Starting phenix.real_space_refine on Mon Feb 19 03:31:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5o_35988/02_2024/8j5o_35988_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5o_35988/02_2024/8j5o_35988.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5o_35988/02_2024/8j5o_35988.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5o_35988/02_2024/8j5o_35988.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5o_35988/02_2024/8j5o_35988_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5o_35988/02_2024/8j5o_35988_updated.pdb" } resolution = 2.9 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 5 7.16 5 P 4 5.49 5 Mg 48 5.21 5 S 75 5.16 5 C 16852 2.51 5 N 3297 2.21 5 O 3411 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 7": "OE1" <-> "OE2" Residue "J GLU 7": "OE1" <-> "OE2" Residue "L GLU 90": "OE1" <-> "OE2" Residue "L GLU 95": "OE1" <-> "OE2" Residue "L PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 341": "OE1" <-> "OE2" Residue "M GLU 348": "OE1" <-> "OE2" Residue "M TYR 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 555": "OE1" <-> "OE2" Residue "M GLU 564": "OE1" <-> "OE2" Residue "N GLU 7": "OE1" <-> "OE2" Residue "V PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 23692 Number of models: 1 Model: "" Number of chains: 69 Chain: "0" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "1" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 266 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "2" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "3" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 295 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "4" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "5" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "6" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "7" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 295 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "8" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "9" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 295 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "A" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "B" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "C" Number of atoms: 2404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2404 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 24, 'TRANS': 290} Chain: "D" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "E" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "F" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 295 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "H" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "I" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "J" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 295 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "K" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "L" Number of atoms: 2364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2364 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 16, 'TRANS': 282} Chain breaks: 1 Chain: "M" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2488 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 16, 'TRANS': 289} Chain: "N" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 295 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "O" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "P" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 295 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "Q" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "R" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "S" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "T" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "U" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "V" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 295 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "W" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "X" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 206 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 1, 'TRANS': 24} Chain: "Y" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 259 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 2, 'TRANS': 29} Chain: "Z" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 362 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 4, 'TRANS': 42} Chain: "0" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 214 Unusual residues: {'BCL': 2, 'KGD': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "1" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 148 Unusual residues: {'BCL': 1, 'KGD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "2" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'KGD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "3" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'KGD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "5" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "6" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'KGD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "7" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "8" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'KGD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "9" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'KGD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 299 Unusual residues: {'HEM': 4, 'KGD': 2, 'PGV': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "D" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 148 Unusual residues: {'BCL': 1, 'KGD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'KGD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'KGD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 148 Unusual residues: {'BCL': 1, 'KGD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'KGD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 438 Unusual residues: {' FE': 1, 'BCL': 2, 'BPH': 2, 'MQE': 1, 'PGV': 3} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'PGV:plan-3': 2} Unresolved non-hydrogen planarities: 7 Chain: "M" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 223 Unusual residues: {'BCL': 1, 'BPH': 1, 'MQE': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'MQE:plan-12': 1, 'MQE:plan-11': 1, 'MQE:plan-10': 1, 'MQE:plan-9': 1, 'MQE:plan-6': 1, 'MQE:plan-5': 1, 'MQE:plan-4': 1, 'MQE:plan-3': 1, 'MQE:plan-2': 1} Unresolved non-hydrogen planarities: 44 Chain: "N" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'KGD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "P" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'KGD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 214 Unusual residues: {'BCL': 2, 'KGD': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "T" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'KGD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "V" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 11.99, per 1000 atoms: 0.51 Number of scatterers: 23692 At special positions: 0 Unit cell: (142.88, 131.271, 126.806, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 5 26.01 S 75 16.00 P 4 15.00 Mg 48 11.99 O 3411 8.00 N 3297 7.00 C 16852 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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=58, symmetry=0 Number of additional bonds: simple=58, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.38 Conformation dependent library (CDL) restraints added in 3.3 seconds 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4346 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 83 helices and 2 sheets defined 62.0% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.31 Creating SS restraints... Processing helix chain '0' and resid 20 through 50 removed outlier: 4.225A pdb=" N LEU 0 24 " --> pdb=" O ASN 0 20 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL 0 25 " --> pdb=" O ALA 0 21 " (cutoff:3.500A) Processing helix chain '1' and resid 8 through 33 Processing helix chain '2' and resid 20 through 50 removed outlier: 3.819A pdb=" N LEU 2 24 " --> pdb=" O ASN 2 20 " (cutoff:3.500A) Processing helix chain '3' and resid 8 through 33 Processing helix chain '4' and resid 20 through 50 removed outlier: 4.274A pdb=" N LEU 4 24 " --> pdb=" O ASN 4 20 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL 4 25 " --> pdb=" O ALA 4 21 " (cutoff:3.500A) Processing helix chain '5' and resid 8 through 33 Processing helix chain '6' and resid 20 through 50 removed outlier: 4.356A pdb=" N LEU 6 24 " --> pdb=" O ASN 6 20 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL 6 25 " --> pdb=" O ALA 6 21 " (cutoff:3.500A) Processing helix chain '7' and resid 8 through 33 Processing helix chain '8' and resid 20 through 50 removed outlier: 4.156A pdb=" N LEU 8 24 " --> pdb=" O ASN 8 20 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL 8 25 " --> pdb=" O ALA 8 21 " (cutoff:3.500A) Processing helix chain '9' and resid 8 through 33 Processing helix chain 'A' and resid 8 through 33 Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 20 through 50 removed outlier: 4.455A pdb=" N LEU B 24 " --> pdb=" O ASN B 20 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 13 No H-bonds generated for 'chain 'C' and resid 10 through 13' Processing helix chain 'C' and resid 16 through 45 removed outlier: 3.941A pdb=" N TYR C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ILE C 22 " --> pdb=" O GLY C 18 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 84 removed outlier: 3.664A pdb=" N ASN C 79 " --> pdb=" O LEU C 75 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA C 80 " --> pdb=" O ALA C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 108 Processing helix chain 'C' and resid 110 through 114 removed outlier: 3.562A pdb=" N LEU C 114 " --> pdb=" O VAL C 110 " (cutoff:3.500A) No H-bonds generated for '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 157 through 159 No H-bonds generated for 'chain 'C' and resid 157 through 159' 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 187 through 189 No H-bonds generated for 'chain 'C' and resid 187 through 189' Processing helix chain 'C' and resid 219 through 234 Processing helix chain 'C' and resid 257 through 273 Processing helix chain 'C' and resid 285 through 288 removed outlier: 4.394A pdb=" N GLY C 288 " --> pdb=" O ILE C 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 285 through 288' Processing helix chain 'C' and resid 293 through 297 Processing helix chain 'D' and resid 8 through 32 Processing helix chain 'E' and resid 15 through 17 No H-bonds generated for 'chain 'E' and resid 15 through 17' Processing helix chain 'E' and resid 20 through 50 removed outlier: 4.085A pdb=" N LEU E 24 " --> pdb=" O ASN E 20 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL E 25 " --> pdb=" O ALA E 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 33 Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 20 through 50 removed outlier: 4.076A pdb=" N LEU G 24 " --> pdb=" O ASN G 20 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL G 25 " --> pdb=" O ALA G 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 32 Processing helix chain 'I' and resid 20 through 50 removed outlier: 4.225A pdb=" N LEU I 24 " --> pdb=" O ASN I 20 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL I 25 " --> pdb=" O ALA I 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 8 through 33 Processing helix chain 'K' and resid 22 through 50 Processing helix chain 'L' and resid 36 through 42 Processing helix chain 'L' and resid 50 through 55 Processing helix chain 'L' and resid 71 through 92 removed outlier: 3.737A pdb=" N ILE L 75 " --> pdb=" O LEU L 71 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLY L 91 " --> pdb=" O TYR L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 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 210 through 236 removed outlier: 4.070A pdb=" N GLU L 236 " --> pdb=" O ALA L 232 " (cutoff:3.500A) Processing helix chain 'L' and resid 245 through 252 Processing helix chain 'L' and resid 260 through 287 removed outlier: 4.361A pdb=" N HIS L 264 " --> pdb=" O GLU L 260 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG L 265 " --> pdb=" O ILE L 261 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL L 275 " --> pdb=" O GLY L 271 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR L 287 " --> pdb=" O PHE L 283 " (cutoff:3.500A) Processing helix chain 'L' and resid 294 through 298 removed outlier: 4.332A pdb=" N PHE L 298 " --> pdb=" O PHE L 295 " (cutoff:3.500A) 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 342 Processing helix chain 'M' and resid 360 through 364 Processing helix chain 'M' and resid 380 through 401 removed outlier: 3.580A pdb=" N VAL M 401 " --> pdb=" O TYR M 397 " (cutoff:3.500A) Processing helix chain 'M' and resid 405 through 410 Processing helix chain 'M' and resid 412 through 414 No H-bonds generated for 'chain 'M' and resid 412 through 414' Processing helix chain 'M' and resid 432 through 434 No H-bonds generated for 'chain 'M' and resid 432 through 434' Processing helix chain 'M' and resid 436 through 463 removed outlier: 3.719A pdb=" N ALA M 440 " --> pdb=" O GLY M 436 " (cutoff:3.500A) Processing helix chain 'M' and resid 468 through 484 removed outlier: 3.821A pdb=" N LEU M 479 " --> pdb=" O SER M 475 " (cutoff:3.500A) 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: 4.393A pdb=" N GLY M 611 " --> pdb=" O LEU M 607 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N THR M 612 " --> pdb=" O PHE M 608 " (cutoff:3.500A) 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 33 Processing helix chain 'O' and resid 20 through 50 removed outlier: 4.506A pdb=" N LEU O 24 " --> pdb=" O ASN O 20 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL O 25 " --> pdb=" O ALA O 21 " (cutoff:3.500A) Processing helix chain 'P' and resid 8 through 33 Processing helix chain 'Q' and resid 15 through 17 No H-bonds generated for 'chain 'Q' and resid 15 through 17' Processing helix chain 'Q' and resid 20 through 50 removed outlier: 4.428A pdb=" N LEU Q 24 " --> pdb=" O ASN Q 20 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL Q 25 " --> pdb=" O ALA Q 21 " (cutoff:3.500A) Processing helix chain 'R' and resid 8 through 33 Processing helix chain 'S' and resid 20 through 50 removed outlier: 4.447A pdb=" N LEU S 24 " --> pdb=" O ASN S 20 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 8 through 33 Processing helix chain 'U' and resid 12 through 14 No H-bonds generated for 'chain 'U' and resid 12 through 14' Processing helix chain 'U' and resid 20 through 50 removed outlier: 4.387A pdb=" N LEU U 24 " --> pdb=" O ASN U 20 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL U 25 " --> pdb=" O ALA U 21 " (cutoff:3.500A) Processing helix chain 'V' and resid 8 through 32 Processing helix chain 'W' and resid 20 through 50 removed outlier: 4.412A pdb=" N LEU W 24 " --> pdb=" O ASN W 20 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL W 25 " --> pdb=" O ALA W 21 " (cutoff:3.500A) Processing helix chain 'X' and resid 2 through 24 Processing helix chain 'Y' and resid 3 through 16 Processing helix chain 'Y' and resid 18 through 29 Processing helix chain 'Z' and resid 17 through 46 Proline residue: Z 26 - end of helix Processing sheet with id= A, first strand: chain 'L' and resid 62 through 64 removed outlier: 3.705A pdb=" N PHE L 62 " --> pdb=" O VAL L 69 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE L 67 " --> pdb=" O ILE L 64 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'M' and resid 349 through 351 1078 hydrogen bonds defined for protein. 3222 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: 6.11 Time building geometry restraints manager: 10.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.37: 6834 1.37 - 1.57: 17569 1.57 - 1.77: 8 1.77 - 1.98: 125 1.98 - 2.18: 208 Bond restraints: 24744 Sorted by residual: bond pdb=" NA BCL K 102 " pdb="MG BCL K 102 " ideal model delta sigma weight residual 2.170 1.997 0.173 2.40e-02 1.74e+03 5.19e+01 bond pdb=" NA BCL W 102 " pdb="MG BCL W 102 " ideal model delta sigma weight residual 2.170 2.000 0.170 2.40e-02 1.74e+03 5.00e+01 bond pdb=" CGD BCL W 102 " pdb=" O2D BCL W 102 " ideal model delta sigma weight residual 1.324 1.450 -0.126 2.10e-02 2.27e+03 3.60e+01 bond pdb=" CAY KGD J 103 " pdb=" CBD KGD J 103 " ideal model delta sigma weight residual 1.500 1.381 0.119 2.00e-02 2.50e+03 3.54e+01 bond pdb=" C1A BCL K 102 " pdb=" CHA BCL K 102 " ideal model delta sigma weight residual 1.368 1.487 -0.119 2.00e-02 2.50e+03 3.52e+01 ... (remaining 24739 not shown) Histogram of bond angle deviations from ideal: 84.54 - 103.53: 730 103.53 - 122.52: 29460 122.52 - 141.51: 4148 141.51 - 160.51: 142 160.51 - 179.50: 13 Bond angle restraints: 34493 Sorted by residual: angle pdb=" N PHE L 185 " pdb=" CA PHE L 185 " pdb=" C PHE L 185 " ideal model delta sigma weight residual 109.93 121.06 -11.13 1.24e+00 6.50e-01 8.06e+01 angle pdb=" C1D BCL K 102 " pdb=" C2D BCL K 102 " pdb=" CMD BCL K 102 " ideal model delta sigma weight residual 125.57 139.17 -13.59 1.83e+00 2.99e-01 5.53e+01 angle pdb=" C1D BCL W 102 " pdb=" C2D BCL W 102 " pdb=" CMD BCL W 102 " ideal model delta sigma weight residual 125.57 138.52 -12.94 1.83e+00 2.99e-01 5.01e+01 angle pdb=" NA BCL W 102 " pdb="MG BCL W 102 " pdb=" NC BCL W 102 " ideal model delta sigma weight residual 160.52 177.34 -16.82 2.84e+00 1.24e-01 3.51e+01 angle pdb=" N HIS L 183 " pdb=" CA HIS L 183 " pdb=" CB HIS L 183 " ideal model delta sigma weight residual 110.91 102.27 8.64 1.58e+00 4.01e-01 2.99e+01 ... (remaining 34488 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 12546 36.00 - 71.99: 364 71.99 - 107.99: 55 107.99 - 143.99: 11 143.99 - 179.98: 2 Dihedral angle restraints: 12978 sinusoidal: 6291 harmonic: 6687 Sorted by residual: dihedral pdb=" C1 BCL L1002 " pdb=" C2 BCL L1002 " pdb=" C3 BCL L1002 " pdb=" C5 BCL L1002 " ideal model delta sinusoidal sigma weight residual 180.00 0.02 179.98 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL W 102 " pdb=" CGA BCL W 102 " pdb=" O2A BCL W 102 " pdb=" CBA BCL W 102 " ideal model delta sinusoidal sigma weight residual 180.00 122.95 57.05 1 6.00e+00 2.78e-02 1.22e+02 dihedral pdb=" C2C HEM C 501 " pdb=" C3C HEM C 501 " pdb=" CAC HEM C 501 " pdb=" CBC HEM C 501 " ideal model delta sinusoidal sigma weight residual 0.00 89.17 -89.17 2 1.00e+01 1.00e-02 4.80e+01 ... (remaining 12975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 3377 0.121 - 0.241: 23 0.241 - 0.362: 4 0.362 - 0.483: 0 0.483 - 0.603: 1 Chirality restraints: 3405 Sorted by residual: chirality pdb=" CA PHE L 185 " pdb=" N PHE L 185 " pdb=" C PHE L 185 " pdb=" CB PHE L 185 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.10e+00 chirality pdb=" CA ALA L 315 " pdb=" N ALA L 315 " pdb=" C ALA L 315 " pdb=" CB ALA L 315 " both_signs ideal model delta sigma weight residual False 2.48 2.14 0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" CA TYR E 34 " pdb=" N TYR E 34 " pdb=" C TYR E 34 " pdb=" CB TYR E 34 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.29 2.00e-01 2.50e+01 2.03e+00 ... (remaining 3402 not shown) Planarity restraints: 4200 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL W 102 " 0.328 3.00e-02 1.11e+03 2.65e-01 3.90e+02 pdb=" CBA BCL W 102 " 0.192 3.00e-02 1.11e+03 pdb=" CGA BCL W 102 " -0.079 3.00e-02 1.11e+03 pdb=" O1A BCL W 102 " 0.006 3.00e-02 1.11e+03 pdb=" O2A BCL W 102 " -0.447 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1A BCL K 102 " 0.035 3.20e-02 9.77e+02 1.72e-01 1.45e+02 pdb=" C4A BCL K 102 " 0.094 3.20e-02 9.77e+02 pdb=" CHA BCL K 102 " -0.173 3.20e-02 9.77e+02 pdb=" CHB BCL K 102 " -0.210 3.20e-02 9.77e+02 pdb=" NA BCL K 102 " 0.254 3.20e-02 9.77e+02 delta sigma weight rms_deltas residual plane pdb=" C1A BCL W 102 " 0.032 3.20e-02 9.77e+02 1.55e-01 1.18e+02 pdb=" C4A BCL W 102 " 0.113 3.20e-02 9.77e+02 pdb=" CHA BCL W 102 " -0.154 3.20e-02 9.77e+02 pdb=" CHB BCL W 102 " -0.200 3.20e-02 9.77e+02 pdb=" NA BCL W 102 " 0.208 3.20e-02 9.77e+02 ... (remaining 4197 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 48 2.46 - 3.07: 14696 3.07 - 3.68: 32462 3.68 - 4.29: 53333 4.29 - 4.90: 89644 Nonbonded interactions: 190183 Sorted by model distance: nonbonded pdb=" CE1 HIS 3 27 " pdb="MG BCL 3 101 " model vdw 1.849 3.130 nonbonded pdb=" CE1 HIS P 27 " pdb="MG BCL P 101 " model vdw 2.084 3.130 nonbonded pdb=" OE2 GLU M 557 " pdb="FE FE L1004 " model vdw 2.086 2.260 nonbonded pdb=" SD MET C 229 " pdb="FE HEM C 503 " model vdw 2.127 3.360 nonbonded pdb=" SD MET C 145 " pdb="FE HEM C 502 " model vdw 2.132 3.360 ... (remaining 190178 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain '0' and (resid 7 through 55 or resid 101)) selection = (chain '2' and (resid 7 through 55 or resid 101)) selection = (chain '4' and (resid 7 through 55 or resid 101)) selection = (chain '6' and (resid 7 through 55 or resid 101)) selection = (chain '8' and (resid 7 through 55 or resid 101)) selection = (chain 'B' and (resid 7 through 55 or resid 101)) selection = (chain 'E' and (resid 7 through 55 or resid 101)) selection = (chain 'G' and (resid 7 through 55 or resid 101)) selection = (chain 'I' and (resid 7 through 55 or resid 101)) selection = (chain 'K' and (resid 7 through 55 or resid 101)) selection = (chain 'O' and (resid 7 through 55 or resid 101)) selection = (chain 'Q' and (resid 7 through 55 or resid 101)) selection = (chain 'S' and (resid 7 through 55 or resid 101)) selection = (chain 'U' and (resid 7 through 55 or resid 101)) selection = (chain 'W' and (resid 7 through 55 or resid 101)) } ncs_group { reference = (chain '1' and resid 7 through 40) selection = (chain '3' and resid 7 through 40) selection = (chain '5' and resid 7 through 40) selection = (chain '7' and resid 7 through 40) selection = (chain '9' and resid 7 through 40) selection = (chain 'A' and resid 7 through 40) selection = (chain 'D' and resid 7 through 40) selection = (chain 'F' and resid 7 through 40) selection = (chain 'H' and resid 7 through 40) selection = (chain 'J' and resid 7 through 40) selection = (chain 'N' and resid 7 through 40) selection = (chain 'P' and resid 7 through 40) selection = (chain 'R' and resid 7 through 40) selection = (chain 'T' and resid 7 through 40) selection = (chain 'V' and resid 7 through 40) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.370 Check model and map are aligned: 0.320 Set scattering table: 0.200 Process input model: 58.680 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.173 24744 Z= 0.373 Angle : 0.980 16.821 34493 Z= 0.403 Chirality : 0.043 0.603 3405 Planarity : 0.008 0.265 4200 Dihedral : 17.270 179.983 8632 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.71 (0.18), residues: 2244 helix: 3.62 (0.13), residues: 1398 sheet: None (None), residues: 0 loop : -1.59 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP L 305 HIS 0.022 0.001 HIS L 192 PHE 0.040 0.002 PHE L 185 TYR 0.030 0.002 TYR L 204 ARG 0.007 0.000 ARG L 251 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 301 time to evaluate : 2.306 Fit side-chains REVERT: 5 22 MET cc_start: 0.9206 (mmp) cc_final: 0.8989 (mmp) REVERT: 7 16 THR cc_start: 0.8956 (m) cc_final: 0.8693 (m) REVERT: N 14 VAL cc_start: 0.8349 (t) cc_final: 0.8131 (t) outliers start: 0 outliers final: 1 residues processed: 301 average time/residue: 1.2596 time to fit residues: 439.6593 Evaluate side-chains 236 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 235 time to evaluate : 2.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 240 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 10.0000 chunk 154 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 104 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 159 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 185 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 20 ASN B 13 GLN C 61 ASN C 225 ASN C 226 GLN ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 ASN C 301 ASN G 13 GLN H 37 ASN I 22 GLN L 183 HIS L 209 ASN L 252 ASN L 264 HIS M 637 GLN N 37 ASN O 13 GLN Q 13 GLN U 13 GLN U 22 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24744 Z= 0.245 Angle : 0.790 11.757 34493 Z= 0.312 Chirality : 0.042 0.172 3405 Planarity : 0.005 0.060 4200 Dihedral : 17.447 179.935 4635 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.63 % Allowed : 6.56 % Favored : 91.81 % 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: 2.49 (0.18), residues: 2244 helix: 3.41 (0.13), residues: 1407 sheet: None (None), residues: 0 loop : -1.70 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP L 305 HIS 0.017 0.002 HIS L 192 PHE 0.022 0.002 PHE L 185 TYR 0.014 0.002 TYR C 205 ARG 0.003 0.000 ARG M 344 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 229 time to evaluate : 2.285 Fit side-chains REVERT: 5 22 MET cc_start: 0.9267 (mmp) cc_final: 0.9012 (mmp) REVERT: 6 20 ASN cc_start: 0.7799 (t0) cc_final: 0.7381 (t0) REVERT: 7 16 THR cc_start: 0.9015 (m) cc_final: 0.8764 (m) REVERT: C 247 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.7934 (ptm160) REVERT: C 272 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7776 (mt-10) REVERT: L 41 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7460 (tt0) REVERT: L 94 ASN cc_start: 0.7088 (m110) cc_final: 0.6802 (m-40) REVERT: N 14 VAL cc_start: 0.8414 (t) cc_final: 0.8205 (t) REVERT: Z 42 ASP cc_start: 0.8276 (t70) cc_final: 0.7934 (t0) outliers start: 32 outliers final: 15 residues processed: 243 average time/residue: 1.3026 time to fit residues: 365.2888 Evaluate side-chains 237 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 219 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 233 ASN Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 41 GLU Chi-restraints excluded: chain L residue 241 ILE Chi-restraints excluded: chain M residue 607 LEU Chi-restraints excluded: chain O residue 31 LYS Chi-restraints excluded: chain Z residue 46 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 5.9990 chunk 57 optimal weight: 0.3980 chunk 154 optimal weight: 7.9990 chunk 126 optimal weight: 8.9990 chunk 51 optimal weight: 0.0370 chunk 185 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 165 optimal weight: 10.0000 chunk 184 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 overall best weight: 1.8864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 20 ASN ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN H 37 ASN I 22 GLN O 13 GLN P 37 ASN Q 13 GLN U 13 GLN U 22 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 24744 Z= 0.185 Angle : 0.708 11.575 34493 Z= 0.276 Chirality : 0.039 0.152 3405 Planarity : 0.004 0.054 4200 Dihedral : 16.344 179.970 4633 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.53 % Allowed : 9.15 % Favored : 89.32 % 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: 2.63 (0.18), residues: 2244 helix: 3.56 (0.13), residues: 1405 sheet: None (None), residues: 0 loop : -1.69 (0.20), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 305 HIS 0.013 0.001 HIS L 192 PHE 0.016 0.001 PHE L 185 TYR 0.013 0.001 TYR C 205 ARG 0.002 0.000 ARG M 399 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 221 time to evaluate : 2.161 Fit side-chains REVERT: 5 22 MET cc_start: 0.9264 (mmp) cc_final: 0.8971 (mmp) REVERT: 6 20 ASN cc_start: 0.7783 (t0) cc_final: 0.7388 (t0) REVERT: 7 16 THR cc_start: 0.8995 (m) cc_final: 0.8748 (m) REVERT: C 247 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.7685 (ptm160) REVERT: C 272 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7743 (mt-10) REVERT: L 41 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7468 (tt0) REVERT: M 367 GLU cc_start: 0.8123 (tp30) cc_final: 0.7811 (tm-30) REVERT: N 14 VAL cc_start: 0.8340 (t) cc_final: 0.8108 (t) REVERT: W 46 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7623 (tp) outliers start: 30 outliers final: 11 residues processed: 235 average time/residue: 1.2271 time to fit residues: 335.7647 Evaluate side-chains 230 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 215 time to evaluate : 2.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 233 ASN Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 41 GLU Chi-restraints excluded: chain L residue 240 ASN Chi-restraints excluded: chain L residue 241 ILE Chi-restraints excluded: chain W residue 46 LEU Chi-restraints excluded: chain Z residue 35 ILE Chi-restraints excluded: chain Z residue 46 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 6.9990 chunk 139 optimal weight: 0.4980 chunk 96 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 88 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 chunk 186 optimal weight: 8.9990 chunk 197 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 176 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 37 ASN ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN H 37 ASN M 572 GLN O 13 GLN U 13 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 24744 Z= 0.302 Angle : 0.839 13.676 34493 Z= 0.332 Chirality : 0.044 0.194 3405 Planarity : 0.005 0.059 4200 Dihedral : 16.621 179.918 4633 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.08 % Allowed : 10.12 % Favored : 87.80 % 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: 2.11 (0.18), residues: 2244 helix: 3.12 (0.13), residues: 1407 sheet: None (None), residues: 0 loop : -1.86 (0.19), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP M 630 HIS 0.014 0.002 HIS L 192 PHE 0.022 0.002 PHE 9 36 TYR 0.018 0.002 TYR C 205 ARG 0.005 0.001 ARG 3 4 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 228 time to evaluate : 2.182 Fit side-chains REVERT: 6 20 ASN cc_start: 0.7789 (t0) cc_final: 0.7404 (t0) REVERT: 7 17 LEU cc_start: 0.8551 (mm) cc_final: 0.8248 (tp) REVERT: C 78 MET cc_start: 0.6428 (tmm) cc_final: 0.6167 (ttm) REVERT: C 247 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.7933 (ptm160) REVERT: C 272 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.7766 (mt-10) REVERT: L 41 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7465 (tt0) REVERT: L 94 ASN cc_start: 0.7484 (m110) cc_final: 0.7165 (m-40) REVERT: L 106 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.7746 (mm-30) REVERT: M 343 TYR cc_start: 0.8189 (m-80) cc_final: 0.7910 (m-80) REVERT: M 367 GLU cc_start: 0.8135 (tp30) cc_final: 0.7872 (tm-30) REVERT: N 14 VAL cc_start: 0.8458 (t) cc_final: 0.8220 (t) REVERT: O 20 ASN cc_start: 0.8899 (t0) cc_final: 0.8666 (t0) REVERT: W 46 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7682 (tp) outliers start: 41 outliers final: 20 residues processed: 250 average time/residue: 1.2517 time to fit residues: 363.3720 Evaluate side-chains 245 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 220 time to evaluate : 2.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain 6 residue 15 LYS Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 233 ASN Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 240 CYS Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 41 GLU Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain M residue 375 VAL Chi-restraints excluded: chain M residue 607 LEU Chi-restraints excluded: chain O residue 31 LYS Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain Q residue 37 LEU Chi-restraints excluded: chain W residue 12 ASP Chi-restraints excluded: chain W residue 46 LEU Chi-restraints excluded: chain Z residue 46 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 0.9980 chunk 111 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 146 optimal weight: 7.9990 chunk 81 optimal weight: 8.9990 chunk 168 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 chunk 176 optimal weight: 0.9990 chunk 49 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 37 ASN ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN H 37 ASN I 22 GLN M 582 ASN O 13 GLN U 13 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 24744 Z= 0.289 Angle : 0.823 13.252 34493 Z= 0.326 Chirality : 0.043 0.208 3405 Planarity : 0.005 0.054 4200 Dihedral : 16.448 179.979 4633 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.34 % Allowed : 10.42 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.18), residues: 2244 helix: 3.08 (0.13), residues: 1398 sheet: None (None), residues: 0 loop : -1.96 (0.19), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 630 HIS 0.012 0.002 HIS L 192 PHE 0.019 0.002 PHE 9 36 TYR 0.019 0.002 TYR C 205 ARG 0.005 0.001 ARG 3 4 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 226 time to evaluate : 2.519 Fit side-chains REVERT: 6 20 ASN cc_start: 0.7813 (t0) cc_final: 0.7429 (t0) REVERT: 7 17 LEU cc_start: 0.8580 (mm) cc_final: 0.8245 (tp) REVERT: A 4 ARG cc_start: 0.7298 (OUTLIER) cc_final: 0.4848 (ppt-90) REVERT: C 78 MET cc_start: 0.6598 (tmm) cc_final: 0.6243 (ttm) REVERT: C 247 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.7853 (ptm160) REVERT: C 272 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.7768 (mt-10) REVERT: J 4 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.6867 (ptt90) REVERT: L 41 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7471 (tt0) REVERT: L 94 ASN cc_start: 0.7647 (m110) cc_final: 0.7275 (m-40) REVERT: L 106 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7789 (mm-30) REVERT: L 145 ASP cc_start: 0.7822 (m-30) cc_final: 0.7602 (m-30) REVERT: M 367 GLU cc_start: 0.8134 (tp30) cc_final: 0.7926 (tm-30) REVERT: N 14 VAL cc_start: 0.8446 (t) cc_final: 0.8201 (t) REVERT: O 20 ASN cc_start: 0.8914 (t0) cc_final: 0.8700 (t0) REVERT: W 46 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7647 (tp) outliers start: 46 outliers final: 22 residues processed: 252 average time/residue: 1.3000 time to fit residues: 381.3416 Evaluate side-chains 250 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 221 time to evaluate : 2.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain 8 residue 45 VAL Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 233 ASN Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 240 CYS Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain J residue 4 ARG Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 41 GLU Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain M residue 348 GLU Chi-restraints excluded: chain M residue 375 VAL Chi-restraints excluded: chain M residue 607 LEU Chi-restraints excluded: chain M residue 630 TRP Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain Q residue 37 LEU Chi-restraints excluded: chain W residue 12 ASP Chi-restraints excluded: chain W residue 46 LEU Chi-restraints excluded: chain Z residue 46 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 0.7980 chunk 177 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 115 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 197 optimal weight: 6.9990 chunk 163 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 16 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 37 ASN C 61 ASN ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN H 37 ASN I 22 GLN ** L 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 205 ASN O 13 GLN U 13 GLN Z 44 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 24744 Z= 0.290 Angle : 0.828 13.457 34493 Z= 0.328 Chirality : 0.043 0.203 3405 Planarity : 0.005 0.057 4200 Dihedral : 16.297 179.870 4633 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.34 % Allowed : 11.18 % Favored : 86.48 % 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: 1.92 (0.18), residues: 2244 helix: 3.02 (0.13), residues: 1402 sheet: None (None), residues: 0 loop : -1.99 (0.19), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 360 HIS 0.013 0.002 HIS L 192 PHE 0.017 0.002 PHE 9 36 TYR 0.019 0.002 TYR C 205 ARG 0.005 0.001 ARG 3 4 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 223 time to evaluate : 2.213 Fit side-chains REVERT: 6 20 ASN cc_start: 0.7825 (t0) cc_final: 0.7447 (t0) REVERT: 7 17 LEU cc_start: 0.8601 (mm) cc_final: 0.8274 (tp) REVERT: A 4 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.4874 (ppt-90) REVERT: C 78 MET cc_start: 0.6592 (tmm) cc_final: 0.6047 (ttm) REVERT: C 247 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.7915 (ptm160) REVERT: C 272 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.7766 (mt-10) REVERT: J 4 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.6899 (ptt90) REVERT: L 41 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7452 (tt0) REVERT: L 94 ASN cc_start: 0.7598 (m110) cc_final: 0.7234 (m-40) REVERT: L 106 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7801 (mm-30) REVERT: L 145 ASP cc_start: 0.7748 (m-30) cc_final: 0.7505 (m-30) REVERT: M 341 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7095 (mp0) REVERT: M 367 GLU cc_start: 0.8200 (tp30) cc_final: 0.7997 (tm-30) REVERT: N 14 VAL cc_start: 0.8443 (t) cc_final: 0.8205 (t) REVERT: O 20 ASN cc_start: 0.8911 (t0) cc_final: 0.8699 (t0) outliers start: 46 outliers final: 21 residues processed: 251 average time/residue: 1.2633 time to fit residues: 367.9828 Evaluate side-chains 245 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 217 time to evaluate : 2.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain 6 residue 15 LYS Chi-restraints excluded: chain 8 residue 45 VAL Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 233 ASN Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 240 CYS Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain J residue 4 ARG Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 41 GLU Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain M residue 341 GLU Chi-restraints excluded: chain M residue 375 VAL Chi-restraints excluded: chain M residue 630 TRP Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain Q residue 37 LEU Chi-restraints excluded: chain W residue 12 ASP Chi-restraints excluded: chain Z residue 46 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 chunk 144 optimal weight: 7.9990 chunk 111 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 chunk 110 optimal weight: 8.9990 chunk 196 optimal weight: 9.9990 chunk 123 optimal weight: 6.9990 chunk 119 optimal weight: 0.8980 chunk 90 optimal weight: 10.0000 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 37 ASN C 61 ASN ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN H 37 ASN ** L 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 13 GLN U 13 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24744 Z= 0.259 Angle : 0.794 13.181 34493 Z= 0.315 Chirality : 0.042 0.199 3405 Planarity : 0.005 0.056 4200 Dihedral : 16.065 179.912 4633 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.08 % Allowed : 11.95 % Favored : 85.97 % 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: 2.03 (0.18), residues: 2244 helix: 3.13 (0.13), residues: 1397 sheet: None (None), residues: 0 loop : -1.98 (0.19), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 360 HIS 0.012 0.001 HIS L 192 PHE 0.016 0.001 PHE L 185 TYR 0.019 0.002 TYR M 424 ARG 0.004 0.000 ARG 3 4 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 221 time to evaluate : 2.475 Fit side-chains REVERT: 6 20 ASN cc_start: 0.7816 (t0) cc_final: 0.7435 (t0) REVERT: 7 17 LEU cc_start: 0.8629 (mm) cc_final: 0.8276 (tp) REVERT: A 4 ARG cc_start: 0.7312 (OUTLIER) cc_final: 0.4888 (ppt-90) REVERT: C 78 MET cc_start: 0.6768 (tmm) cc_final: 0.6189 (ttm) REVERT: C 247 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.7755 (ptm160) REVERT: C 272 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7717 (mt-10) REVERT: J 4 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.6864 (ptt90) REVERT: L 41 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7471 (tt0) REVERT: L 94 ASN cc_start: 0.7597 (m110) cc_final: 0.7216 (m-40) REVERT: L 106 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7793 (mm-30) REVERT: L 145 ASP cc_start: 0.7718 (m-30) cc_final: 0.7455 (m-30) REVERT: M 341 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.6936 (mp0) REVERT: M 367 GLU cc_start: 0.8180 (tp30) cc_final: 0.7974 (tm-30) REVERT: M 609 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7772 (mp) REVERT: N 14 VAL cc_start: 0.8395 (t) cc_final: 0.8158 (t) outliers start: 41 outliers final: 22 residues processed: 248 average time/residue: 1.3041 time to fit residues: 377.7181 Evaluate side-chains 251 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 221 time to evaluate : 2.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 37 ASN Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 233 ASN Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 240 CYS Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain J residue 4 ARG Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 41 GLU Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 240 ASN Chi-restraints excluded: chain M residue 341 GLU Chi-restraints excluded: chain M residue 375 VAL Chi-restraints excluded: chain M residue 609 LEU Chi-restraints excluded: chain M residue 630 TRP Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain Q residue 37 LEU Chi-restraints excluded: chain W residue 12 ASP Chi-restraints excluded: chain Z residue 46 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 117 optimal weight: 0.9980 chunk 59 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 chunk 125 optimal weight: 8.9990 chunk 133 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 154 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 37 ASN C 61 ASN ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN H 37 ASN I 22 GLN ** L 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 637 GLN O 13 GLN U 13 GLN Z 44 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 24744 Z= 0.271 Angle : 0.806 13.328 34493 Z= 0.321 Chirality : 0.042 0.200 3405 Planarity : 0.005 0.057 4200 Dihedral : 16.073 179.911 4633 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.14 % Allowed : 12.10 % Favored : 85.77 % 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 (0.18), residues: 2244 helix: 3.07 (0.13), residues: 1402 sheet: None (None), residues: 0 loop : -1.99 (0.19), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 360 HIS 0.012 0.001 HIS L 192 PHE 0.018 0.002 PHE 1 36 TYR 0.019 0.002 TYR M 424 ARG 0.004 0.000 ARG 3 4 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 226 time to evaluate : 2.138 Fit side-chains REVERT: 6 20 ASN cc_start: 0.7810 (t0) cc_final: 0.7433 (t0) REVERT: 7 17 LEU cc_start: 0.8623 (mm) cc_final: 0.8273 (tp) REVERT: A 4 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.4885 (ppt-90) REVERT: C 78 MET cc_start: 0.6788 (tmm) cc_final: 0.6182 (ttm) REVERT: C 85 ASN cc_start: 0.7146 (m110) cc_final: 0.6874 (m110) REVERT: C 247 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.7787 (ptm160) REVERT: C 272 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7706 (mt-10) REVERT: J 4 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.6846 (ptt90) REVERT: L 41 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7476 (tt0) REVERT: L 94 ASN cc_start: 0.7524 (m110) cc_final: 0.7140 (m-40) REVERT: L 106 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7804 (mm-30) REVERT: L 145 ASP cc_start: 0.7722 (m-30) cc_final: 0.7467 (m-30) REVERT: M 341 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7007 (mp0) REVERT: M 367 GLU cc_start: 0.8182 (tp30) cc_final: 0.7973 (tm-30) REVERT: M 609 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7821 (mp) REVERT: N 14 VAL cc_start: 0.8405 (t) cc_final: 0.8169 (t) REVERT: X 18 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7236 (mm) outliers start: 42 outliers final: 24 residues processed: 253 average time/residue: 1.2382 time to fit residues: 363.4814 Evaluate side-chains 256 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 223 time to evaluate : 2.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 37 ASN Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain 6 residue 15 LYS Chi-restraints excluded: chain 8 residue 45 VAL Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 233 ASN Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 240 CYS Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain H residue 37 ASN Chi-restraints excluded: chain J residue 4 ARG Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 41 GLU Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 240 ASN Chi-restraints excluded: chain M residue 341 GLU Chi-restraints excluded: chain M residue 375 VAL Chi-restraints excluded: chain M residue 609 LEU Chi-restraints excluded: chain M residue 630 TRP Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain Q residue 37 LEU Chi-restraints excluded: chain W residue 12 ASP Chi-restraints excluded: chain X residue 18 LEU Chi-restraints excluded: chain Z residue 46 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 10.0000 chunk 171 optimal weight: 5.9990 chunk 183 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 143 optimal weight: 0.5980 chunk 56 optimal weight: 5.9990 chunk 165 optimal weight: 9.9990 chunk 173 optimal weight: 7.9990 chunk 182 optimal weight: 6.9990 chunk 120 optimal weight: 4.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 37 ASN C 61 ASN ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN H 37 ASN I 22 GLN ** L 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 13 GLN U 13 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 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 0.043 24744 Z= 0.266 Angle : 0.803 13.369 34493 Z= 0.320 Chirality : 0.042 0.203 3405 Planarity : 0.005 0.056 4200 Dihedral : 16.055 179.902 4633 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.03 % Allowed : 12.51 % Favored : 85.46 % 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 (0.18), residues: 2244 helix: 3.07 (0.13), residues: 1403 sheet: None (None), residues: 0 loop : -1.98 (0.19), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 360 HIS 0.012 0.001 HIS L 192 PHE 0.016 0.002 PHE 1 36 TYR 0.019 0.002 TYR M 424 ARG 0.006 0.000 ARG 9 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 219 time to evaluate : 2.529 Fit side-chains REVERT: 6 20 ASN cc_start: 0.7797 (t0) cc_final: 0.7419 (t0) REVERT: 7 17 LEU cc_start: 0.8621 (mm) cc_final: 0.8270 (tp) REVERT: A 4 ARG cc_start: 0.7308 (OUTLIER) cc_final: 0.4873 (ppt-90) REVERT: C 78 MET cc_start: 0.6815 (tmm) cc_final: 0.6210 (ttm) REVERT: C 85 ASN cc_start: 0.7142 (m110) cc_final: 0.6868 (m110) REVERT: C 247 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.7754 (ptm160) REVERT: C 272 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7700 (mt-10) REVERT: J 4 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.6865 (ptt90) REVERT: L 41 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7472 (tt0) REVERT: L 94 ASN cc_start: 0.7571 (m110) cc_final: 0.7200 (m-40) REVERT: L 106 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7802 (mm-30) REVERT: L 145 ASP cc_start: 0.7740 (m-30) cc_final: 0.7518 (m-30) REVERT: M 341 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7006 (mp0) REVERT: M 367 GLU cc_start: 0.8186 (tp30) cc_final: 0.7980 (tm-30) REVERT: M 609 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7809 (mp) REVERT: N 14 VAL cc_start: 0.8402 (t) cc_final: 0.8160 (t) REVERT: X 18 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7224 (mm) REVERT: Z 43 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8046 (ttpt) outliers start: 40 outliers final: 25 residues processed: 244 average time/residue: 1.2575 time to fit residues: 356.2506 Evaluate side-chains 253 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 218 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 37 ASN Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain 6 residue 15 LYS Chi-restraints excluded: chain 8 residue 45 VAL Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 233 ASN Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 240 CYS Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain H residue 37 ASN Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain J residue 4 ARG Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 41 GLU Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 240 ASN Chi-restraints excluded: chain M residue 341 GLU Chi-restraints excluded: chain M residue 375 VAL Chi-restraints excluded: chain M residue 609 LEU Chi-restraints excluded: chain M residue 630 TRP Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain Q residue 37 LEU Chi-restraints excluded: chain W residue 12 ASP Chi-restraints excluded: chain X residue 18 LEU Chi-restraints excluded: chain Z residue 43 LYS Chi-restraints excluded: chain Z residue 46 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 9.9990 chunk 118 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 134 optimal weight: 10.0000 chunk 203 optimal weight: 4.9990 chunk 187 optimal weight: 1.9990 chunk 161 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 125 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 chunk 128 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 37 ASN C 61 ASN ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN H 37 ASN ** L 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 13 GLN U 13 GLN Z 44 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24744 Z= 0.250 Angle : 0.789 13.213 34493 Z= 0.314 Chirality : 0.041 0.196 3405 Planarity : 0.005 0.056 4200 Dihedral : 15.984 179.913 4633 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.93 % Allowed : 12.66 % Favored : 85.41 % 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: 2.03 (0.18), residues: 2244 helix: 3.10 (0.13), residues: 1403 sheet: None (None), residues: 0 loop : -1.96 (0.19), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 360 HIS 0.012 0.001 HIS L 192 PHE 0.015 0.001 PHE M 387 TYR 0.020 0.002 TYR M 424 ARG 0.006 0.000 ARG 9 40 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 218 time to evaluate : 2.302 Fit side-chains REVERT: 6 20 ASN cc_start: 0.7795 (t0) cc_final: 0.7417 (t0) REVERT: A 4 ARG cc_start: 0.7267 (OUTLIER) cc_final: 0.4795 (ppt-90) REVERT: C 78 MET cc_start: 0.6778 (tmm) cc_final: 0.6205 (ttm) REVERT: C 247 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.7748 (ptm160) REVERT: C 272 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7689 (mt-10) REVERT: J 4 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.6851 (ptt90) REVERT: L 41 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7472 (tt0) REVERT: L 94 ASN cc_start: 0.7485 (m110) cc_final: 0.7107 (m-40) REVERT: L 106 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7798 (mm-30) REVERT: L 145 ASP cc_start: 0.7729 (m-30) cc_final: 0.7507 (m-30) REVERT: M 341 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.6937 (mp0) REVERT: M 367 GLU cc_start: 0.8179 (tp30) cc_final: 0.7970 (tm-30) REVERT: M 609 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7762 (mp) REVERT: N 14 VAL cc_start: 0.8393 (t) cc_final: 0.8151 (t) REVERT: W 46 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7636 (tp) REVERT: X 18 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7223 (mm) REVERT: Z 43 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8033 (ttpt) outliers start: 38 outliers final: 23 residues processed: 242 average time/residue: 1.2887 time to fit residues: 361.6566 Evaluate side-chains 251 residues out of total 1967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 217 time to evaluate : 2.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 37 ASN Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain 6 residue 15 LYS Chi-restraints excluded: chain 8 residue 45 VAL Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 233 ASN Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 240 CYS Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain H residue 37 ASN Chi-restraints excluded: chain J residue 4 ARG Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 41 GLU Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 240 ASN Chi-restraints excluded: chain M residue 341 GLU Chi-restraints excluded: chain M residue 375 VAL Chi-restraints excluded: chain M residue 609 LEU Chi-restraints excluded: chain M residue 630 TRP Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain Q residue 37 LEU Chi-restraints excluded: chain W residue 12 ASP Chi-restraints excluded: chain W residue 46 LEU Chi-restraints excluded: chain X residue 18 LEU Chi-restraints excluded: chain Z residue 43 LYS Chi-restraints excluded: chain Z residue 46 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 162 optimal weight: 9.9990 chunk 67 optimal weight: 0.7980 chunk 166 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 29 optimal weight: 7.9990 chunk 142 optimal weight: 8.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 37 ASN C 61 ASN ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN H 37 ASN I 22 GLN ** L 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 13 GLN U 13 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.120680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.101512 restraints weight = 28351.688| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.11 r_work: 0.2789 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24744 Z= 0.236 Angle : 0.773 13.145 34493 Z= 0.308 Chirality : 0.041 0.192 3405 Planarity : 0.005 0.055 4200 Dihedral : 15.899 179.925 4633 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.03 % Allowed : 12.86 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.18), residues: 2244 helix: 3.14 (0.13), residues: 1405 sheet: None (None), residues: 0 loop : -1.95 (0.19), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 360 HIS 0.012 0.001 HIS L 192 PHE 0.015 0.001 PHE M 387 TYR 0.021 0.002 TYR M 424 ARG 0.006 0.000 ARG 9 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6492.87 seconds wall clock time: 116 minutes 41.54 seconds (7001.54 seconds total)