Starting phenix.real_space_refine on Mon Feb 19 06:01:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hju_34838/02_2024/8hju_34838_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hju_34838/02_2024/8hju_34838.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hju_34838/02_2024/8hju_34838.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hju_34838/02_2024/8hju_34838.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hju_34838/02_2024/8hju_34838_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hju_34838/02_2024/8hju_34838_updated.pdb" } resolution = 2.8 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= 0.008 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 7 5.49 5 Mg 48 5.21 5 S 75 5.16 5 C 17010 2.51 5 N 3312 2.21 5 O 3460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 ARG 55": "NH1" <-> "NH2" Residue "1 GLU 7": "OE1" <-> "OE2" Residue "1 ARG 40": "NH1" <-> "NH2" Residue "2 ARG 55": "NH1" <-> "NH2" Residue "3 ARG 4": "NH1" <-> "NH2" Residue "3 GLU 7": "OE1" <-> "OE2" Residue "3 ARG 40": "NH1" <-> "NH2" Residue "4 ARG 55": "NH1" <-> "NH2" Residue "5 ARG 4": "NH1" <-> "NH2" Residue "5 GLU 7": "OE1" <-> "OE2" Residue "5 ARG 40": "NH1" <-> "NH2" Residue "6 ARG 55": "NH1" <-> "NH2" Residue "7 GLU 7": "OE1" <-> "OE2" Residue "7 ARG 40": "NH1" <-> "NH2" Residue "8 ARG 55": "NH1" <-> "NH2" Residue "9 GLU 7": "OE1" <-> "OE2" Residue "9 ARG 40": "NH1" <-> "NH2" Residue "A ARG 4": "NH1" <-> "NH2" Residue "A GLU 7": "OE1" <-> "OE2" Residue "A ARG 40": "NH1" <-> "NH2" Residue "B ARG 55": "NH1" <-> "NH2" Residue "D GLU 7": "OE1" <-> "OE2" Residue "D ARG 40": "NH1" <-> "NH2" Residue "E ARG 55": "NH1" <-> "NH2" Residue "F ARG 4": "NH1" <-> "NH2" Residue "F PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 7": "OE1" <-> "OE2" Residue "F ARG 40": "NH1" <-> "NH2" Residue "G ARG 55": "NH1" <-> "NH2" Residue "H ARG 4": "NH1" <-> "NH2" Residue "H GLU 7": "OE1" <-> "OE2" Residue "H ARG 40": "NH1" <-> "NH2" Residue "I ARG 55": "NH1" <-> "NH2" Residue "J GLU 7": "OE1" <-> "OE2" Residue "K ARG 55": "NH1" <-> "NH2" Residue "L GLU 14": "OE1" <-> "OE2" Residue "L GLU 19": "OE1" <-> "OE2" Residue "L GLU 41": "OE1" <-> "OE2" Residue "L GLU 106": "OE1" <-> "OE2" Residue "M GLU 341": "OE1" <-> "OE2" Residue "M ARG 363": "NH1" <-> "NH2" Residue "M ARG 410": "NH1" <-> "NH2" Residue "M GLU 555": "OE1" <-> "OE2" Residue "M GLU 622": "OE1" <-> "OE2" Residue "N GLU 7": "OE1" <-> "OE2" Residue "O ARG 55": "NH1" <-> "NH2" Residue "P ARG 4": "NH1" <-> "NH2" Residue "P GLU 7": "OE1" <-> "OE2" Residue "P ARG 40": "NH1" <-> "NH2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "R ARG 4": "NH1" <-> "NH2" Residue "R GLU 7": "OE1" <-> "OE2" Residue "R ARG 40": "NH1" <-> "NH2" Residue "S ARG 55": "NH1" <-> "NH2" Residue "T GLU 7": "OE1" <-> "OE2" Residue "T ARG 40": "NH1" <-> "NH2" Residue "U ARG 55": "NH1" <-> "NH2" Residue "V ARG 4": "NH1" <-> "NH2" Residue "V GLU 7": "OE1" <-> "OE2" Residue "W ARG 55": "NH1" <-> "NH2" Residue "C ARG 19": "NH1" <-> "NH2" Residue "C GLU 73": "OE1" <-> "OE2" Residue "C TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 202": "OE1" <-> "OE2" Residue "C GLU 221": "OE1" <-> "OE2" Residue "C GLU 223": "OE1" <-> "OE2" Residue "C ARG 280": "NH1" <-> "NH2" Residue "Z ARG 39": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 23917 Number of models: 1 Model: "" Number of chains: 71 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: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 271 Classifications: {'peptide': 35} Link IDs: {'TRANS': 34} 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: "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: 2389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2389 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 16, 'TRANS': 285} 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: "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: "X" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 206 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 1, 'TRANS': 24} Chain: "Y" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 259 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 2, 'TRANS': 29} Chain: "Z" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 362 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 4, 'TRANS': 42} Chain: "0" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 214 Unusual residues: {'BCL': 2, 'KGD': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "1" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "2" 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: "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: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "6" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'KGD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "7" Number of atoms: 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: 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: "B" 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: "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: 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: "F" 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: "G" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 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: "I" 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: "J" 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: "K" 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: "L" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 404 Unusual residues: {'BCL': 2, 'BPH': 2, 'MQE': 1, 'PGV': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 258 Unusual residues: {' FE': 1, 'BCL': 1, 'BPH': 1, 'MQE': 2, 'PGV': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'MQE:plan-12': 1, 'MQE:plan-11': 1, 'MQE:plan-10': 1, 'PGV:plan-3': 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: 48 Chain: "N" 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: "O" 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: "P" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 185 Unusual residues: {'BCL': 1, 'KGD': 1, 'PGV': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'PGV:plan-3': 2} Unresolved non-hydrogen planarities: 5 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: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 214 Unusual residues: {'BCL': 2, 'KGD': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "T" Number of atoms: 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: "W" 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: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 258 Unusual residues: {'HEM': 4, 'KGD': 1, 'PGV': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "X" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'DGA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'PGV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 13.29, per 1000 atoms: 0.56 Number of scatterers: 23917 At special positions: 0 Unit cell: (138.24, 122.04, 143.64, 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 7 15.00 Mg 48 11.99 O 3460 8.00 N 3312 7.00 C 17010 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=61, symmetry=0 Number of additional bonds: simple=61, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.47 Conformation dependent library (CDL) restraints added in 3.3 seconds 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4370 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 82 helices and 2 sheets defined 61.8% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.33 Creating SS restraints... Processing helix chain '0' and resid 20 through 50 removed outlier: 3.834A pdb=" N LEU 0 24 " --> pdb=" O ASN 0 20 " (cutoff:3.500A) Processing helix chain '1' and resid 8 through 32 Processing helix chain '2' and resid 20 through 50 removed outlier: 3.834A pdb=" N LEU 2 24 " --> pdb=" O ASN 2 20 " (cutoff:3.500A) Processing helix chain '3' and resid 8 through 32 Processing helix chain '4' and resid 20 through 50 removed outlier: 3.834A pdb=" N LEU 4 24 " --> pdb=" O ASN 4 20 " (cutoff:3.500A) Processing helix chain '5' and resid 8 through 32 Processing helix chain '6' and resid 20 through 50 removed outlier: 3.834A pdb=" N LEU 6 24 " --> pdb=" O ASN 6 20 " (cutoff:3.500A) Processing helix chain '7' and resid 8 through 32 Processing helix chain '8' and resid 20 through 50 removed outlier: 3.833A pdb=" N LEU 8 24 " --> pdb=" O ASN 8 20 " (cutoff:3.500A) Processing helix chain '9' and resid 8 through 32 Processing helix chain 'A' and resid 8 through 32 Processing helix chain 'B' and resid 12 through 14 No H-bonds generated for 'chain 'B' and resid 12 through 14' Processing helix chain 'B' and resid 20 through 50 removed outlier: 3.834A pdb=" N LEU B 24 " --> pdb=" O ASN B 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 32 Processing helix chain 'E' and resid 12 through 14 No H-bonds generated for 'chain 'E' and resid 12 through 14' Processing helix chain 'E' and resid 20 through 50 removed outlier: 3.833A pdb=" N LEU E 24 " --> pdb=" O ASN E 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 32 Processing helix chain 'G' and resid 20 through 50 removed outlier: 3.833A pdb=" N LEU G 24 " --> pdb=" O ASN G 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 32 Processing helix chain 'I' and resid 12 through 14 No H-bonds generated for 'chain 'I' and resid 12 through 14' Processing helix chain 'I' and resid 20 through 50 removed outlier: 3.834A pdb=" N LEU I 24 " --> pdb=" O ASN I 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 8 through 32 Processing helix chain 'K' and resid 20 through 50 removed outlier: 3.833A pdb=" N LEU K 24 " --> pdb=" O ASN K 20 " (cutoff:3.500A) Processing helix chain 'L' and resid 36 through 42 Processing helix chain 'L' and resid 50 through 54 Processing helix chain 'L' and resid 71 through 92 removed outlier: 4.108A 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 149 Processing helix chain 'L' and resid 155 through 171 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 235 Processing helix chain 'L' and resid 245 through 252 Processing helix chain 'L' and resid 260 through 287 removed outlier: 3.780A pdb=" N HIS L 264 " --> pdb=" O GLU L 260 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL L 275 " --> pdb=" O GLY L 271 " (cutoff:3.500A) Processing helix chain 'L' and resid 292 through 301 removed outlier: 4.031A pdb=" N TRP L 296 " --> pdb=" O TRP L 292 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY L 297 " --> pdb=" O ASN L 293 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N PHE L 298 " --> pdb=" O ALA L 294 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N TRP L 299 " --> pdb=" O PHE L 295 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASP L 300 " --> pdb=" O TRP L 296 " (cutoff:3.500A) removed outlier: 4.202A 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 Processing helix chain 'M' and resid 360 through 365 Processing helix chain 'M' and resid 379 through 400 Processing helix chain 'M' and resid 405 through 411 removed outlier: 3.512A pdb=" N LEU M 409 " --> pdb=" O PRO M 405 " (cutoff:3.500A) Processing helix chain 'M' and resid 436 through 463 removed outlier: 3.576A pdb=" N ALA M 440 " --> pdb=" O GLY M 436 " (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 Processing helix chain 'M' and resid 587 through 612 removed outlier: 3.999A pdb=" N GLY M 611 " --> pdb=" O LEU M 607 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR M 612 " --> pdb=" O PHE M 608 " (cutoff:3.500A) Processing helix chain 'M' and resid 617 through 623 Processing helix chain 'M' and resid 635 through 638 Processing helix chain 'N' and resid 8 through 32 Processing helix chain 'O' and resid 20 through 50 removed outlier: 3.834A pdb=" N LEU O 24 " --> pdb=" O ASN O 20 " (cutoff:3.500A) Processing helix chain 'P' and resid 8 through 32 Processing helix chain 'Q' and resid 20 through 50 removed outlier: 3.834A pdb=" N LEU Q 24 " --> pdb=" O ASN Q 20 " (cutoff:3.500A) Processing helix chain 'R' and resid 8 through 32 Processing helix chain 'S' and resid 20 through 50 removed outlier: 3.834A pdb=" N LEU S 24 " --> pdb=" O ASN S 20 " (cutoff:3.500A) Processing helix chain 'T' and resid 8 through 32 Processing helix chain 'U' and resid 20 through 50 removed outlier: 3.834A pdb=" N LEU U 24 " --> pdb=" O ASN U 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 8 through 32 Processing helix chain 'V' and resid 37 through 39 No H-bonds generated for 'chain 'V' and resid 37 through 39' Processing helix chain 'W' and resid 20 through 50 removed outlier: 3.834A pdb=" N LEU W 24 " --> pdb=" O ASN W 20 " (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: 3.650A pdb=" N ILE C 22 " --> pdb=" O GLY C 18 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 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 205 through 207 No H-bonds generated for 'chain 'C' and resid 205 through 207' Processing helix chain 'C' and resid 219 through 235 Processing helix chain 'C' and resid 240 through 242 No H-bonds generated for 'chain 'C' and resid 240 through 242' 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 297 Processing helix chain 'X' and resid 2 through 24 Processing helix chain 'Y' and resid 2 through 30 Proline residue: Y 19 - end of helix Processing helix chain 'Z' and resid 17 through 46 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 62 through 64 removed outlier: 3.868A pdb=" N PHE L 62 " --> pdb=" O VAL L 69 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'M' and resid 349 through 351 removed outlier: 3.766A pdb=" N GLY M 349 " --> pdb=" O VAL M 375 " (cutoff:3.500A) 1098 hydrogen bonds defined for protein. 3285 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.02 Time building geometry restraints manager: 11.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.29: 3053 1.29 - 1.49: 11699 1.49 - 1.69: 9879 1.69 - 1.88: 126 1.88 - 2.08: 208 Bond restraints: 24965 Sorted by residual: bond pdb=" C VAL W 25 " pdb=" N HIS W 26 " ideal model delta sigma weight residual 1.335 1.432 -0.097 1.31e-02 5.83e+03 5.49e+01 bond pdb=" C1 PGV P 103 " pdb=" C2 PGV P 103 " ideal model delta sigma weight residual 1.504 1.365 0.139 2.00e-02 2.50e+03 4.82e+01 bond pdb=" C LEU C 295 " pdb=" N CYS C 296 " ideal model delta sigma weight residual 1.331 1.227 0.104 1.73e-02 3.34e+03 3.63e+01 bond pdb=" CAB KGD C 401 " pdb=" CAF KGD C 401 " ideal model delta sigma weight residual 1.536 1.417 0.119 2.00e-02 2.50e+03 3.56e+01 bond pdb=" C VAL 4 25 " pdb=" N HIS 4 26 " ideal model delta sigma weight residual 1.335 1.415 -0.080 1.38e-02 5.25e+03 3.39e+01 ... (remaining 24960 not shown) Histogram of bond angle deviations from ideal: 81.08 - 99.51: 288 99.51 - 117.95: 19094 117.95 - 136.38: 15173 136.38 - 154.82: 101 154.82 - 173.25: 104 Bond angle restraints: 34760 Sorted by residual: angle pdb=" N ALA V 35 " pdb=" CA ALA V 35 " pdb=" C ALA V 35 " ideal model delta sigma weight residual 111.69 99.18 12.51 1.23e+00 6.61e-01 1.03e+02 angle pdb=" N GLY M 425 " pdb=" CA GLY M 425 " pdb=" C GLY M 425 " ideal model delta sigma weight residual 112.50 123.52 -11.02 1.16e+00 7.43e-01 9.03e+01 angle pdb=" N GLY L 307 " pdb=" CA GLY L 307 " pdb=" C GLY L 307 " ideal model delta sigma weight residual 113.37 123.41 -10.04 1.34e+00 5.57e-01 5.61e+01 angle pdb=" N PHE L 206 " pdb=" CA PHE L 206 " pdb=" C PHE L 206 " ideal model delta sigma weight residual 113.01 104.24 8.77 1.20e+00 6.94e-01 5.34e+01 angle pdb=" N THR L 97 " pdb=" CA THR L 97 " pdb=" C THR L 97 " ideal model delta sigma weight residual 111.36 119.32 -7.96 1.09e+00 8.42e-01 5.33e+01 ... (remaining 34755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.94: 12117 28.94 - 57.87: 880 57.87 - 86.81: 116 86.81 - 115.74: 24 115.74 - 144.68: 24 Dihedral angle restraints: 13161 sinusoidal: 6438 harmonic: 6723 Sorted by residual: dihedral pdb=" C1 BCL S 102 " pdb=" CGA BCL S 102 " pdb=" O2A BCL S 102 " pdb=" CBA BCL S 102 " ideal model delta sinusoidal sigma weight residual -180.00 -54.93 -125.07 1 6.00e+00 2.78e-02 4.20e+02 dihedral pdb=" C1 BCL F 102 " pdb=" CGA BCL F 102 " pdb=" O2A BCL F 102 " pdb=" CBA BCL F 102 " ideal model delta sinusoidal sigma weight residual -180.00 -54.97 -125.03 1 6.00e+00 2.78e-02 4.20e+02 dihedral pdb=" C1 BCL 8 101 " pdb=" CGA BCL 8 101 " pdb=" O2A BCL 8 101 " pdb=" CBA BCL 8 101 " ideal model delta sinusoidal sigma weight residual -180.00 -54.98 -125.02 1 6.00e+00 2.78e-02 4.20e+02 ... (remaining 13158 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.118: 3408 1.118 - 2.236: 0 2.236 - 3.353: 0 3.353 - 4.471: 0 4.471 - 5.589: 16 Chirality restraints: 3424 Sorted by residual: chirality pdb=" C18 BCL X 101 " pdb=" C17 BCL X 101 " pdb=" C19 BCL X 101 " pdb=" C20 BCL X 101 " both_signs ideal model delta sigma weight residual False 2.71 -2.88 5.59 2.00e-01 2.50e+01 7.81e+02 chirality pdb=" C18 BCL W 102 " pdb=" C17 BCL W 102 " pdb=" C19 BCL W 102 " pdb=" C20 BCL W 102 " both_signs ideal model delta sigma weight residual False 2.71 -2.84 5.55 2.00e-01 2.50e+01 7.71e+02 chirality pdb=" C18 BCL 5 101 " pdb=" C17 BCL 5 101 " pdb=" C19 BCL 5 101 " pdb=" C20 BCL 5 101 " both_signs ideal model delta sigma weight residual False 2.71 -2.84 5.55 2.00e-01 2.50e+01 7.69e+02 ... (remaining 3421 not shown) Planarity restraints: 4222 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL L1001 " 0.343 1.50e-02 4.44e+03 2.91e-01 1.88e+03 pdb=" C2 BCL L1001 " -0.400 1.50e-02 4.44e+03 pdb=" C3 BCL L1001 " -0.247 1.50e-02 4.44e+03 pdb=" C4 BCL L1001 " 0.016 1.50e-02 4.44e+03 pdb=" C5 BCL L1001 " 0.289 1.50e-02 4.44e+03 delta sigma weight rms_deltas residual plane pdb=" C3D BCL L1001 " 0.051 5.00e-03 4.00e+04 9.26e-02 1.37e+03 pdb=" CAD BCL L1001 " -0.160 5.00e-03 4.00e+04 pdb=" CBD BCL L1001 " 0.043 5.00e-03 4.00e+04 pdb=" OBD BCL L1001 " 0.066 5.00e-03 4.00e+04 delta sigma weight rms_deltas residual plane pdb=" C3D BCL B 101 " 0.043 5.00e-03 4.00e+04 7.89e-02 9.96e+02 pdb=" CAD BCL B 101 " -0.136 5.00e-03 4.00e+04 pdb=" CBD BCL B 101 " 0.036 5.00e-03 4.00e+04 pdb=" OBD BCL B 101 " 0.056 5.00e-03 4.00e+04 ... (remaining 4219 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 96 2.44 - 3.06: 14865 3.06 - 3.67: 37113 3.67 - 4.29: 62541 4.29 - 4.90: 100320 Nonbonded interactions: 214935 Sorted by model distance: nonbonded pdb=" OE2 GLU M 557 " pdb="FE FE M 702 " model vdw 1.827 2.260 nonbonded pdb=" NE2 HIS L 229 " pdb="FE FE M 702 " model vdw 2.065 2.340 nonbonded pdb=" NE2 HIS C 122 " pdb="FE HEM C 402 " model vdw 2.105 3.080 nonbonded pdb=" O06 PGV P 103 " pdb=" O12 PGV P 103 " model vdw 2.109 2.440 nonbonded pdb=" NE2 HIS C 297 " pdb="FE HEM C 405 " model vdw 2.114 3.080 ... (remaining 214930 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) selection = (chain '2' and resid 7 through 55) selection = (chain '4' and resid 7 through 55) selection = (chain '6' and resid 7 through 55) selection = (chain '8' and resid 7 through 55) selection = (chain 'B' and resid 7 through 55) selection = (chain 'E' and resid 7 through 55) selection = (chain 'G' and resid 7 through 55) selection = (chain 'I' and resid 7 through 55) selection = (chain 'K' and resid 7 through 55) selection = (chain 'O' and resid 7 through 55) selection = (chain 'Q' and resid 7 through 55) selection = (chain 'S' and resid 7 through 55) selection = (chain 'U' and resid 7 through 55) selection = (chain 'W' and resid 7 through 55) } ncs_group { reference = (chain '1' and resid 7 through 41) selection = (chain '3' and resid 7 through 41) selection = (chain '5' and resid 7 through 41) selection = (chain '7' and resid 7 through 41) selection = (chain '9' and resid 7 through 41) selection = (chain 'A' and resid 7 through 41) selection = (chain 'D' and resid 7 through 41) selection = (chain 'F' and resid 7 through 41) selection = (chain 'H' and resid 7 through 41) selection = (chain 'J' and resid 7 through 41) selection = (chain 'N' and resid 7 through 41) selection = (chain 'P' and resid 7 through 41) selection = (chain 'R' and resid 7 through 41) selection = (chain 'T' and resid 7 through 41) selection = (chain 'V' and resid 7 through 41) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 5.300 Check model and map are aligned: 0.400 Set scattering table: 0.250 Process input model: 62.310 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 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 : 0.020 0.139 24965 Z= 0.998 Angle : 2.080 16.829 34760 Z= 0.863 Chirality : 0.397 5.589 3424 Planarity : 0.031 0.293 4222 Dihedral : 20.784 144.679 8791 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 25.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.63 % Favored : 96.32 % Rotamer: Outliers : 0.66 % Allowed : 9.24 % Favored : 90.10 % Cbeta Deviations : 0.05 % 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: -0.29 (0.16), residues: 2256 helix: 0.58 (0.12), residues: 1410 sheet: None (None), residues: 0 loop : -1.47 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 38 HIS 0.007 0.001 HIS M 589 PHE 0.025 0.002 PHE L 206 TYR 0.018 0.002 TYR C 156 ARG 0.004 0.000 ARG V 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 455 time to evaluate : 2.286 Fit side-chains REVERT: 0 19 ASN cc_start: 0.6837 (t0) cc_final: 0.6614 (t0) REVERT: 3 22 MET cc_start: 0.8708 (mmm) cc_final: 0.8482 (mmp) REVERT: 9 17 LEU cc_start: 0.8112 (tp) cc_final: 0.7725 (mm) REVERT: A 22 MET cc_start: 0.9140 (mmm) cc_final: 0.8901 (mmp) REVERT: D 9 ARG cc_start: 0.6433 (ttp-170) cc_final: 0.5951 (tmt170) REVERT: D 10 THR cc_start: 0.8295 (m) cc_final: 0.8082 (m) REVERT: G 31 LYS cc_start: 0.8370 (mttt) cc_final: 0.8160 (mttp) REVERT: J 4 ARG cc_start: 0.6410 (tpt-90) cc_final: 0.6183 (mtp180) REVERT: L 151 ASP cc_start: 0.8847 (m-30) cc_final: 0.8551 (m-30) REVERT: N 9 ARG cc_start: 0.7503 (ttp-170) cc_final: 0.7282 (ttm170) REVERT: S 19 ASN cc_start: 0.7880 (t0) cc_final: 0.7636 (t0) REVERT: C 223 GLU cc_start: 0.8303 (tt0) cc_final: 0.7995 (tt0) REVERT: X 8 PHE cc_start: 0.6827 (t80) cc_final: 0.6595 (t80) REVERT: Z 43 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8190 (ttpp) outliers start: 13 outliers final: 6 residues processed: 466 average time/residue: 1.1868 time to fit residues: 645.0639 Evaluate side-chains 329 residues out of total 1969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 322 time to evaluate : 2.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 305 TRP Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain Z residue 39 ARG Chi-restraints excluded: chain Z residue 43 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 5.9990 chunk 155 optimal weight: 7.9990 chunk 86 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 160 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 119 optimal weight: 0.9990 chunk 186 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 13 GLN ** 8 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN E 13 GLN G 19 ASN I 19 ASN L 120 GLN ** L 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 369 GLN M 572 GLN O 13 GLN Q 13 GLN W 13 GLN C 56 ASN C 87 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 24965 Z= 0.237 Angle : 0.926 18.995 34760 Z= 0.330 Chirality : 0.042 0.223 3424 Planarity : 0.005 0.065 4222 Dihedral : 21.378 177.961 4800 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.74 % Allowed : 14.22 % Favored : 83.04 % 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: 1.53 (0.17), residues: 2256 helix: 2.12 (0.13), residues: 1408 sheet: None (None), residues: 0 loop : -0.94 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 50 HIS 0.007 0.001 HIS L 192 PHE 0.015 0.001 PHE C 39 TYR 0.012 0.001 TYR C 230 ARG 0.005 0.000 ARG 9 40 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 355 time to evaluate : 2.263 Fit side-chains revert: symmetry clash REVERT: 6 17 LEU cc_start: 0.8038 (mt) cc_final: 0.7817 (mt) REVERT: 8 45 VAL cc_start: 0.8759 (t) cc_final: 0.8478 (m) REVERT: 9 17 LEU cc_start: 0.8227 (tp) cc_final: 0.7751 (mp) REVERT: D 9 ARG cc_start: 0.6486 (ttp-170) cc_final: 0.5929 (tmt170) REVERT: D 10 THR cc_start: 0.8265 (m) cc_final: 0.7967 (m) REVERT: E 31 LYS cc_start: 0.8307 (mttm) cc_final: 0.8099 (mtpp) REVERT: G 31 LYS cc_start: 0.8295 (mttt) cc_final: 0.7991 (mtpp) REVERT: J 9 ARG cc_start: 0.7633 (ttp-110) cc_final: 0.7244 (ptt90) REVERT: L 151 ASP cc_start: 0.8837 (m-30) cc_final: 0.8502 (m-30) REVERT: M 348 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7305 (mm-30) REVERT: N 17 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8462 (tp) REVERT: P 38 TRP cc_start: 0.8825 (OUTLIER) cc_final: 0.8509 (t60) REVERT: R 9 ARG cc_start: 0.8507 (tmm160) cc_final: 0.8306 (ttm110) REVERT: S 19 ASN cc_start: 0.7591 (t0) cc_final: 0.7382 (t0) REVERT: W 9 LEU cc_start: 0.7983 (mt) cc_final: 0.7778 (mp) REVERT: W 17 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7604 (mm) REVERT: C 73 GLU cc_start: 0.7271 (mt-10) cc_final: 0.6944 (mp0) REVERT: C 145 MET cc_start: 0.7970 (mmt) cc_final: 0.7110 (mmt) REVERT: C 223 GLU cc_start: 0.8265 (tt0) cc_final: 0.7948 (tt0) REVERT: C 272 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.6942 (mp0) REVERT: Z 43 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8452 (tttp) outliers start: 54 outliers final: 16 residues processed: 378 average time/residue: 1.1756 time to fit residues: 519.8891 Evaluate side-chains 343 residues out of total 1969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 321 time to evaluate : 2.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 28 ILE Chi-restraints excluded: chain 3 residue 15 SER Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain 5 residue 21 VAL Chi-restraints excluded: chain 7 residue 38 TRP Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain I residue 8 ASP Chi-restraints excluded: chain L residue 285 SER Chi-restraints excluded: chain L residue 305 TRP Chi-restraints excluded: chain M residue 348 GLU Chi-restraints excluded: chain M residue 375 VAL Chi-restraints excluded: chain M residue 632 ASN Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 LEU Chi-restraints excluded: chain P residue 38 TRP Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain Z residue 43 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 103 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 154 optimal weight: 0.0670 chunk 126 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 186 optimal weight: 0.8980 chunk 201 optimal weight: 0.9980 chunk 166 optimal weight: 4.9990 chunk 184 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 13 GLN 5 37 ASN ** 8 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 ASN E 13 GLN G 19 ASN I 19 ASN L 120 GLN S 22 GLN W 13 GLN ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 24965 Z= 0.196 Angle : 0.728 14.650 34760 Z= 0.289 Chirality : 0.038 0.175 3424 Planarity : 0.004 0.043 4222 Dihedral : 19.031 179.884 4792 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.69 % Allowed : 15.44 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.09 (0.17), residues: 2256 helix: 2.57 (0.13), residues: 1431 sheet: None (None), residues: 0 loop : -0.82 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP T 38 HIS 0.006 0.001 HIS L 192 PHE 0.025 0.001 PHE X 8 TYR 0.013 0.001 TYR C 230 ARG 0.004 0.000 ARG U 55 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 348 time to evaluate : 2.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 9 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7520 (mp) REVERT: 6 8 ASP cc_start: 0.7136 (OUTLIER) cc_final: 0.6675 (p0) REVERT: 6 17 LEU cc_start: 0.8017 (mt) cc_final: 0.7736 (mt) REVERT: 6 24 LEU cc_start: 0.8491 (mt) cc_final: 0.8257 (mt) REVERT: 9 17 LEU cc_start: 0.8226 (tp) cc_final: 0.7764 (mp) REVERT: D 9 ARG cc_start: 0.6502 (ttp-170) cc_final: 0.5971 (tmt170) REVERT: G 31 LYS cc_start: 0.8294 (mttt) cc_final: 0.8072 (mttp) REVERT: H 4 ARG cc_start: 0.6006 (ttp-170) cc_final: 0.5655 (ttm170) REVERT: J 4 ARG cc_start: 0.6758 (tpt-90) cc_final: 0.6505 (ttt-90) REVERT: J 9 ARG cc_start: 0.7576 (ttp-110) cc_final: 0.7139 (ptt90) REVERT: L 151 ASP cc_start: 0.8814 (m-30) cc_final: 0.8488 (m-30) REVERT: L 181 TRP cc_start: 0.6252 (OUTLIER) cc_final: 0.4569 (t-100) REVERT: M 348 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7328 (mm-30) REVERT: M 553 LYS cc_start: 0.8183 (mmpt) cc_final: 0.7980 (mmmt) REVERT: N 17 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8489 (tp) REVERT: P 9 ARG cc_start: 0.8109 (ttp-170) cc_final: 0.7668 (ttp-110) REVERT: Q 34 TYR cc_start: 0.7653 (m-10) cc_final: 0.7448 (m-10) REVERT: Q 55 ARG cc_start: 0.7325 (ttm170) cc_final: 0.7078 (mtp180) REVERT: W 9 LEU cc_start: 0.7899 (mt) cc_final: 0.7584 (mp) REVERT: C 223 GLU cc_start: 0.8261 (tt0) cc_final: 0.7938 (tt0) REVERT: C 272 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7264 (mp0) REVERT: Z 43 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8345 (tttm) outliers start: 53 outliers final: 23 residues processed: 374 average time/residue: 1.2088 time to fit residues: 527.8804 Evaluate side-chains 352 residues out of total 1969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 322 time to evaluate : 2.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 9 LEU Chi-restraints excluded: chain 3 residue 15 SER Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain 6 residue 8 ASP Chi-restraints excluded: chain 8 residue 31 LYS Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain I residue 8 ASP Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 181 TRP Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain L residue 285 SER Chi-restraints excluded: chain L residue 305 TRP Chi-restraints excluded: chain M residue 345 ASP Chi-restraints excluded: chain M residue 348 GLU Chi-restraints excluded: chain M residue 375 VAL Chi-restraints excluded: chain M residue 509 THR Chi-restraints excluded: chain M residue 595 PHE Chi-restraints excluded: chain M residue 613 LEU Chi-restraints excluded: chain M residue 632 ASN Chi-restraints excluded: chain N residue 11 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 LEU Chi-restraints excluded: chain Q residue 13 GLN Chi-restraints excluded: chain S residue 31 LYS Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain Z residue 43 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 184 optimal weight: 0.8980 chunk 140 optimal weight: 7.9990 chunk 96 optimal weight: 0.3980 chunk 20 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 chunk 125 optimal weight: 6.9990 chunk 187 optimal weight: 0.7980 chunk 198 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 177 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 13 GLN ** 8 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN G 19 ASN I 19 ASN L 120 GLN L 293 ASN O 13 GLN S 22 GLN W 13 GLN C 126 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24965 Z= 0.172 Angle : 0.669 13.986 34760 Z= 0.270 Chirality : 0.037 0.196 3424 Planarity : 0.004 0.044 4222 Dihedral : 18.175 179.939 4792 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.23 % Allowed : 17.12 % Favored : 80.65 % 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: 2.42 (0.17), residues: 2256 helix: 2.86 (0.13), residues: 1427 sheet: None (None), residues: 0 loop : -0.73 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP T 38 HIS 0.005 0.001 HIS L 192 PHE 0.024 0.001 PHE X 8 TYR 0.012 0.001 TYR C 230 ARG 0.006 0.000 ARG U 55 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 342 time to evaluate : 2.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 6 17 LEU cc_start: 0.8018 (mt) cc_final: 0.7786 (mt) REVERT: 6 24 LEU cc_start: 0.8501 (mt) cc_final: 0.8262 (mt) REVERT: 7 9 ARG cc_start: 0.6837 (OUTLIER) cc_final: 0.6407 (ttt180) REVERT: 9 17 LEU cc_start: 0.8253 (tp) cc_final: 0.7795 (mp) REVERT: D 9 ARG cc_start: 0.6449 (ttp-170) cc_final: 0.5926 (tmt170) REVERT: J 4 ARG cc_start: 0.6729 (tpt-90) cc_final: 0.6485 (ttt-90) REVERT: J 9 ARG cc_start: 0.7567 (ttp-110) cc_final: 0.7180 (ttp-110) REVERT: L 151 ASP cc_start: 0.8774 (m-30) cc_final: 0.8461 (m-30) REVERT: N 17 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8533 (tp) REVERT: P 9 ARG cc_start: 0.7974 (ttp-170) cc_final: 0.7604 (ttp-110) REVERT: Q 34 TYR cc_start: 0.7590 (m-10) cc_final: 0.7380 (m-10) REVERT: Q 55 ARG cc_start: 0.7274 (ttm170) cc_final: 0.7059 (mtp180) REVERT: S 31 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8228 (mptt) REVERT: C 31 MET cc_start: 0.6273 (ttm) cc_final: 0.6047 (ttm) REVERT: C 145 MET cc_start: 0.8261 (mmt) cc_final: 0.7276 (mmt) REVERT: C 223 GLU cc_start: 0.8271 (tt0) cc_final: 0.7953 (tt0) REVERT: Z 43 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8298 (tttm) outliers start: 44 outliers final: 22 residues processed: 367 average time/residue: 1.1546 time to fit residues: 499.0907 Evaluate side-chains 339 residues out of total 1969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 313 time to evaluate : 2.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 15 SER Chi-restraints excluded: chain 7 residue 9 ARG Chi-restraints excluded: chain 7 residue 38 TRP Chi-restraints excluded: chain 8 residue 31 LYS Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain J residue 22 MET Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain L residue 285 SER Chi-restraints excluded: chain L residue 305 TRP Chi-restraints excluded: chain M residue 345 ASP Chi-restraints excluded: chain M residue 375 VAL Chi-restraints excluded: chain M residue 509 THR Chi-restraints excluded: chain M residue 595 PHE Chi-restraints excluded: chain M residue 613 LEU Chi-restraints excluded: chain M residue 632 ASN Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 LEU Chi-restraints excluded: chain Q residue 13 GLN Chi-restraints excluded: chain S residue 31 LYS Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain Z residue 43 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 165 optimal weight: 0.8980 chunk 112 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 147 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 169 optimal weight: 9.9990 chunk 136 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 1.9990 chunk 177 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 13 GLN ** 8 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 ASN E 13 GLN I 19 ASN L 120 GLN L 227 HIS O 13 GLN S 22 GLN W 13 GLN C 269 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 24965 Z= 0.287 Angle : 0.802 18.314 34760 Z= 0.317 Chirality : 0.041 0.209 3424 Planarity : 0.005 0.051 4222 Dihedral : 18.073 179.891 4792 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.64 % Allowed : 16.56 % Favored : 80.80 % 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: 2.16 (0.17), residues: 2256 helix: 2.57 (0.13), residues: 1436 sheet: None (None), residues: 0 loop : -0.70 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP T 38 HIS 0.007 0.001 HIS M 589 PHE 0.024 0.002 PHE X 8 TYR 0.016 0.002 TYR C 230 ARG 0.008 0.001 ARG 8 55 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 320 time to evaluate : 2.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 19 ASN cc_start: 0.7422 (t0) cc_final: 0.7116 (t0) REVERT: 3 9 ARG cc_start: 0.7068 (ttp-170) cc_final: 0.6649 (ttm110) REVERT: 6 8 ASP cc_start: 0.7142 (OUTLIER) cc_final: 0.6464 (p0) REVERT: 6 17 LEU cc_start: 0.8208 (mt) cc_final: 0.7990 (mt) REVERT: 7 9 ARG cc_start: 0.6929 (OUTLIER) cc_final: 0.6468 (ttt180) REVERT: 9 17 LEU cc_start: 0.8270 (tp) cc_final: 0.7807 (mp) REVERT: D 9 ARG cc_start: 0.6543 (ttp-170) cc_final: 0.6143 (tmt170) REVERT: J 22 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.6980 (mpm) REVERT: L 151 ASP cc_start: 0.8784 (m-30) cc_final: 0.8422 (m-30) REVERT: L 181 TRP cc_start: 0.6776 (OUTLIER) cc_final: 0.5138 (t-100) REVERT: M 541 MET cc_start: 0.8171 (mtp) cc_final: 0.7960 (mtp) REVERT: N 17 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8534 (tp) REVERT: P 9 ARG cc_start: 0.7981 (ttp-170) cc_final: 0.7575 (ttp-110) REVERT: P 38 TRP cc_start: 0.8870 (OUTLIER) cc_final: 0.8395 (t60) REVERT: Q 55 ARG cc_start: 0.7326 (ttm170) cc_final: 0.7093 (mtp180) REVERT: C 31 MET cc_start: 0.6380 (ttm) cc_final: 0.6131 (ttm) REVERT: C 223 GLU cc_start: 0.8292 (tt0) cc_final: 0.8041 (tt0) outliers start: 52 outliers final: 24 residues processed: 350 average time/residue: 1.1651 time to fit residues: 479.5278 Evaluate side-chains 334 residues out of total 1969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 304 time to evaluate : 2.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 15 SER Chi-restraints excluded: chain 5 residue 21 VAL Chi-restraints excluded: chain 6 residue 8 ASP Chi-restraints excluded: chain 7 residue 9 ARG Chi-restraints excluded: chain 8 residue 31 LYS Chi-restraints excluded: chain 8 residue 32 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain J residue 22 MET Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 181 TRP Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain L residue 285 SER Chi-restraints excluded: chain L residue 290 LYS Chi-restraints excluded: chain L residue 305 TRP Chi-restraints excluded: chain M residue 375 VAL Chi-restraints excluded: chain M residue 509 THR Chi-restraints excluded: chain M residue 519 PHE Chi-restraints excluded: chain M residue 613 LEU Chi-restraints excluded: chain M residue 632 ASN Chi-restraints excluded: chain N residue 11 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 LEU Chi-restraints excluded: chain P residue 38 TRP Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 243 CYS 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: 1.9990 chunk 39 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 198 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 13 GLN 1 37 ASN 8 22 GLN E 13 GLN I 19 ASN L 112 GLN L 120 GLN L 227 HIS O 13 GLN S 22 GLN W 13 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 24965 Z= 0.361 Angle : 0.875 17.286 34760 Z= 0.343 Chirality : 0.044 0.270 3424 Planarity : 0.005 0.047 4222 Dihedral : 18.243 179.865 4788 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.25 % Allowed : 15.79 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.83 (0.17), residues: 2256 helix: 2.30 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : -0.78 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP T 38 HIS 0.009 0.001 HIS M 589 PHE 0.026 0.002 PHE X 8 TYR 0.020 0.002 TYR M 424 ARG 0.007 0.001 ARG 8 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 321 time to evaluate : 2.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 38 ILE cc_start: 0.8475 (mm) cc_final: 0.8191 (mt) REVERT: 2 7 ASN cc_start: 0.7049 (p0) cc_final: 0.6722 (p0) REVERT: 3 9 ARG cc_start: 0.7022 (ttp-170) cc_final: 0.6596 (ttm110) REVERT: 4 34 TYR cc_start: 0.7745 (m-10) cc_final: 0.7038 (m-10) REVERT: 6 8 ASP cc_start: 0.7170 (OUTLIER) cc_final: 0.6482 (p0) REVERT: 7 9 ARG cc_start: 0.6933 (OUTLIER) cc_final: 0.6469 (ttt180) REVERT: 8 20 ASN cc_start: 0.8245 (m-40) cc_final: 0.7985 (m110) REVERT: 9 17 LEU cc_start: 0.8139 (tp) cc_final: 0.7705 (mp) REVERT: J 22 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.7102 (mpm) REVERT: L 151 ASP cc_start: 0.8805 (m-30) cc_final: 0.8436 (m-30) REVERT: L 181 TRP cc_start: 0.6991 (OUTLIER) cc_final: 0.5364 (t-100) REVERT: M 541 MET cc_start: 0.8167 (mtp) cc_final: 0.7924 (mtp) REVERT: N 17 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8532 (tp) REVERT: P 38 TRP cc_start: 0.8896 (OUTLIER) cc_final: 0.8382 (t60) REVERT: Q 55 ARG cc_start: 0.7392 (ttm170) cc_final: 0.7061 (mtp180) REVERT: U 8 ASP cc_start: 0.7238 (p0) cc_final: 0.6940 (p0) REVERT: U 13 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7532 (tp40) REVERT: W 7 ASN cc_start: 0.6530 (p0) cc_final: 0.6290 (p0) REVERT: C 31 MET cc_start: 0.6399 (ttm) cc_final: 0.6027 (ttt) REVERT: C 188 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7482 (pt0) REVERT: C 223 GLU cc_start: 0.8300 (tt0) cc_final: 0.8050 (tt0) outliers start: 64 outliers final: 33 residues processed: 360 average time/residue: 1.2426 time to fit residues: 525.2190 Evaluate side-chains 343 residues out of total 1969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 302 time to evaluate : 2.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 15 SER Chi-restraints excluded: chain 5 residue 21 VAL Chi-restraints excluded: chain 6 residue 8 ASP Chi-restraints excluded: chain 7 residue 9 ARG Chi-restraints excluded: chain 8 residue 31 LYS Chi-restraints excluded: chain 8 residue 32 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain J residue 22 MET Chi-restraints excluded: chain J residue 27 HIS Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 181 TRP Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain L residue 266 VAL Chi-restraints excluded: chain L residue 285 SER Chi-restraints excluded: chain L residue 290 LYS Chi-restraints excluded: chain L residue 305 TRP Chi-restraints excluded: chain M residue 375 VAL Chi-restraints excluded: chain M residue 509 THR Chi-restraints excluded: chain M residue 519 PHE Chi-restraints excluded: chain M residue 613 LEU Chi-restraints excluded: chain M residue 632 ASN Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 11 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 LEU Chi-restraints excluded: chain P residue 11 SER Chi-restraints excluded: chain P residue 38 TRP Chi-restraints excluded: chain Q residue 13 GLN Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain U residue 13 GLN Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 205 TYR Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain X residue 23 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 191 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 113 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 166 optimal weight: 8.9990 chunk 110 optimal weight: 0.9980 chunk 197 optimal weight: 9.9990 chunk 123 optimal weight: 0.6980 chunk 120 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 13 GLN E 13 GLN I 19 ASN L 120 GLN L 227 HIS O 13 GLN S 22 GLN W 13 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24965 Z= 0.207 Angle : 0.722 16.519 34760 Z= 0.288 Chirality : 0.038 0.199 3424 Planarity : 0.004 0.043 4222 Dihedral : 17.638 179.894 4787 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.59 % Allowed : 17.06 % Favored : 80.35 % 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 (0.17), residues: 2256 helix: 2.62 (0.13), residues: 1433 sheet: None (None), residues: 0 loop : -0.75 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 594 HIS 0.008 0.001 HIS L 227 PHE 0.026 0.001 PHE X 8 TYR 0.015 0.001 TYR C 133 ARG 0.010 0.000 ARG 8 55 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 321 time to evaluate : 2.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 7 ASN cc_start: 0.7188 (p0) cc_final: 0.6674 (p0) REVERT: 3 9 ARG cc_start: 0.7026 (ttp-170) cc_final: 0.6581 (ttm110) REVERT: 4 34 TYR cc_start: 0.7701 (m-10) cc_final: 0.6835 (m-10) REVERT: 6 8 ASP cc_start: 0.7152 (OUTLIER) cc_final: 0.6477 (p0) REVERT: 7 9 ARG cc_start: 0.6906 (OUTLIER) cc_final: 0.6461 (ttt180) REVERT: 9 17 LEU cc_start: 0.8174 (tp) cc_final: 0.7799 (mm) REVERT: E 20 ASN cc_start: 0.8007 (OUTLIER) cc_final: 0.7689 (m-40) REVERT: L 41 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6761 (mt-10) REVERT: L 151 ASP cc_start: 0.8761 (m-30) cc_final: 0.8416 (m-30) REVERT: M 505 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8694 (pt) REVERT: N 17 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8541 (tp) REVERT: S 55 ARG cc_start: 0.7290 (mtp85) cc_final: 0.6502 (mtt-85) REVERT: U 8 ASP cc_start: 0.7073 (p0) cc_final: 0.6755 (p0) REVERT: U 13 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.7552 (tp40) REVERT: W 7 ASN cc_start: 0.6500 (p0) cc_final: 0.6272 (p0) REVERT: C 223 GLU cc_start: 0.8272 (tt0) cc_final: 0.7998 (tt0) outliers start: 51 outliers final: 23 residues processed: 354 average time/residue: 1.1805 time to fit residues: 489.4905 Evaluate side-chains 336 residues out of total 1969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 306 time to evaluate : 2.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 11 SER Chi-restraints excluded: chain 3 residue 15 SER Chi-restraints excluded: chain 6 residue 8 ASP Chi-restraints excluded: chain 7 residue 9 ARG Chi-restraints excluded: chain 8 residue 31 LYS Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain E residue 20 ASN Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain J residue 22 MET Chi-restraints excluded: chain J residue 27 HIS Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 41 GLU Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 285 SER Chi-restraints excluded: chain L residue 305 TRP Chi-restraints excluded: chain M residue 375 VAL Chi-restraints excluded: chain M residue 505 ILE Chi-restraints excluded: chain M residue 509 THR Chi-restraints excluded: chain M residue 595 PHE Chi-restraints excluded: chain M residue 613 LEU Chi-restraints excluded: chain M residue 632 ASN Chi-restraints excluded: chain N residue 11 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 LEU Chi-restraints excluded: chain Q residue 13 GLN Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain U residue 13 GLN Chi-restraints excluded: chain C residue 106 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 122 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 125 optimal weight: 3.9990 chunk 134 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 179 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 13 GLN B 13 GLN E 13 GLN I 19 ASN L 120 GLN L 227 HIS O 13 GLN S 22 GLN W 13 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 24965 Z= 0.429 Angle : 0.932 17.523 34760 Z= 0.365 Chirality : 0.046 0.336 3424 Planarity : 0.005 0.047 4222 Dihedral : 18.208 179.827 4787 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.59 % Allowed : 17.12 % Favored : 80.29 % 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: 1.72 (0.17), residues: 2256 helix: 2.20 (0.13), residues: 1438 sheet: None (None), residues: 0 loop : -0.85 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 181 HIS 0.014 0.002 HIS L 227 PHE 0.026 0.002 PHE X 8 TYR 0.022 0.002 TYR Z 20 ARG 0.012 0.001 ARG 8 55 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 322 time to evaluate : 2.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 7 ASN cc_start: 0.7328 (p0) cc_final: 0.6961 (p0) REVERT: 3 9 ARG cc_start: 0.7051 (ttp-170) cc_final: 0.6622 (ttm110) REVERT: 4 34 TYR cc_start: 0.7747 (m-10) cc_final: 0.7025 (m-10) REVERT: 6 8 ASP cc_start: 0.7141 (OUTLIER) cc_final: 0.6442 (p0) REVERT: 7 9 ARG cc_start: 0.6912 (OUTLIER) cc_final: 0.6405 (ttt180) REVERT: 9 17 LEU cc_start: 0.8249 (tp) cc_final: 0.7779 (mm) REVERT: J 22 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7109 (mpm) REVERT: K 13 GLN cc_start: 0.7546 (tt0) cc_final: 0.7301 (tt0) REVERT: K 55 ARG cc_start: 0.7474 (ttp-110) cc_final: 0.6995 (ttm170) REVERT: L 41 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6825 (mt-10) REVERT: L 151 ASP cc_start: 0.8815 (m-30) cc_final: 0.8443 (m-30) REVERT: L 181 TRP cc_start: 0.6832 (OUTLIER) cc_final: 0.5315 (t-100) REVERT: N 17 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8584 (tp) REVERT: S 55 ARG cc_start: 0.7406 (mtp85) cc_final: 0.6623 (mtt-85) REVERT: U 8 ASP cc_start: 0.7155 (p0) cc_final: 0.6861 (p0) REVERT: U 13 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7477 (tp40) REVERT: C 188 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7456 (pt0) REVERT: C 223 GLU cc_start: 0.8307 (tt0) cc_final: 0.8061 (tt0) REVERT: X 26 SER cc_start: 0.6799 (OUTLIER) cc_final: 0.6423 (p) outliers start: 51 outliers final: 27 residues processed: 354 average time/residue: 1.2620 time to fit residues: 525.7973 Evaluate side-chains 342 residues out of total 1969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 306 time to evaluate : 2.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 11 SER Chi-restraints excluded: chain 3 residue 15 SER Chi-restraints excluded: chain 5 residue 17 LEU Chi-restraints excluded: chain 5 residue 21 VAL Chi-restraints excluded: chain 6 residue 8 ASP Chi-restraints excluded: chain 7 residue 9 ARG Chi-restraints excluded: chain 8 residue 31 LYS Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain J residue 22 MET Chi-restraints excluded: chain J residue 27 HIS Chi-restraints excluded: chain L residue 41 GLU Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 181 TRP Chi-restraints excluded: chain L residue 285 SER Chi-restraints excluded: chain L residue 305 TRP Chi-restraints excluded: chain M residue 375 VAL Chi-restraints excluded: chain M residue 442 THR Chi-restraints excluded: chain M residue 509 THR Chi-restraints excluded: chain M residue 595 PHE Chi-restraints excluded: chain M residue 613 LEU Chi-restraints excluded: chain M residue 632 ASN Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 LEU Chi-restraints excluded: chain Q residue 13 GLN Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain U residue 13 GLN Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain X residue 23 MET Chi-restraints excluded: chain X residue 26 SER Chi-restraints excluded: chain Y residue 11 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 189 optimal weight: 0.9980 chunk 172 optimal weight: 6.9990 chunk 184 optimal weight: 0.6980 chunk 110 optimal weight: 0.4980 chunk 80 optimal weight: 0.9980 chunk 144 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 166 optimal weight: 5.9990 chunk 174 optimal weight: 4.9990 chunk 183 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 13 GLN B 13 GLN E 13 GLN I 19 ASN L 120 GLN O 13 GLN S 22 GLN W 13 GLN Y 2 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24965 Z= 0.195 Angle : 0.739 17.930 34760 Z= 0.293 Chirality : 0.038 0.206 3424 Planarity : 0.004 0.054 4222 Dihedral : 17.545 179.974 4787 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.23 % Allowed : 17.88 % Favored : 79.89 % 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: 2.14 (0.17), residues: 2256 helix: 2.59 (0.13), residues: 1432 sheet: None (None), residues: 0 loop : -0.77 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 41 HIS 0.005 0.001 HIS L 192 PHE 0.027 0.001 PHE X 8 TYR 0.017 0.001 TYR C 133 ARG 0.012 0.000 ARG 8 55 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 320 time to evaluate : 2.489 Fit side-chains revert: symmetry clash REVERT: 2 7 ASN cc_start: 0.7376 (p0) cc_final: 0.6781 (p0) REVERT: 3 9 ARG cc_start: 0.7022 (ttp-170) cc_final: 0.6580 (ttm110) REVERT: 4 34 TYR cc_start: 0.7705 (m-10) cc_final: 0.6863 (m-10) REVERT: 5 12 VAL cc_start: 0.8677 (t) cc_final: 0.8445 (t) REVERT: 6 8 ASP cc_start: 0.7147 (OUTLIER) cc_final: 0.6458 (p0) REVERT: 7 9 ARG cc_start: 0.6884 (OUTLIER) cc_final: 0.6462 (ttt180) REVERT: 9 17 LEU cc_start: 0.8068 (tp) cc_final: 0.7715 (mm) REVERT: J 9 ARG cc_start: 0.7976 (ttp-110) cc_final: 0.7280 (ptt90) REVERT: K 13 GLN cc_start: 0.7506 (tt0) cc_final: 0.7296 (tt0) REVERT: K 55 ARG cc_start: 0.7330 (ttp-110) cc_final: 0.6890 (ttm170) REVERT: L 41 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6736 (mt-10) REVERT: L 151 ASP cc_start: 0.8764 (m-30) cc_final: 0.8432 (m-30) REVERT: N 17 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8562 (tp) REVERT: P 9 ARG cc_start: 0.7974 (ttp-170) cc_final: 0.7524 (ttp-110) REVERT: S 55 ARG cc_start: 0.7289 (mtp85) cc_final: 0.6485 (mtt-85) REVERT: U 8 ASP cc_start: 0.7141 (p0) cc_final: 0.6836 (p0) REVERT: C 223 GLU cc_start: 0.8289 (tt0) cc_final: 0.8005 (tt0) outliers start: 44 outliers final: 28 residues processed: 348 average time/residue: 1.2227 time to fit residues: 497.2980 Evaluate side-chains 341 residues out of total 1969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 309 time to evaluate : 2.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 11 SER Chi-restraints excluded: chain 3 residue 15 SER Chi-restraints excluded: chain 5 residue 13 VAL Chi-restraints excluded: chain 5 residue 17 LEU Chi-restraints excluded: chain 5 residue 21 VAL Chi-restraints excluded: chain 6 residue 8 ASP Chi-restraints excluded: chain 7 residue 9 ARG Chi-restraints excluded: chain 8 residue 31 LYS Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain J residue 22 MET Chi-restraints excluded: chain J residue 27 HIS Chi-restraints excluded: chain L residue 41 GLU Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 285 SER Chi-restraints excluded: chain L residue 305 TRP Chi-restraints excluded: chain M residue 375 VAL Chi-restraints excluded: chain M residue 442 THR Chi-restraints excluded: chain M residue 509 THR Chi-restraints excluded: chain M residue 595 PHE Chi-restraints excluded: chain M residue 613 LEU Chi-restraints excluded: chain M residue 632 ASN Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 LEU Chi-restraints excluded: chain Q residue 13 GLN Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain Y residue 11 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 194 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 135 optimal weight: 8.9990 chunk 204 optimal weight: 9.9990 chunk 187 optimal weight: 4.9990 chunk 162 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 125 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 129 optimal weight: 0.0470 overall best weight: 2.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 13 GLN B 13 GLN E 13 GLN I 19 ASN L 120 GLN O 13 GLN S 22 GLN W 13 GLN Y 2 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 24965 Z= 0.312 Angle : 0.827 17.079 34760 Z= 0.327 Chirality : 0.041 0.254 3424 Planarity : 0.005 0.050 4222 Dihedral : 17.752 179.850 4787 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.44 % Allowed : 18.13 % Favored : 79.43 % 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: 1.98 (0.17), residues: 2256 helix: 2.44 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : -0.79 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 41 HIS 0.007 0.001 HIS M 589 PHE 0.027 0.002 PHE X 8 TYR 0.017 0.002 TYR M 424 ARG 0.014 0.001 ARG 8 55 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 315 time to evaluate : 2.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 7 ASN cc_start: 0.7412 (p0) cc_final: 0.6846 (p0) REVERT: 3 9 ARG cc_start: 0.7041 (ttp-170) cc_final: 0.6622 (ttm110) REVERT: 4 34 TYR cc_start: 0.7679 (m-10) cc_final: 0.6937 (m-10) REVERT: 5 4 ARG cc_start: 0.6744 (ttt180) cc_final: 0.6510 (ttt180) REVERT: 6 8 ASP cc_start: 0.7175 (OUTLIER) cc_final: 0.6492 (p0) REVERT: 7 9 ARG cc_start: 0.6863 (OUTLIER) cc_final: 0.6439 (ttt180) REVERT: 9 17 LEU cc_start: 0.8180 (tp) cc_final: 0.7745 (mm) REVERT: J 22 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.7140 (mpm) REVERT: K 13 GLN cc_start: 0.7536 (tt0) cc_final: 0.7301 (tt0) REVERT: K 55 ARG cc_start: 0.7366 (ttp-110) cc_final: 0.6921 (ttm170) REVERT: L 41 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6791 (mt-10) REVERT: L 151 ASP cc_start: 0.8781 (m-30) cc_final: 0.8441 (m-30) REVERT: N 17 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8565 (tp) REVERT: P 9 ARG cc_start: 0.8019 (ttp-170) cc_final: 0.7548 (ttp-110) REVERT: S 55 ARG cc_start: 0.7293 (mtp85) cc_final: 0.6497 (mtt-85) REVERT: U 8 ASP cc_start: 0.7212 (p0) cc_final: 0.6922 (p0) REVERT: C 188 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7472 (pt0) REVERT: C 223 GLU cc_start: 0.8296 (tt0) cc_final: 0.8024 (tt0) outliers start: 48 outliers final: 31 residues processed: 348 average time/residue: 1.2084 time to fit residues: 490.1266 Evaluate side-chains 343 residues out of total 1969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 306 time to evaluate : 2.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 11 SER Chi-restraints excluded: chain 3 residue 15 SER Chi-restraints excluded: chain 5 residue 13 VAL Chi-restraints excluded: chain 5 residue 17 LEU Chi-restraints excluded: chain 5 residue 21 VAL Chi-restraints excluded: chain 6 residue 8 ASP Chi-restraints excluded: chain 7 residue 9 ARG Chi-restraints excluded: chain 8 residue 31 LYS Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain J residue 22 MET Chi-restraints excluded: chain J residue 27 HIS Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 41 GLU Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain L residue 285 SER Chi-restraints excluded: chain L residue 305 TRP Chi-restraints excluded: chain M residue 375 VAL Chi-restraints excluded: chain M residue 442 THR Chi-restraints excluded: chain M residue 509 THR Chi-restraints excluded: chain M residue 595 PHE Chi-restraints excluded: chain M residue 613 LEU Chi-restraints excluded: chain M residue 632 ASN Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 LEU Chi-restraints excluded: chain Q residue 13 GLN Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain Y residue 11 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 0.0980 chunk 49 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 162 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 167 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 143 optimal weight: 2.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 13 GLN B 13 GLN E 13 GLN I 19 ASN L 115 ASN L 120 GLN M 414 ASN O 13 GLN S 22 GLN W 13 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.114120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.097217 restraints weight = 30805.505| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.05 r_work: 0.2810 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 24965 Z= 0.244 Angle : 0.766 16.839 34760 Z= 0.306 Chirality : 0.039 0.224 3424 Planarity : 0.004 0.053 4222 Dihedral : 17.541 179.904 4787 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.13 % Allowed : 18.38 % Favored : 79.48 % 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: 2.09 (0.17), residues: 2256 helix: 2.55 (0.13), residues: 1431 sheet: None (None), residues: 0 loop : -0.78 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 41 HIS 0.007 0.001 HIS L 192 PHE 0.027 0.001 PHE X 8 TYR 0.016 0.002 TYR C 133 ARG 0.013 0.000 ARG 8 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8172.45 seconds wall clock time: 146 minutes 9.53 seconds (8769.53 seconds total)