000 ARG B 55 *********************** 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 319 residues out of total 1971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 261 time to evaluate : 2.457 Fit side-chains REVERT: 9 22 MET cc_start: 0.8830 (mmm) cc_final: 0.8516 (mmm) REVERT: C 73 GLU cc_start: 0.6533 (pp20) cc_final: 0.5601 (pt0) REVERT: C 106 MET cc_start: 0.8836 (mmt) cc_final: 0.8050 (mmt) REVERT: M 553 LYS cc_start: 0.7665 (mmmt) cc_final: 0.7295 (mttm) REVERT: U 19 ASN cc_start: 0.7619 (t0) cc_final: 0.7348 (t0) REVERT: U 31 LYS cc_start: 0.8179 (mtpt) cc_final: 0.7921 (mtmt) REVERT: X 17 THR cc_start: 0.8443 (t) cc_final: 0.8165 (t) REVERT: X 21 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7761 (mp) REVERT: Z 22 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.7121 (mp) outliers start: 58 outliers final: 44 residues processed: 294 average time/residue: 0.3336 time to fit residues: 160.2995 Evaluate side-chains 299 residues out of total 1971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 253 time to evaluate : 2.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 45 VAL Chi-restraints excluded: chain 1 residue 33 SER 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 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 32 SER Chi-restraints excluded: chain B residue 8 ASP Chi-restraints excluded: chain B residue 19 ASN 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 68 ASP 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 E residue 45 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain L residue 14 GLU Chi-restraints excluded: chain L residue 94 ASN 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 S residue 20 ASN Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain V residue 16 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 66 optimal weight: 6.9990 chunk 178 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 116 optimal weight: 0.6980 chunk 48 optimal weight: 6.9990 chunk 198 optimal weight: 0.9990 chunk 164 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 238 GLN E 19 ASN K 7 ASN ** M 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 7 ASN Z 58 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24792 Z= 0.142 Angle : 0.643 10.433 34567 Z= 0.254 Chirality : 0.038 0.185 3413 Planarity : 0.004 0.049 4217 Dihedral : 16.537 179.986 4590 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.54 % Favored : 96.41 % Rotamer: Outliers : 1.52 % Allowed : 13.55 % Favored : 84.93 % 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: 2.65 (0.18), residues: 2257 helix: 3.59 (0.13), residues: 1405 sheet: 0.42 (1.44), residues: 8 loop : -1.67 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 594 HIS 0.005 0.001 HIS L 192 PHE 0.012 0.001 PHE S 18 TYR 0.010 0.001 TYR Y 26 ARG 0.003 0.000 ARG V 40 *********************** 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 279 residues out of total 1971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 249 time to evaluate : 1.990 Fit side-chains REVERT: C 73 GLU cc_start: 0.6410 (pp20) cc_final: 0.5652 (pt0) REVERT: C 106 MET cc_start: 0.8750 (mmt) cc_final: 0.8087 (mmt) REVERT: E 13 GLN cc_start: 0.6881 (tp40) cc_final: 0.6558 (tp40) REVERT: L 61 ASP cc_start: 0.8439 (t0) cc_final: 0.8190 (t70) REVERT: U 31 LYS cc_start: 0.8149 (mtpt) cc_final: 0.7877 (mtmt) REVERT: X 17 THR cc_start: 0.8425 (t) cc_final: 0.8167 (t) REVERT: X 21 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7684 (mp) REVERT: Z 22 LEU cc_start: 0.7195 (tp) cc_final: 0.6988 (mt) outliers start: 30 outliers final: 22 residues processed: 266 average time/residue: 0.3288 time to fit residues: 143.2133 Evaluate side-chains 269 residues out of total 1971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 246 time to evaluate : 3.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 45 VAL Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain 5 residue 24 LEU Chi-restraints excluded: chain 6 residue 41 VAL Chi-restraints excluded: chain B residue 8 ASP Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain L residue 14 GLU Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain M residue 561 MET 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 X residue 21 LEU Chi-restraints excluded: chain Y residue 24 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 191 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 chunk 144 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 166 optimal weight: 7.9990 chunk 110 optimal weight: 0.8980 chunk 197 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 91 optimal weight: 0.0770 overall best weight: 1.5944 ------------------------------------------------------------------------------- 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 238 GLN M 493 ASN S 20 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 24792 Z= 0.162 Angle : 0.656 11.327 34567 Z= 0.257 Chirality : 0.038 0.157 3413 Planarity : 0.004 0.051 4217 Dihedral : 16.251 179.920 4590 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.99 % Favored : 95.97 % Rotamer: Outliers : 1.73 % Allowed : 13.70 % Favored : 84.58 % 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: 2.65 (0.18), residues: 2257 helix: 3.59 (0.13), residues: 1405 sheet: 0.44 (1.41), residues: 8 loop : -1.67 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 594 HIS 0.007 0.001 HIS L 192 PHE 0.011 0.001 PHE M 383 TYR 0.010 0.001 TYR C 230 ARG 0.004 0.000 ARG V 40 *********************** 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 285 residues out of total 1971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 251 time to evaluate : 2.177 Fit side-chains REVERT: C 106 MET cc_start: 0.8742 (mmt) cc_final: 0.8008 (mmt) REVERT: E 13 GLN cc_start: 0.6851 (tp40) cc_final: 0.6525 (tp40) REVERT: L 61 ASP cc_start: 0.8449 (t0) cc_final: 0.8201 (t70) REVERT: U 19 ASN cc_start: 0.7670 (t0) cc_final: 0.7453 (t0) REVERT: U 31 LYS cc_start: 0.8169 (mtpt) cc_final: 0.7900 (mtmt) REVERT: X 17 THR cc_start: 0.8459 (t) cc_final: 0.8218 (t) REVERT: X 21 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7716 (mp) REVERT: Y 17 PHE cc_start: 0.7531 (OUTLIER) cc_final: 0.6657 (t80) outliers start: 34 outliers final: 28 residues processed: 270 average time/residue: 0.3240 time to fit residues: 143.1448 Evaluate side-chains 278 residues out of total 1971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 248 time to evaluate : 2.382 ------------------------------------------------------------------------------- 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 24 LEU Chi-restraints excluded: chain 6 residue 41 VAL Chi-restraints excluded: chain 7 residue 29 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 30 VAL Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain L residue 14 GLU Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain M residue 561 MET 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 V residue 16 THR Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain Y residue 17 PHE Chi-restraints excluded: chain Y residue 24 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 122 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 118 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 125 optimal weight: 10.0000 chunk 134 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 179 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 493 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 24792 Z= 0.432 Angle : 0.910 15.297 34567 Z= 0.364 Chirality : 0.047 0.256 3413 Planarity : 0.006 0.055 4217 Dihedral : 17.348 179.716 4590 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.87 % Favored : 95.08 % Rotamer: Outliers : 2.49 % Allowed : 13.09 % Favored : 84.42 % 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: 1.77 (0.18), residues: 2257 helix: 2.82 (0.13), residues: 1407 sheet: 0.60 (1.71), residues: 8 loop : -1.89 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP V 38 HIS 0.008 0.002 HIS C 122 PHE 0.019 0.002 PHE V 36 TYR 0.029 0.002 TYR M 424 ARG 0.008 0.001 ARG C 143 *********************** 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 304 residues out of total 1971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 255 time to evaluate : 2.260 Fit side-chains REVERT: C 106 MET cc_start: 0.8858 (mmt) cc_final: 0.8013 (mmt) REVERT: E 13 GLN cc_start: 0.6977 (tp40) cc_final: 0.6646 (tp40) REVERT: G 7 ASN cc_start: 0.6396 (p0) cc_final: 0.6088 (p0) REVERT: M 553 LYS cc_start: 0.7740 (mmmt) cc_final: 0.7337 (mttm) REVERT: N 6 PHE cc_start: 0.8397 (m-80) cc_final: 0.8031 (m-80) REVERT: U 31 LYS cc_start: 0.8166 (mtpt) cc_final: 0.7914 (mtmt) REVERT: X 17 THR cc_start: 0.8454 (t) cc_final: 0.8165 (t) REVERT: X 21 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7672 (mp) outliers start: 49 outliers final: 33 residues processed: 286 average time/residue: 0.3340 time to fit residues: 156.0032 Evaluate side-chains 287 residues out of total 1971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 253 time to evaluate : 2.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 45 VAL Chi-restraints excluded: chain 1 residue 33 SER 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 6 residue 45 VAL Chi-restraints excluded: chain 7 residue 29 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 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 68 ASP Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain L residue 14 GLU Chi-restraints excluded: chain L residue 94 ASN 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 R residue 32 SER Chi-restraints excluded: chain V residue 16 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 189 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 184 optimal weight: 8.9990 chunk 110 optimal weight: 0.0970 chunk 80 optimal weight: 4.9990 chunk 144 optimal weight: 7.9990 chunk 56 optimal weight: 7.9990 chunk 166 optimal weight: 9.9990 chunk 174 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 20 ASN ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 ASN M 493 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 24792 Z= 0.233 Angle : 0.736 12.719 34567 Z= 0.294 Chirality : 0.040 0.209 3413 Planarity : 0.005 0.051 4217 Dihedral : 16.818 179.892 4587 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.12 % Favored : 95.84 % Rotamer: Outliers : 2.03 % Allowed : 13.34 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.18 (0.18), residues: 2257 helix: 3.26 (0.13), residues: 1392 sheet: 0.07 (1.50), residues: 8 loop : -1.86 (0.20), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP V 38 HIS 0.007 0.001 HIS L 192 PHE 0.015 0.001 PHE L 185 TYR 0.013 0.001 TYR M 424 ARG 0.004 0.000 ARG C 143 *********************** 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 293 residues out of total 1971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 253 time to evaluate : 2.307 Fit side-chains REVERT: C 106 MET cc_start: 0.8809 (mmt) cc_final: 0.8041 (mmt) REVERT: G 7 ASN cc_start: 0.6289 (p0) cc_final: 0.6016 (p0) REVERT: L 243 ASP cc_start: 0.6160 (t0) cc_final: 0.5721 (t70) REVERT: N 6 PHE cc_start: 0.8380 (m-80) cc_final: 0.8025 (m-80) REVERT: U 31 LYS cc_start: 0.8162 (mtpt) cc_final: 0.7908 (mtmt) REVERT: X 17 THR cc_start: 0.8430 (t) cc_final: 0.8172 (t) REVERT: X 21 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7692 (mp) outliers start: 40 outliers final: 35 residues processed: 276 average time/residue: 0.3242 time to fit residues: 147.7225 Evaluate side-chains 288 residues out of total 1971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 252 time to evaluate : 2.421 ------------------------------------------------------------------------------- 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 7 residue 29 VAL Chi-restraints excluded: chain A residue 7 GLU 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 B residue 37 LEU 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 C residue 68 ASP Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain L residue 14 GLU Chi-restraints excluded: chain L residue 94 ASN Chi-restraints excluded: chain M residue 423 GLU 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 V residue 16 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 194 optimal weight: 9.9990 chunk 118 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 135 optimal weight: 7.9990 chunk 204 optimal weight: 2.9990 chunk 187 optimal weight: 10.0000 chunk 162 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 chunk 99 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 GLN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 493 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 24792 Z= 0.296 Angle : 0.799 13.913 34567 Z= 0.319 Chirality : 0.042 0.243 3413 Planarity : 0.005 0.052 4217 Dihedral : 16.985 179.796 4587 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.92 % Favored : 95.04 % Rotamer: Outliers : 1.98 % Allowed : 13.60 % Favored : 84.42 % 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: 1.96 (0.18), residues: 2257 helix: 3.06 (0.13), residues: 1392 sheet: -0.12 (1.48), residues: 8 loop : -1.91 (0.20), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP V 38 HIS 0.007 0.001 HIS C 122 PHE 0.019 0.002 PHE L 185 TYR 0.019 0.002 TYR M 424 ARG 0.005 0.000 ARG C 143 ********************** 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 294 residues out of total 1971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 255 time to evaluate : 2.531 Fit side-chains REVERT: C 73 GLU cc_start: 0.6343 (pp20) cc_final: 0.6006 (pt0) REVERT: C 106 MET cc_start: 0.8826 (mmt) cc_final: 0.8031 (mmt) REVERT: G 7 ASN cc_start: 0.6218 (p0) cc_final: 0.5959 (p0) REVERT: L 243 ASP cc_start: 0.6199 (t0) cc_final: 0.5759 (t70) REVERT: M 553 LYS cc_start: 0.7679 (mmmt) cc_final: 0.7324 (mttm) REVERT: N 6 PHE cc_start: 0.8351 (m-80) cc_final: 0.7942 (m-80) REVERT: U 31 LYS cc_start: 0.8158 (mtpt) cc_final: 0.7913 (mtmt) outliers start: 39 outliers final: 37 residues processed: 279 average time/residue: 0.3345 time to fit residues: 152.0371 Evaluate side-chains 292 residues out of total 1971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 255 time to evaluate : 2.519 ------------------------------------------------------------------------------- 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 6 residue 45 VAL Chi-restraints excluded: chain 7 residue 29 VAL Chi-restraints excluded: chain 9 residue 21 VAL Chi-restraints excluded: chain A residue 7 GLU 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 30 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain L residue 14 GLU Chi-restraints excluded: chain L residue 94 ASN 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 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 16 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 149 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 167 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 143 optimal weight: 2.9990 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 B 13 GLN B 20 ASN ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 493 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.106157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.089917 restraints weight = 37696.040| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.42 r_work: 0.2799 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 24792 Z= 0.257 Angle : 0.757 13.061 34567 Z= 0.303 Chirality : 0.041 0.244 3413 Planarity : 0.005 0.052 4217 Dihedral : 16.812 179.868 4587 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.34 % Favored : 95.61 % Rotamer: Outliers : 2.08 % Allowed : 13.70 % 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: 2.08 (0.18), residues: 2257 helix: 3.18 (0.13), residues: 1392 sheet: -0.12 (1.52), residues: 8 loop : -1.90 (0.20), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP M 360 HIS 0.007 0.001 HIS L 192 PHE 0.016 0.001 PHE L 185 TYR 0.016 0.001 TYR M 424 ARG 0.004 0.000 ARG C 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4482.00 seconds wall clock time: 82 minutes 49.40 seconds (4969.40 seconds total)