Starting phenix.real_space_refine on Fri Aug 9 07:18:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hju_34838/08_2024/8hju_34838.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hju_34838/08_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_34838/08_2024/8hju_34838.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hju_34838/08_2024/8hju_34838.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hju_34838/08_2024/8hju_34838.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hju_34838/08_2024/8hju_34838.cif" } 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 12.18, per 1000 atoms: 0.51 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: 10.86 Conformation dependent library (CDL) restraints added in 3.7 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... Secondary structure from input PDB file: 82 helices and 3 sheets defined 68.9% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain '0' and resid 19 through 51 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 33 Processing helix chain '2' and resid 19 through 51 removed outlier: 3.834A pdb=" N LEU 2 24 " --> pdb=" O ASN 2 20 " (cutoff:3.500A) Processing helix chain '3' and resid 7 through 34 removed outlier: 3.975A pdb=" N GLY 3 34 " --> pdb=" O VAL 3 30 " (cutoff:3.500A) Processing helix chain '4' and resid 19 through 51 removed outlier: 3.834A pdb=" N LEU 4 24 " --> pdb=" O ASN 4 20 " (cutoff:3.500A) Processing helix chain '5' and resid 7 through 34 removed outlier: 3.974A pdb=" N GLY 5 34 " --> pdb=" O VAL 5 30 " (cutoff:3.500A) Processing helix chain '6' and resid 19 through 51 removed outlier: 3.834A pdb=" N LEU 6 24 " --> pdb=" O ASN 6 20 " (cutoff:3.500A) Processing helix chain '7' and resid 7 through 34 removed outlier: 3.974A pdb=" N GLY 7 34 " --> pdb=" O VAL 7 30 " (cutoff:3.500A) Processing helix chain '8' and resid 19 through 51 removed outlier: 3.833A pdb=" N LEU 8 24 " --> pdb=" O ASN 8 20 " (cutoff:3.500A) Processing helix chain '9' and resid 7 through 34 removed outlier: 3.974A pdb=" N GLY 9 34 " --> pdb=" O VAL 9 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 34 removed outlier: 3.974A pdb=" N GLY A 34 " --> pdb=" O VAL A 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 15 Processing helix chain 'B' and resid 19 through 51 removed outlier: 3.834A pdb=" N LEU B 24 " --> pdb=" O ASN B 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 34 removed outlier: 3.974A pdb=" N GLY D 34 " --> pdb=" O VAL D 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 15 Processing helix chain 'E' and resid 19 through 51 removed outlier: 3.833A pdb=" N LEU E 24 " --> pdb=" O ASN E 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 34 removed outlier: 3.974A pdb=" N GLY F 34 " --> pdb=" O VAL F 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 51 removed outlier: 3.833A pdb=" N LEU G 24 " --> pdb=" O ASN G 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 34 removed outlier: 3.974A pdb=" N GLY H 34 " --> pdb=" O VAL H 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 11 through 15 Processing helix chain 'I' and resid 19 through 51 removed outlier: 3.834A pdb=" N LEU I 24 " --> pdb=" O ASN I 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 34 removed outlier: 3.974A pdb=" N GLY J 34 " --> pdb=" O VAL J 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 51 removed outlier: 3.833A pdb=" N LEU K 24 " --> pdb=" O ASN K 20 " (cutoff:3.500A) Processing helix chain 'L' and resid 35 through 43 Processing helix chain 'L' and resid 49 through 55 Processing helix chain 'L' and resid 70 through 93 removed outlier: 4.108A pdb=" N GLY L 91 " --> pdb=" O TYR L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 109 through 113 Processing helix chain 'L' and resid 122 through 150 Processing helix chain 'L' and resid 154 through 172 Processing helix chain 'L' and resid 172 through 179 Processing helix chain 'L' and resid 191 through 203 Processing helix chain 'L' and resid 205 through 208 Processing helix chain 'L' and resid 209 through 236 Processing helix chain 'L' and resid 244 through 253 Processing helix chain 'L' and resid 259 through 288 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 291 through 296 removed outlier: 4.031A pdb=" N TRP L 296 " --> pdb=" O TRP L 292 " (cutoff:3.500A) Processing helix chain 'L' and resid 297 through 302 removed outlier: 4.036A pdb=" N ASP L 300 " --> pdb=" O GLY L 297 " (cutoff:3.500A) Processing helix chain 'L' and resid 310 through 314 removed outlier: 3.869A pdb=" N VAL L 314 " --> pdb=" O GLY L 311 " (cutoff:3.500A) Processing helix chain 'M' and resid 337 through 344 Processing helix chain 'M' and resid 359 through 366 Processing helix chain 'M' and resid 378 through 401 Processing helix chain 'M' and resid 404 through 412 removed outlier: 3.512A pdb=" N LEU M 409 " --> pdb=" O PRO M 405 " (cutoff:3.500A) Processing helix chain 'M' and resid 435 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 467 through 485 Processing helix chain 'M' and resid 493 through 497 removed outlier: 3.558A pdb=" N ALA M 496 " --> pdb=" O ASN M 493 " (cutoff:3.500A) Processing helix chain 'M' and resid 503 through 516 Processing helix chain 'M' and resid 518 through 521 Processing helix chain 'M' and resid 522 through 549 Processing helix chain 'M' and resid 550 through 553 Processing helix chain 'M' and resid 556 through 561 Processing helix chain 'M' and resid 565 through 580 Processing helix chain 'M' and resid 586 through 613 removed outlier: 3.602A pdb=" N ILE M 590 " --> pdb=" O TYR M 586 " (cutoff:3.500A) 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 616 through 624 Processing helix chain 'N' and resid 7 through 34 removed outlier: 3.974A pdb=" N GLY N 34 " --> pdb=" O VAL N 30 " (cutoff:3.500A) Processing helix chain 'O' and resid 19 through 51 removed outlier: 3.834A pdb=" N LEU O 24 " --> pdb=" O ASN O 20 " (cutoff:3.500A) Processing helix chain 'P' and resid 7 through 34 removed outlier: 3.974A pdb=" N GLY P 34 " --> pdb=" O VAL P 30 " (cutoff:3.500A) Processing helix chain 'Q' and resid 19 through 51 removed outlier: 3.834A pdb=" N LEU Q 24 " --> pdb=" O ASN Q 20 " (cutoff:3.500A) Processing helix chain 'R' and resid 7 through 34 removed outlier: 3.974A pdb=" N GLY R 34 " --> pdb=" O VAL R 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 19 through 51 removed outlier: 3.834A pdb=" N LEU S 24 " --> pdb=" O ASN S 20 " (cutoff:3.500A) Processing helix chain 'T' and resid 7 through 34 removed outlier: 3.974A pdb=" N GLY T 34 " --> pdb=" O VAL T 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 11 through 15 Processing helix chain 'U' and resid 19 through 51 removed outlier: 3.834A pdb=" N LEU U 24 " --> pdb=" O ASN U 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 7 through 33 Processing helix chain 'V' and resid 36 through 40 Processing helix chain 'W' and resid 19 through 51 removed outlier: 3.834A pdb=" N LEU W 24 " --> pdb=" O ASN W 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 14 Processing helix chain 'C' and resid 15 through 47 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 71 through 85 Processing helix chain 'C' and resid 98 through 109 Processing helix chain 'C' and resid 109 through 115 Processing helix chain 'C' and resid 117 through 121 Processing helix chain 'C' and resid 135 through 156 removed outlier: 3.509A pdb=" N LYS C 139 " --> pdb=" O ASN C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 175 removed outlier: 3.920A pdb=" N CYS C 174 " --> pdb=" O THR C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 236 Processing helix chain 'C' and resid 239 through 243 removed outlier: 3.506A pdb=" N PHE C 242 " --> pdb=" O GLY C 239 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N CYS C 243 " --> pdb=" O CYS C 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 239 through 243' Processing helix chain 'C' and resid 255 through 274 removed outlier: 3.593A pdb=" N HIS C 259 " --> pdb=" O ALA C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 289 removed outlier: 4.323A pdb=" N GLY C 288 " --> pdb=" O ILE C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 298 removed outlier: 4.430A pdb=" N CYS C 296 " --> pdb=" O SER C 292 " (cutoff:3.500A) Processing helix chain 'X' and resid 2 through 25 Processing helix chain 'Y' and resid 2 through 31 Proline residue: Y 19 - end of helix Processing helix chain 'Z' and resid 16 through 47 Proline residue: Z 26 - end of helix Processing helix chain 'Z' and resid 53 through 58 Processing sheet with id=AA1, first strand: chain 'L' and resid 32 through 34 removed outlier: 3.992A pdb=" N TYR Z 49 " --> pdb=" O ILE L 34 " (cutoff:3.500A) Processing sheet with id=AA2, 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=AA3, 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) 1246 hydrogen bonds defined for protein. 3663 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: 7.34 Time building geometry restraints manager: 11.34 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: 14798 3.06 - 3.67: 36960 3.67 - 4.29: 62204 4.29 - 4.90: 100285 Nonbonded interactions: 214343 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 3.040 nonbonded pdb=" NE2 HIS C 297 " pdb="FE HEM C 405 " model vdw 2.114 3.080 ... (remaining 214338 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '0' and resid 7 through 55) 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: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.950 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 61.740 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.210 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: 0.020 Load rotamer database and sin/cos tables:13.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.910 ------------------------------------------------------------------------------- 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= 1.009 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 : 2.077 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: 1.1649 time to fit residues: 633.9005 Evaluate side-chains 329 residues out of total 1969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 322 time to evaluate : 2.302 ------------------------------------------------------------------------------- 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: 8.9990 chunk 155 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 160 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 chunk 186 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: