Starting phenix.real_space_refine on Sat Jun 29 00:58:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r0w_14224/06_2024/7r0w_14224_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r0w_14224/06_2024/7r0w_14224.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r0w_14224/06_2024/7r0w_14224.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r0w_14224/06_2024/7r0w_14224.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r0w_14224/06_2024/7r0w_14224_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r0w_14224/06_2024/7r0w_14224_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.036 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 12 7.16 5 P 6 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 11209 2.51 5 N 2586 2.21 5 O 2933 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "X ASP 34": "OD1" <-> "OD2" Residue "X ASP 50": "OD1" <-> "OD2" Residue "X GLU 59": "OE1" <-> "OE2" Residue "I GLU 8": "OE1" <-> "OE2" Residue "I ASP 170": "OD1" <-> "OD2" Residue "I GLU 180": "OE1" <-> "OE2" Residue "J ASP 8": "OD1" <-> "OD2" Residue "J ASP 13": "OD1" <-> "OD2" Residue "J GLU 74": "OE1" <-> "OE2" Residue "J GLU 115": "OE1" <-> "OE2" Residue "K GLU 35": "OE1" <-> "OE2" Residue "K ASP 55": "OD1" <-> "OD2" Residue "K TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 108": "OE1" <-> "OE2" Residue "K ASP 139": "OD1" <-> "OD2" Residue "K ASP 206": "OD1" <-> "OD2" Residue "P ASP 2": "OD1" <-> "OD2" Residue "A GLU 5": "OE1" <-> "OE2" Residue "A ASP 17": "OD1" <-> "OD2" Residue "A GLU 20": "OE1" <-> "OE2" Residue "A ASP 26": "OD1" <-> "OD2" Residue "A GLU 71": "OE1" <-> "OE2" Residue "A GLU 82": "OE1" <-> "OE2" Residue "A ASP 170": "OD1" <-> "OD2" Residue "B ASP 13": "OD1" <-> "OD2" Residue "B GLU 29": "OE1" <-> "OE2" Residue "B GLU 64": "OE1" <-> "OE2" Residue "B TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 115": "OE1" <-> "OE2" Residue "C ASP 43": "OD1" <-> "OD2" Residue "C ASP 55": "OD1" <-> "OD2" Residue "C TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 206": "OD1" <-> "OD2" Residue "C PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 21": "OD1" <-> "OD2" Residue "D ASP 75": "OD1" <-> "OD2" Residue "D PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 99": "OD1" <-> "OD2" Residue "D TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 188": "OD1" <-> "OD2" Residue "E PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 2": "OD1" <-> "OD2" Residue "L PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 148": "OE1" <-> "OE2" Residue "L GLU 187": "OE1" <-> "OE2" Residue "L ASP 188": "OD1" <-> "OD2" Residue "V TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 60": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 16830 Number of models: 1 Model: "" Number of chains: 32 Chain: "X" Number of atoms: 500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 500 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "I" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1769 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 212} Chain: "J" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1223 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 141} Chain: "K" Number of atoms: 2115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2115 Classifications: {'peptide': 279} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 257} Chain breaks: 1 Chain: "M" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 238 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "N" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 248 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "O" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 242 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 2, 'TRANS': 29} Chain: "P" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 234 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "A" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1769 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 212} Chain: "B" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1223 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 141} Chain: "C" Number of atoms: 2115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2115 Classifications: {'peptide': 279} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 257} Chain breaks: 1 Chain: "D" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1256 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 10, 'TRANS': 158} Chain breaks: 1 Chain: "E" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 238 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "F" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 248 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "G" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 242 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 2, 'TRANS': 29} Chain: "H" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 234 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "L" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1256 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 10, 'TRANS': 158} Chain breaks: 1 Chain: "V" Number of atoms: 500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 500 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "I" Number of atoms: 209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 209 Unusual residues: {'ECH': 1, 'HEM': 3, 'PGV': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 161 Unusual residues: {'CLA': 1, 'PGV': 1, 'PL9': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "K" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 55 Unusual residues: {'LMG': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'6PL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 182 Unusual residues: {'ECH': 1, 'HEM': 2, 'PL9': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 199 Unusual residues: {'2WA': 1, 'CLA': 1, 'HEM': 1, 'PGV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 90 Unusual residues: {'HEC': 1, 'PGV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'FES': 1, 'SQD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'LFA': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'6PL': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'FES': 1, 'SQD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12395 SG CYS D 120 39.548 55.252 52.072 1.00132.65 S ATOM 12535 SG CYS D 138 40.960 50.958 51.417 1.00140.44 S ATOM 14613 SG CYS L 120 102.025 55.430 44.575 1.00143.08 S ATOM 14753 SG CYS L 138 100.229 57.365 42.020 1.00145.78 S Time building chain proxies: 9.61, per 1000 atoms: 0.57 Number of scatterers: 16830 At special positions: 0 Unit cell: (138.86, 125.08, 135.68, 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 12 26.01 S 82 16.00 P 6 15.00 Mg 2 11.99 O 2933 8.00 N 2586 7.00 C 11209 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS D 125 " - pdb=" SG CYS D 140 " distance=2.04 Simple disulfide: pdb=" SG CYS L 125 " - pdb=" SG CYS L 140 " distance=2.03 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.62 Conformation dependent library (CDL) restraints added in 2.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES D 201 " pdb="FE2 FES D 201 " - pdb=" ND1 HIS D 141 " pdb="FE1 FES D 201 " - pdb=" SG CYS D 138 " pdb="FE1 FES D 201 " - pdb=" SG CYS D 120 " pdb="FE2 FES D 201 " - pdb=" NE2 HIS D 122 " pdb=" FES L 202 " pdb="FE2 FES L 202 " - pdb=" ND1 HIS L 141 " pdb="FE1 FES L 202 " - pdb=" SG CYS L 120 " pdb="FE2 FES L 202 " - pdb=" NE2 HIS L 122 " pdb="FE1 FES L 202 " - pdb=" SG CYS L 138 " Number of angles added : 6 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3672 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 62 helices and 13 sheets defined 45.1% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.77 Creating SS restraints... Processing helix chain 'X' and resid 20 through 25 Processing helix chain 'X' and resid 39 through 41 No H-bonds generated for 'chain 'X' and resid 39 through 41' Processing helix chain 'I' and resid 4 through 8 Processing helix chain 'I' and resid 10 through 19 Processing helix chain 'I' and resid 21 through 30 removed outlier: 3.562A pdb=" N SER I 30 " --> pdb=" O ASP I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 39 through 62 removed outlier: 4.102A pdb=" N GLY I 44 " --> pdb=" O TYR I 41 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N CYS I 50 " --> pdb=" O THR I 47 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE I 53 " --> pdb=" O CYS I 50 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR I 57 " --> pdb=" O GLN I 54 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY I 58 " --> pdb=" O PHE I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 81 Processing helix chain 'I' and resid 86 through 114 Processing helix chain 'I' and resid 122 through 143 Processing helix chain 'I' and resid 149 through 164 Proline residue: I 162 - end of helix Processing helix chain 'I' and resid 168 through 177 Processing helix chain 'I' and resid 184 through 195 Processing helix chain 'I' and resid 197 through 216 Processing helix chain 'J' and resid 12 through 19 Processing helix chain 'J' and resid 24 through 26 No H-bonds generated for 'chain 'J' and resid 24 through 26' Processing helix chain 'J' and resid 39 through 57 removed outlier: 3.503A pdb=" N CYS J 43 " --> pdb=" O MET J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 90 Proline residue: J 83 - end of helix removed outlier: 3.572A pdb=" N GLN J 86 " --> pdb=" O PRO J 83 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE J 87 " --> pdb=" O THR J 84 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE J 90 " --> pdb=" O ILE J 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 117 Proline residue: J 105 - end of helix Proline residue: J 112 - end of helix removed outlier: 4.578A pdb=" N VAL J 117 " --> pdb=" O PHE J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 123 through 125 No H-bonds generated for 'chain 'J' and resid 123 through 125' Processing helix chain 'J' and resid 127 through 148 removed outlier: 3.949A pdb=" N THR J 148 " --> pdb=" O GLY J 144 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 8 Processing helix chain 'K' and resid 21 through 24 Processing helix chain 'K' and resid 92 through 98 Processing helix chain 'K' and resid 248 through 283 Processing helix chain 'M' and resid 2 through 28 Processing helix chain 'N' and resid 4 through 32 removed outlier: 4.564A pdb=" N ASN N 9 " --> pdb=" O MET N 6 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLY N 10 " --> pdb=" O LEU N 7 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE N 13 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR N 18 " --> pdb=" O ILE N 15 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU N 19 " --> pdb=" O GLY N 16 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU N 20 " --> pdb=" O LEU N 17 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA N 23 " --> pdb=" O LEU N 20 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN N 32 " --> pdb=" O ILE N 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 29 Proline residue: O 15 - end of helix Processing helix chain 'P' and resid 3 through 26 Processing helix chain 'A' and resid 10 through 19 Processing helix chain 'A' and resid 21 through 30 Processing helix chain 'A' and resid 39 through 62 removed outlier: 4.204A pdb=" N GLY A 44 " --> pdb=" O TYR A 41 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS A 50 " --> pdb=" O THR A 47 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 53 " --> pdb=" O CYS A 50 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR A 57 " --> pdb=" O GLN A 54 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY A 58 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR A 62 " --> pdb=" O PHE A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 86 through 114 removed outlier: 3.525A pdb=" N SER A 98 " --> pdb=" O ARG A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 143 Processing helix chain 'A' and resid 149 through 164 Proline residue: A 162 - end of helix Processing helix chain 'A' and resid 169 through 177 Processing helix chain 'A' and resid 184 through 195 Processing helix chain 'A' and resid 197 through 216 Processing helix chain 'B' and resid 12 through 19 Processing helix chain 'B' and resid 24 through 26 No H-bonds generated for 'chain 'B' and resid 24 through 26' Processing helix chain 'B' and resid 39 through 57 Processing helix chain 'B' and resid 79 through 90 Proline residue: B 83 - end of helix removed outlier: 3.615A pdb=" N GLN B 86 " --> pdb=" O PRO B 83 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE B 90 " --> pdb=" O ILE B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 109 Proline residue: B 105 - end of helix Processing helix chain 'B' and resid 111 through 117 removed outlier: 4.554A pdb=" N VAL B 117 " --> pdb=" O PHE B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 125 No H-bonds generated for 'chain 'B' and resid 123 through 125' Processing helix chain 'B' and resid 127 through 148 removed outlier: 3.784A pdb=" N THR B 148 " --> pdb=" O GLY B 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 8 Processing helix chain 'C' and resid 21 through 24 Processing helix chain 'C' and resid 92 through 98 Processing helix chain 'C' and resid 248 through 283 Processing helix chain 'D' and resid 25 through 54 Proline residue: D 49 - end of helix Processing helix chain 'D' and resid 78 through 83 Processing helix chain 'D' and resid 96 through 98 No H-bonds generated for 'chain 'D' and resid 96 through 98' Processing helix chain 'E' and resid 2 through 28 Processing helix chain 'F' and resid 4 through 6 No H-bonds generated for 'chain 'F' and resid 4 through 6' Processing helix chain 'F' and resid 8 through 31 Processing helix chain 'G' and resid 4 through 29 Proline residue: G 15 - end of helix Processing helix chain 'H' and resid 3 through 25 Processing helix chain 'L' and resid 25 through 54 Proline residue: L 49 - end of helix Processing helix chain 'L' and resid 78 through 83 Processing helix chain 'L' and resid 96 through 98 No H-bonds generated for 'chain 'L' and resid 96 through 98' Processing helix chain 'V' and resid 20 through 25 Processing sheet with id= A, first strand: chain 'X' and resid 62 through 64 removed outlier: 6.492A pdb=" N VAL X 46 " --> pdb=" O LYS X 33 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'K' and resid 33 through 35 removed outlier: 3.641A pdb=" N VAL K 49 " --> pdb=" O GLU K 35 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'K' and resid 39 through 41 removed outlier: 7.984A pdb=" N VAL K 40 " --> pdb=" O GLU K 242 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL K 244 " --> pdb=" O VAL K 40 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'K' and resid 191 through 193 Processing sheet with id= E, first strand: chain 'C' and resid 33 through 35 removed outlier: 3.639A pdb=" N VAL C 49 " --> pdb=" O GLU C 35 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 39 through 41 removed outlier: 7.889A pdb=" N VAL C 40 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL C 244 " --> pdb=" O VAL C 40 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 113 through 116 Processing sheet with id= H, first strand: chain 'C' and resid 191 through 193 Processing sheet with id= I, first strand: chain 'D' and resid 91 through 93 removed outlier: 4.024A pdb=" N VAL D 91 " --> pdb=" O ILE D 103 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 114 through 116 Processing sheet with id= K, first strand: chain 'L' and resid 90 through 94 removed outlier: 3.873A pdb=" N VAL L 91 " --> pdb=" O ILE L 103 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'L' and resid 135 through 137 Processing sheet with id= M, first strand: chain 'V' and resid 62 through 64 removed outlier: 6.898A pdb=" N VAL V 46 " --> pdb=" O LYS V 33 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N PHE V 35 " --> pdb=" O GLY V 44 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLY V 44 " --> pdb=" O PHE V 35 " (cutoff:3.500A) 721 hydrogen bonds defined for protein. 1926 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: 4.76 Time building geometry restraints manager: 8.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.39: 6605 1.39 - 1.59: 10468 1.59 - 1.80: 97 1.80 - 2.00: 52 2.00 - 2.21: 48 Bond restraints: 17270 Sorted by residual: bond pdb=" C5 LMG N 101 " pdb=" O6 LMG N 101 " ideal model delta sigma weight residual 1.413 1.342 0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" CD LYS X 63 " pdb=" CE LYS X 63 " ideal model delta sigma weight residual 1.520 1.454 0.066 3.00e-02 1.11e+03 4.83e+00 bond pdb=" C4 LMG N 101 " pdb=" C5 LMG N 101 " ideal model delta sigma weight residual 1.531 1.491 0.040 2.00e-02 2.50e+03 4.08e+00 bond pdb=" C1 LMG N 101 " pdb=" C2 LMG N 101 " ideal model delta sigma weight residual 1.525 1.563 -0.038 2.00e-02 2.50e+03 3.70e+00 bond pdb=" C2 LMG N 101 " pdb=" C3 LMG N 101 " ideal model delta sigma weight residual 1.525 1.563 -0.038 2.00e-02 2.50e+03 3.57e+00 ... (remaining 17265 not shown) Histogram of bond angle deviations from ideal: 75.74 - 96.55: 50 96.55 - 117.36: 12557 117.36 - 138.16: 10890 138.16 - 158.97: 2 158.97 - 179.78: 20 Bond angle restraints: 23519 Sorted by residual: angle pdb=" CA LYS D 97 " pdb=" CB LYS D 97 " pdb=" CG LYS D 97 " ideal model delta sigma weight residual 114.10 125.34 -11.24 2.00e+00 2.50e-01 3.16e+01 angle pdb=" C10 CLA B 302 " pdb=" C8 CLA B 302 " pdb=" C9 CLA B 302 " ideal model delta sigma weight residual 110.21 125.73 -15.52 3.00e+00 1.11e-01 2.68e+01 angle pdb=" C1 6PL P 101 " pdb=" C2 6PL P 101 " pdb=" C3 6PL P 101 " ideal model delta sigma weight residual 114.77 127.74 -12.97 3.00e+00 1.11e-01 1.87e+01 angle pdb=" CA ARG X 52 " pdb=" CB ARG X 52 " pdb=" CG ARG X 52 " ideal model delta sigma weight residual 114.10 122.14 -8.04 2.00e+00 2.50e-01 1.62e+01 angle pdb=" CB LYS X 63 " pdb=" CG LYS X 63 " pdb=" CD LYS X 63 " ideal model delta sigma weight residual 111.30 120.19 -8.89 2.30e+00 1.89e-01 1.49e+01 ... (remaining 23514 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.13: 9449 34.13 - 68.25: 485 68.25 - 102.38: 77 102.38 - 136.50: 9 136.50 - 170.63: 5 Dihedral angle restraints: 10025 sinusoidal: 4271 harmonic: 5754 Sorted by residual: dihedral pdb=" CB CYS D 125 " pdb=" SG CYS D 125 " pdb=" SG CYS D 140 " pdb=" CB CYS D 140 " ideal model delta sinusoidal sigma weight residual 93.00 18.01 74.99 1 1.00e+01 1.00e-02 7.11e+01 dihedral pdb=" C2C HEM B 301 " pdb=" C3C HEM B 301 " pdb=" CAC HEM B 301 " pdb=" CBC HEM B 301 " ideal model delta sinusoidal sigma weight residual -180.00 -102.88 -77.12 2 1.00e+01 1.00e-02 4.56e+01 dihedral pdb=" C2C HEC K 301 " pdb=" C3C HEC K 301 " pdb=" CAC HEC K 301 " pdb=" CBC HEC K 301 " ideal model delta sinusoidal sigma weight residual 240.00 169.44 70.56 2 1.00e+01 1.00e-02 4.27e+01 ... (remaining 10022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.631: 2551 0.631 - 1.261: 0 1.261 - 1.892: 0 1.892 - 2.522: 5 2.522 - 3.153: 1 Chirality restraints: 2557 Sorted by residual: chirality pdb=" C5 LMG N 101 " pdb=" C4 LMG N 101 " pdb=" C6 LMG N 101 " pdb=" O6 LMG N 101 " both_signs ideal model delta sigma weight residual False -2.46 0.69 -3.15 2.00e-01 2.50e+01 2.49e+02 chirality pdb=" C2 6PL H 101 " pdb=" C1 6PL H 101 " pdb=" C3 6PL H 101 " pdb=" O2 6PL H 101 " both_signs ideal model delta sigma weight residual False -2.33 0.11 -2.44 2.00e-01 2.50e+01 1.49e+02 chirality pdb=" C2 6PL P 101 " pdb=" C1 6PL P 101 " pdb=" C3 6PL P 101 " pdb=" O2 6PL P 101 " both_signs ideal model delta sigma weight residual False -2.33 -0.08 -2.25 2.00e-01 2.50e+01 1.27e+02 ... (remaining 2554 not shown) Planarity restraints: 2868 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC K 301 " -0.018 2.00e-02 2.50e+03 5.53e-02 6.88e+01 pdb=" C2C HEC K 301 " 0.152 2.00e-02 2.50e+03 pdb=" C3C HEC K 301 " -0.028 2.00e-02 2.50e+03 pdb=" C4C HEC K 301 " -0.009 2.00e-02 2.50e+03 pdb=" CAC HEC K 301 " -0.026 2.00e-02 2.50e+03 pdb=" CHC HEC K 301 " -0.026 2.00e-02 2.50e+03 pdb=" CHD HEC K 301 " 0.006 2.00e-02 2.50e+03 pdb=" CMC HEC K 301 " -0.043 2.00e-02 2.50e+03 pdb=" NC HEC K 301 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG X 52 " -0.021 2.00e-02 2.50e+03 4.20e-02 1.77e+01 pdb=" C ARG X 52 " 0.073 2.00e-02 2.50e+03 pdb=" O ARG X 52 " -0.027 2.00e-02 2.50e+03 pdb=" N THR X 53 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU N 22 " 0.015 2.00e-02 2.50e+03 3.08e-02 9.47e+00 pdb=" C LEU N 22 " -0.053 2.00e-02 2.50e+03 pdb=" O LEU N 22 " 0.020 2.00e-02 2.50e+03 pdb=" N ALA N 23 " 0.018 2.00e-02 2.50e+03 ... (remaining 2865 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 192 2.62 - 3.19: 16092 3.19 - 3.76: 28380 3.76 - 4.33: 41452 4.33 - 4.90: 65130 Nonbonded interactions: 151246 Sorted by model distance: nonbonded pdb=" O ARG V 52 " pdb=" NH1 ARG V 52 " model vdw 2.048 2.520 nonbonded pdb=" N GLU A 180 " pdb=" OE1 GLU A 180 " model vdw 2.169 2.520 nonbonded pdb=" O ASN L 134 " pdb=" OD1 ASN L 134 " model vdw 2.184 3.040 nonbonded pdb=" OD1 ASP V 21 " pdb=" N VAL V 22 " model vdw 2.189 2.520 nonbonded pdb=" OD1 ASP D 70 " pdb=" N ALA D 71 " model vdw 2.198 2.520 ... (remaining 151241 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 'A' and (resid 1 through 222 or resid 301 through 302)) selection = (chain 'I' and (resid 1 through 222 or resid 301 through 302)) } ncs_group { reference = (chain 'B' and (resid 2 through 160 or resid 302)) selection = (chain 'J' and (resid 2 through 160 or resid 202)) } ncs_group { reference = (chain 'C' and resid 1 through 285) selection = (chain 'K' and resid 1 through 285) } ncs_group { reference = (chain 'D' and resid 21 through 192) selection = (chain 'L' and resid 21 through 192) } ncs_group { reference = (chain 'E' and resid 1 through 32) selection = chain 'M' } ncs_group { reference = chain 'F' selection = (chain 'N' and resid 1 through 34) } ncs_group { reference = chain 'G' selection = chain 'O' } ncs_group { reference = (chain 'H' and (resid 1 through 29 or (resid 101 and (name N or name C1 or name \ C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or n \ ame C18 or name C19 or name C2 or name C20 or name C21 or name C22 or name C23 o \ r name C24 or name C25 or name C26 or name C3 or name C31 or name C32 or name C3 \ 3 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or nam \ e C4 or name C40 or name C41 or name C42 or name C43 or name C44 or name C45 or \ name C46 or name C47 or name C5 or name C6 or name C7 or name C8 or name O11 or \ name O1P or name O2 or name O2P or name O3 or name O31 or name O3P or name O4P o \ r name P )))) selection = chain 'P' } ncs_group { reference = chain 'V' selection = chain 'X' } 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: 0.720 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: 2.240 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 50.360 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 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 : 0.005 0.071 17270 Z= 0.302 Angle : 0.963 15.517 23519 Z= 0.449 Chirality : 0.124 3.153 2557 Planarity : 0.006 0.055 2868 Dihedral : 20.394 170.631 6347 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.84 % Allowed : 22.89 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.16), residues: 1996 helix: -1.54 (0.14), residues: 959 sheet: -2.80 (0.32), residues: 195 loop : -1.52 (0.18), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP N 24 HIS 0.009 0.002 HIS I 209 PHE 0.032 0.002 PHE I 138 TYR 0.032 0.002 TYR X 12 ARG 0.012 0.001 ARG X 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 407 time to evaluate : 1.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 28 LYS cc_start: 0.7946 (mmmm) cc_final: 0.7297 (tptm) REVERT: I 20 GLU cc_start: 0.8376 (mt-10) cc_final: 0.7935 (tm-30) REVERT: D 81 PHE cc_start: 0.8954 (t80) cc_final: 0.8647 (t80) REVERT: D 99 ASP cc_start: 0.7776 (m-30) cc_final: 0.7419 (m-30) REVERT: D 187 GLU cc_start: 0.6650 (pm20) cc_final: 0.6370 (pm20) REVERT: E 1 MET cc_start: 0.7039 (mmm) cc_final: 0.6686 (mmm) REVERT: G 1 MET cc_start: 0.7693 (ptp) cc_final: 0.7480 (ptt) REVERT: L 135 LYS cc_start: 0.8630 (ttmm) cc_final: 0.8329 (ttpp) REVERT: V 33 LYS cc_start: 0.9215 (ptmm) cc_final: 0.8905 (ptpp) outliers start: 14 outliers final: 8 residues processed: 416 average time/residue: 1.1295 time to fit residues: 526.2251 Evaluate side-chains 360 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 352 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 155 ARG Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain L residue 120 CYS Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 60 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 0.4980 chunk 147 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 152 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 176 optimal weight: 7.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 9 ASN D 86 ASN ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 ASN L 32 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 17270 Z= 0.380 Angle : 0.817 21.640 23519 Z= 0.357 Chirality : 0.048 0.452 2557 Planarity : 0.005 0.051 2868 Dihedral : 18.511 179.186 2812 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.98 % Allowed : 20.30 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.17), residues: 1996 helix: 0.35 (0.15), residues: 947 sheet: -1.88 (0.33), residues: 209 loop : -0.68 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP N 24 HIS 0.015 0.003 HIS A 209 PHE 0.026 0.002 PHE I 138 TYR 0.022 0.002 TYR X 12 ARG 0.007 0.001 ARG X 13 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 366 time to evaluate : 1.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 12 TYR cc_start: 0.8770 (p90) cc_final: 0.8557 (p90) REVERT: I 20 GLU cc_start: 0.8454 (mt-10) cc_final: 0.7904 (tm-30) REVERT: I 82 GLU cc_start: 0.9074 (OUTLIER) cc_final: 0.8439 (mp0) REVERT: J 3 ILE cc_start: 0.8431 (tp) cc_final: 0.8176 (pp) REVERT: A 13 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.8845 (mm-40) REVERT: B 15 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.8283 (mtm110) REVERT: C 43 ASP cc_start: 0.8954 (t0) cc_final: 0.8729 (t0) REVERT: C 55 ASP cc_start: 0.7810 (t0) cc_final: 0.7506 (t0) REVERT: C 262 MET cc_start: 0.9292 (mtp) cc_final: 0.9015 (mtt) REVERT: D 97 LYS cc_start: 0.7636 (tmmt) cc_final: 0.7406 (tmtt) REVERT: D 99 ASP cc_start: 0.7651 (m-30) cc_final: 0.6895 (m-30) REVERT: D 133 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7876 (mt-10) REVERT: D 150 LYS cc_start: 0.9257 (ptpp) cc_final: 0.8972 (ptpt) REVERT: F 1 MET cc_start: 0.7951 (ptp) cc_final: 0.7511 (ptm) REVERT: F 30 LYS cc_start: 0.9140 (tptt) cc_final: 0.8898 (tppt) REVERT: G 1 MET cc_start: 0.8030 (ptp) cc_final: 0.7653 (ptt) REVERT: L 69 LYS cc_start: 0.7709 (mtmm) cc_final: 0.7469 (mmmt) REVERT: L 97 LYS cc_start: 0.7766 (tmtt) cc_final: 0.7433 (tmtt) REVERT: L 144 GLN cc_start: 0.8727 (mt0) cc_final: 0.8295 (mm-40) REVERT: V 13 ARG cc_start: 0.8053 (ptm-80) cc_final: 0.7814 (ptm-80) REVERT: V 33 LYS cc_start: 0.9107 (ptmm) cc_final: 0.8752 (ptpp) REVERT: V 51 ASP cc_start: 0.8410 (p0) cc_final: 0.8201 (p0) REVERT: V 60 ASP cc_start: 0.8456 (t0) cc_final: 0.7964 (t0) outliers start: 66 outliers final: 25 residues processed: 395 average time/residue: 1.1140 time to fit residues: 497.1030 Evaluate side-chains 372 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 344 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 31 VAL Chi-restraints excluded: chain X residue 51 ASP Chi-restraints excluded: chain X residue 65 ILE Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain K residue 77 MET Chi-restraints excluded: chain M residue 11 TYR Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain D residue 122 HIS Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain L residue 120 CYS Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 11 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 97 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 146 optimal weight: 2.9990 chunk 119 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 chunk 176 optimal weight: 50.0000 chunk 190 optimal weight: 5.9990 chunk 157 optimal weight: 5.9990 chunk 175 optimal weight: 0.9990 chunk 60 optimal weight: 30.0000 chunk 141 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 36 HIS J 118 ASN C 284 ASN ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 ASN L 32 ASN L 144 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 17270 Z= 0.474 Angle : 0.815 20.613 23519 Z= 0.356 Chirality : 0.049 0.356 2557 Planarity : 0.005 0.046 2868 Dihedral : 17.813 174.962 2804 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.88 % Allowed : 20.18 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.18), residues: 1996 helix: 0.91 (0.16), residues: 949 sheet: -1.64 (0.33), residues: 220 loop : -0.54 (0.20), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP N 24 HIS 0.012 0.002 HIS A 209 PHE 0.024 0.002 PHE M 15 TYR 0.021 0.002 TYR C 54 ARG 0.008 0.001 ARG D 27 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 349 time to evaluate : 1.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 12 TYR cc_start: 0.8763 (p90) cc_final: 0.8447 (p90) REVERT: I 82 GLU cc_start: 0.9121 (OUTLIER) cc_final: 0.8455 (mp0) REVERT: J 153 LYS cc_start: 0.9118 (mtmm) cc_final: 0.8912 (mtmt) REVERT: N 4 GLU cc_start: 0.8411 (tm-30) cc_final: 0.8209 (tm-30) REVERT: A 5 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8393 (mp0) REVERT: B 119 LYS cc_start: 0.9095 (pttp) cc_final: 0.8834 (pptt) REVERT: C 43 ASP cc_start: 0.8970 (t0) cc_final: 0.8705 (t0) REVERT: C 262 MET cc_start: 0.9281 (mtp) cc_final: 0.9034 (mtt) REVERT: D 69 LYS cc_start: 0.7290 (mtpp) cc_final: 0.7027 (mmmm) REVERT: D 99 ASP cc_start: 0.7351 (m-30) cc_final: 0.6558 (m-30) REVERT: D 150 LYS cc_start: 0.9410 (ptpp) cc_final: 0.9142 (ptpp) REVERT: F 30 LYS cc_start: 0.9200 (tptt) cc_final: 0.8956 (tppt) REVERT: G 1 MET cc_start: 0.8156 (ptp) cc_final: 0.7767 (ptt) REVERT: L 133 GLU cc_start: 0.8950 (tt0) cc_final: 0.8624 (tt0) REVERT: L 144 GLN cc_start: 0.8700 (mt0) cc_final: 0.8407 (mm-40) REVERT: V 51 ASP cc_start: 0.8569 (p0) cc_final: 0.8275 (p0) REVERT: V 60 ASP cc_start: 0.8431 (t0) cc_final: 0.7990 (t0) outliers start: 81 outliers final: 34 residues processed: 399 average time/residue: 1.1158 time to fit residues: 499.8878 Evaluate side-chains 371 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 336 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain X residue 41 SER Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain J residue 13 ASP Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 77 MET Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 11 TYR Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 122 HIS Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain L residue 28 ARG Chi-restraints excluded: chain V residue 2 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 174 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 177 optimal weight: 9.9990 chunk 187 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN C 192 GLN C 284 ASN ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 ASN ** L 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 17270 Z= 0.267 Angle : 0.742 19.804 23519 Z= 0.324 Chirality : 0.045 0.334 2557 Planarity : 0.004 0.048 2868 Dihedral : 17.253 170.791 2802 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.61 % Allowed : 21.87 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.18), residues: 1996 helix: 1.20 (0.16), residues: 949 sheet: -1.45 (0.33), residues: 212 loop : -0.51 (0.20), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP I 14 HIS 0.006 0.001 HIS D 122 PHE 0.020 0.002 PHE M 15 TYR 0.018 0.001 TYR C 54 ARG 0.008 0.001 ARG D 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 363 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 8 LYS cc_start: 0.8457 (tptt) cc_final: 0.8108 (tppt) REVERT: X 12 TYR cc_start: 0.8729 (p90) cc_final: 0.8437 (p90) REVERT: X 28 LYS cc_start: 0.8439 (mmmm) cc_final: 0.7822 (tttt) REVERT: I 24 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8879 (mp) REVERT: I 82 GLU cc_start: 0.9108 (OUTLIER) cc_final: 0.8430 (mp0) REVERT: J 101 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8205 (mtt) REVERT: K 284 ASN cc_start: 0.8415 (p0) cc_final: 0.8176 (p0) REVERT: N 4 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8282 (tm-30) REVERT: C 43 ASP cc_start: 0.8985 (t0) cc_final: 0.8658 (t0) REVERT: C 55 ASP cc_start: 0.8196 (t0) cc_final: 0.7831 (t0) REVERT: C 262 MET cc_start: 0.9246 (mtp) cc_final: 0.8969 (mtt) REVERT: D 69 LYS cc_start: 0.7224 (mtpp) cc_final: 0.6945 (mmmm) REVERT: D 99 ASP cc_start: 0.7552 (m-30) cc_final: 0.6998 (m-30) REVERT: D 187 GLU cc_start: 0.7110 (pm20) cc_final: 0.6878 (pm20) REVERT: H 29 PHE cc_start: 0.7313 (OUTLIER) cc_final: 0.6842 (t80) REVERT: L 90 ARG cc_start: 0.8752 (mmt-90) cc_final: 0.8357 (mmt90) REVERT: L 133 GLU cc_start: 0.8889 (tt0) cc_final: 0.8541 (tt0) REVERT: L 144 GLN cc_start: 0.8661 (mt0) cc_final: 0.8407 (mm-40) REVERT: L 150 LYS cc_start: 0.8766 (mmmm) cc_final: 0.8513 (mmtp) REVERT: V 51 ASP cc_start: 0.8581 (p0) cc_final: 0.8317 (p0) REVERT: V 60 ASP cc_start: 0.8246 (t0) cc_final: 0.7919 (t0) outliers start: 60 outliers final: 27 residues processed: 396 average time/residue: 1.1247 time to fit residues: 499.5682 Evaluate side-chains 382 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 351 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain X residue 51 ASP Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain J residue 13 ASP Chi-restraints excluded: chain J residue 101 MET Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 140 LYS Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 11 TYR Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 122 HIS Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain L residue 28 ARG Chi-restraints excluded: chain V residue 2 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 156 optimal weight: 6.9990 chunk 106 optimal weight: 0.5980 chunk 2 optimal weight: 8.9990 chunk 139 optimal weight: 50.0000 chunk 77 optimal weight: 2.9990 chunk 160 optimal weight: 9.9990 chunk 129 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 95 optimal weight: 6.9990 chunk 168 optimal weight: 0.9980 chunk 47 optimal weight: 10.0000 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 ASN C 284 ASN ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 ASN ** L 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 17270 Z= 0.387 Angle : 0.774 20.121 23519 Z= 0.336 Chirality : 0.047 0.295 2557 Planarity : 0.004 0.047 2868 Dihedral : 17.026 163.269 2802 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.40 % Allowed : 21.27 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.18), residues: 1996 helix: 1.27 (0.16), residues: 947 sheet: -2.06 (0.37), residues: 162 loop : -0.60 (0.19), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 190 HIS 0.011 0.002 HIS A 209 PHE 0.022 0.002 PHE M 15 TYR 0.022 0.002 TYR C 54 ARG 0.009 0.001 ARG D 27 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 350 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 12 TYR cc_start: 0.8699 (p90) cc_final: 0.8408 (p90) REVERT: X 28 LYS cc_start: 0.8592 (mmmm) cc_final: 0.7950 (tttt) REVERT: I 19 LEU cc_start: 0.9600 (OUTLIER) cc_final: 0.9364 (mm) REVERT: I 24 ILE cc_start: 0.9115 (OUTLIER) cc_final: 0.8852 (mp) REVERT: I 82 GLU cc_start: 0.9134 (OUTLIER) cc_final: 0.8436 (mp0) REVERT: K 55 ASP cc_start: 0.8252 (t0) cc_final: 0.8001 (t0) REVERT: K 283 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9075 (tm) REVERT: N 4 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8261 (tm-30) REVERT: C 43 ASP cc_start: 0.8997 (t0) cc_final: 0.8671 (t0) REVERT: C 262 MET cc_start: 0.9265 (mtp) cc_final: 0.9016 (mtt) REVERT: D 69 LYS cc_start: 0.7223 (mtpp) cc_final: 0.6959 (mmmm) REVERT: D 97 LYS cc_start: 0.7484 (OUTLIER) cc_final: 0.7168 (tmtt) REVERT: D 150 LYS cc_start: 0.9427 (ptpp) cc_final: 0.9142 (ptpp) REVERT: D 187 GLU cc_start: 0.7122 (pm20) cc_final: 0.6919 (pm20) REVERT: H 29 PHE cc_start: 0.7384 (OUTLIER) cc_final: 0.6849 (t80) REVERT: L 90 ARG cc_start: 0.8771 (mmt-90) cc_final: 0.8395 (mmt90) REVERT: L 133 GLU cc_start: 0.8956 (tt0) cc_final: 0.8542 (tt0) REVERT: L 144 GLN cc_start: 0.8659 (mt0) cc_final: 0.8381 (mm-40) REVERT: L 150 LYS cc_start: 0.8778 (mmmm) cc_final: 0.8564 (mmtp) REVERT: V 13 ARG cc_start: 0.7746 (ptm-80) cc_final: 0.7230 (ptm-80) REVERT: V 51 ASP cc_start: 0.8623 (p0) cc_final: 0.8329 (p0) REVERT: V 60 ASP cc_start: 0.8291 (t0) cc_final: 0.7845 (t0) outliers start: 73 outliers final: 36 residues processed: 393 average time/residue: 1.1150 time to fit residues: 492.2301 Evaluate side-chains 384 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 342 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain X residue 51 ASP Chi-restraints excluded: chain I residue 19 LEU Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 77 MET Chi-restraints excluded: chain K residue 275 ILE Chi-restraints excluded: chain K residue 283 LEU Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 11 TYR Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 97 LYS Chi-restraints excluded: chain D residue 122 HIS Chi-restraints excluded: chain D residue 144 GLN Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain L residue 28 ARG Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 8 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 63 optimal weight: 6.9990 chunk 168 optimal weight: 0.5980 chunk 37 optimal weight: 0.3980 chunk 110 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 187 optimal weight: 20.0000 chunk 155 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 ASN ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 ASN L 32 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 17270 Z= 0.231 Angle : 0.724 18.567 23519 Z= 0.318 Chirality : 0.044 0.208 2557 Planarity : 0.004 0.047 2868 Dihedral : 16.516 159.282 2802 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.67 % Allowed : 22.41 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.18), residues: 1996 helix: 1.41 (0.16), residues: 947 sheet: -1.92 (0.36), residues: 172 loop : -0.58 (0.20), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 190 HIS 0.005 0.001 HIS D 122 PHE 0.018 0.001 PHE M 15 TYR 0.020 0.001 TYR C 54 ARG 0.009 0.000 ARG D 27 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 364 time to evaluate : 2.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 28 LYS cc_start: 0.8513 (mmmm) cc_final: 0.7857 (tttt) REVERT: I 19 LEU cc_start: 0.9534 (OUTLIER) cc_final: 0.9322 (mm) REVERT: I 24 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8851 (mp) REVERT: I 82 GLU cc_start: 0.9125 (OUTLIER) cc_final: 0.8446 (mp0) REVERT: K 55 ASP cc_start: 0.8295 (t0) cc_final: 0.7990 (t0) REVERT: K 283 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9127 (tm) REVERT: N 4 GLU cc_start: 0.8536 (tm-30) cc_final: 0.8178 (tm-30) REVERT: B 15 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.8301 (mtm110) REVERT: C 43 ASP cc_start: 0.9004 (t0) cc_final: 0.8737 (t0) REVERT: C 55 ASP cc_start: 0.8220 (t0) cc_final: 0.7870 (t0) REVERT: C 262 MET cc_start: 0.9216 (mtp) cc_final: 0.8986 (mtt) REVERT: D 69 LYS cc_start: 0.7172 (mtpp) cc_final: 0.6941 (mmmm) REVERT: D 97 LYS cc_start: 0.7334 (OUTLIER) cc_final: 0.7066 (tmmt) REVERT: D 99 ASP cc_start: 0.6991 (m-30) cc_final: 0.6347 (m-30) REVERT: D 150 LYS cc_start: 0.9405 (ptpp) cc_final: 0.9011 (ptpp) REVERT: D 175 LEU cc_start: 0.8647 (mt) cc_final: 0.8445 (mt) REVERT: D 187 GLU cc_start: 0.7152 (pm20) cc_final: 0.6945 (pm20) REVERT: H 29 PHE cc_start: 0.7330 (OUTLIER) cc_final: 0.6859 (t80) REVERT: L 133 GLU cc_start: 0.8865 (tt0) cc_final: 0.8618 (tt0) REVERT: L 144 GLN cc_start: 0.8612 (mt0) cc_final: 0.8375 (mm-40) REVERT: L 150 LYS cc_start: 0.8814 (mmmm) cc_final: 0.8583 (mmtp) REVERT: V 13 ARG cc_start: 0.7790 (ptm-80) cc_final: 0.7327 (ptm-80) REVERT: V 48 SER cc_start: 0.9462 (t) cc_final: 0.9258 (p) REVERT: V 51 ASP cc_start: 0.8692 (p0) cc_final: 0.8402 (p0) REVERT: V 57 PHE cc_start: 0.9312 (m-80) cc_final: 0.9009 (m-80) REVERT: V 60 ASP cc_start: 0.8304 (t0) cc_final: 0.7884 (t0) outliers start: 61 outliers final: 24 residues processed: 400 average time/residue: 1.1309 time to fit residues: 508.8236 Evaluate side-chains 379 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 348 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain X residue 65 ILE Chi-restraints excluded: chain I residue 19 LEU Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain K residue 180 ILE Chi-restraints excluded: chain K residue 275 ILE Chi-restraints excluded: chain K residue 283 LEU Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 11 TYR Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain D residue 97 LYS Chi-restraints excluded: chain D residue 122 HIS Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain L residue 28 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 180 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 137 optimal weight: 30.0000 chunk 158 optimal weight: 10.0000 chunk 104 optimal weight: 0.9980 chunk 186 optimal weight: 20.0000 chunk 117 optimal weight: 6.9990 chunk 113 optimal weight: 8.9990 chunk 86 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 7 GLN ** K 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 ASN ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 ASN L 74 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 17270 Z= 0.313 Angle : 0.751 18.920 23519 Z= 0.328 Chirality : 0.045 0.203 2557 Planarity : 0.004 0.048 2868 Dihedral : 16.310 154.251 2801 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.92 % Allowed : 22.83 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.18), residues: 1996 helix: 1.42 (0.16), residues: 947 sheet: -1.89 (0.36), residues: 172 loop : -0.52 (0.20), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 190 HIS 0.006 0.001 HIS A 209 PHE 0.018 0.002 PHE M 15 TYR 0.053 0.002 TYR X 12 ARG 0.008 0.001 ARG D 27 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 352 time to evaluate : 1.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 10 LYS cc_start: 0.9192 (tmmm) cc_final: 0.8716 (ttmm) REVERT: X 12 TYR cc_start: 0.8562 (p90) cc_final: 0.8334 (p90) REVERT: X 28 LYS cc_start: 0.8441 (mmmm) cc_final: 0.8216 (tttt) REVERT: I 1 MET cc_start: 0.7728 (ttt) cc_final: 0.7465 (ttt) REVERT: I 19 LEU cc_start: 0.9557 (OUTLIER) cc_final: 0.9324 (mm) REVERT: I 24 ILE cc_start: 0.9078 (OUTLIER) cc_final: 0.8844 (mp) REVERT: I 82 GLU cc_start: 0.9136 (OUTLIER) cc_final: 0.8436 (mp0) REVERT: K 55 ASP cc_start: 0.8316 (t0) cc_final: 0.7987 (t0) REVERT: K 283 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9032 (tm) REVERT: N 4 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8251 (tm-30) REVERT: C 55 ASP cc_start: 0.8258 (t0) cc_final: 0.7862 (t0) REVERT: C 155 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.7792 (ptp-170) REVERT: C 262 MET cc_start: 0.9237 (mtp) cc_final: 0.9007 (mtt) REVERT: D 69 LYS cc_start: 0.7225 (mtpp) cc_final: 0.7015 (mmmm) REVERT: D 97 LYS cc_start: 0.7340 (OUTLIER) cc_final: 0.7025 (tmmt) REVERT: D 99 ASP cc_start: 0.7028 (m-30) cc_final: 0.6294 (m-30) REVERT: D 150 LYS cc_start: 0.9433 (ptpp) cc_final: 0.9096 (ptpp) REVERT: D 175 LEU cc_start: 0.8639 (mt) cc_final: 0.8406 (mt) REVERT: H 29 PHE cc_start: 0.7382 (OUTLIER) cc_final: 0.6885 (t80) REVERT: L 133 GLU cc_start: 0.8865 (tt0) cc_final: 0.8565 (tt0) REVERT: L 144 GLN cc_start: 0.8611 (mt0) cc_final: 0.8361 (mm-40) REVERT: L 150 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8576 (mmtp) REVERT: V 13 ARG cc_start: 0.7867 (ptm-80) cc_final: 0.7434 (ptm-80) REVERT: V 48 SER cc_start: 0.9490 (t) cc_final: 0.9262 (p) REVERT: V 49 PHE cc_start: 0.8258 (m-80) cc_final: 0.7866 (m-80) REVERT: V 51 ASP cc_start: 0.8789 (p0) cc_final: 0.8428 (p0) REVERT: V 57 PHE cc_start: 0.9360 (m-80) cc_final: 0.9016 (m-80) REVERT: V 60 ASP cc_start: 0.8316 (t0) cc_final: 0.7885 (t0) outliers start: 65 outliers final: 35 residues processed: 389 average time/residue: 1.1059 time to fit residues: 483.3832 Evaluate side-chains 389 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 346 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain X residue 19 SER Chi-restraints excluded: chain X residue 51 ASP Chi-restraints excluded: chain I residue 19 LEU Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 172 LEU Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 180 ILE Chi-restraints excluded: chain K residue 275 ILE Chi-restraints excluded: chain K residue 283 LEU Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 11 TYR Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 155 ARG Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 97 LYS Chi-restraints excluded: chain D residue 122 HIS Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain L residue 28 ARG Chi-restraints excluded: chain L residue 150 LYS Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain V residue 2 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 74 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 chunk 118 optimal weight: 4.9990 chunk 127 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 146 optimal weight: 0.9980 chunk 170 optimal weight: 0.9980 chunk 179 optimal weight: 20.0000 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 7 GLN ** K 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 ASN ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 ASN L 134 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17270 Z= 0.213 Angle : 0.732 17.361 23519 Z= 0.325 Chirality : 0.044 0.211 2557 Planarity : 0.004 0.044 2868 Dihedral : 15.813 151.412 2801 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.89 % Allowed : 24.10 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.18), residues: 1996 helix: 1.43 (0.16), residues: 949 sheet: -1.26 (0.34), residues: 222 loop : -0.42 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP L 190 HIS 0.005 0.001 HIS D 122 PHE 0.016 0.001 PHE M 15 TYR 0.030 0.001 TYR X 12 ARG 0.011 0.001 ARG X 13 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 364 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 19 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9293 (mm) REVERT: I 24 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8769 (mp) REVERT: I 82 GLU cc_start: 0.9118 (OUTLIER) cc_final: 0.8435 (mp0) REVERT: K 55 ASP cc_start: 0.8342 (t0) cc_final: 0.8001 (t0) REVERT: K 283 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9055 (tm) REVERT: N 4 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8216 (tm-30) REVERT: A 1 MET cc_start: 0.7506 (ttt) cc_final: 0.7296 (ttm) REVERT: C 55 ASP cc_start: 0.8284 (t0) cc_final: 0.7865 (t0) REVERT: C 155 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.7787 (ptp-170) REVERT: C 262 MET cc_start: 0.9198 (mtp) cc_final: 0.8974 (mtt) REVERT: D 97 LYS cc_start: 0.7305 (OUTLIER) cc_final: 0.6952 (tmmt) REVERT: D 99 ASP cc_start: 0.6949 (m-30) cc_final: 0.6230 (m-30) REVERT: D 150 LYS cc_start: 0.9426 (ptpp) cc_final: 0.9069 (ptpp) REVERT: D 175 LEU cc_start: 0.8673 (mt) cc_final: 0.8432 (mt) REVERT: H 29 PHE cc_start: 0.7337 (OUTLIER) cc_final: 0.6869 (t80) REVERT: L 90 ARG cc_start: 0.8609 (mmt-90) cc_final: 0.7713 (mpt-90) REVERT: V 13 ARG cc_start: 0.7864 (ptm-80) cc_final: 0.7432 (ptm-80) REVERT: V 48 SER cc_start: 0.9516 (t) cc_final: 0.9266 (p) REVERT: V 51 ASP cc_start: 0.8824 (p0) cc_final: 0.8437 (p0) REVERT: V 52 ARG cc_start: 0.8433 (tpm170) cc_final: 0.8205 (tpm170) REVERT: V 55 THR cc_start: 0.9104 (m) cc_final: 0.8899 (m) REVERT: V 60 ASP cc_start: 0.8300 (t0) cc_final: 0.7861 (t0) outliers start: 48 outliers final: 28 residues processed: 389 average time/residue: 1.1949 time to fit residues: 521.3126 Evaluate side-chains 383 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 348 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain X residue 51 ASP Chi-restraints excluded: chain I residue 19 LEU Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 172 LEU Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain J residue 13 ASP Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain K residue 180 ILE Chi-restraints excluded: chain K residue 275 ILE Chi-restraints excluded: chain K residue 283 LEU Chi-restraints excluded: chain M residue 11 TYR Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 155 ARG Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain D residue 97 LYS Chi-restraints excluded: chain D residue 122 HIS Chi-restraints excluded: chain D residue 130 ASN Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain L residue 28 ARG Chi-restraints excluded: chain L residue 179 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 5.9990 chunk 174 optimal weight: 6.9990 chunk 179 optimal weight: 20.0000 chunk 104 optimal weight: 7.9990 chunk 75 optimal weight: 0.6980 chunk 136 optimal weight: 20.0000 chunk 53 optimal weight: 2.9990 chunk 157 optimal weight: 8.9990 chunk 164 optimal weight: 9.9990 chunk 173 optimal weight: 0.9990 chunk 114 optimal weight: 0.8980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 17270 Z= 0.293 Angle : 0.755 18.379 23519 Z= 0.334 Chirality : 0.045 0.209 2557 Planarity : 0.004 0.040 2868 Dihedral : 15.676 147.888 2801 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.77 % Allowed : 24.94 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.18), residues: 1996 helix: 1.43 (0.16), residues: 947 sheet: -1.22 (0.34), residues: 218 loop : -0.40 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP L 190 HIS 0.006 0.001 HIS A 209 PHE 0.018 0.002 PHE M 15 TYR 0.027 0.002 TYR X 12 ARG 0.009 0.001 ARG D 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 345 time to evaluate : 1.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 28 LYS cc_start: 0.8404 (mmmm) cc_final: 0.7980 (tttt) REVERT: I 19 LEU cc_start: 0.9536 (OUTLIER) cc_final: 0.9304 (mm) REVERT: I 24 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8754 (mp) REVERT: I 82 GLU cc_start: 0.9132 (OUTLIER) cc_final: 0.8435 (mp0) REVERT: K 55 ASP cc_start: 0.8361 (t0) cc_final: 0.8021 (t0) REVERT: K 283 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9020 (tm) REVERT: N 4 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8226 (tm-30) REVERT: C 155 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.7817 (ptp-170) REVERT: C 262 MET cc_start: 0.9252 (mtp) cc_final: 0.9022 (mtt) REVERT: D 97 LYS cc_start: 0.7231 (OUTLIER) cc_final: 0.6911 (tmtt) REVERT: D 99 ASP cc_start: 0.6977 (m-30) cc_final: 0.6332 (m-30) REVERT: D 150 LYS cc_start: 0.9435 (ptpp) cc_final: 0.9101 (ptpp) REVERT: H 29 PHE cc_start: 0.7387 (OUTLIER) cc_final: 0.6850 (t80) REVERT: L 90 ARG cc_start: 0.8645 (mmt-90) cc_final: 0.7663 (mpt-90) REVERT: L 137 MET cc_start: 0.8858 (mtp) cc_final: 0.8527 (mtp) REVERT: V 13 ARG cc_start: 0.7883 (ptm-80) cc_final: 0.7465 (ptm-80) REVERT: V 25 LYS cc_start: 0.9211 (tppp) cc_final: 0.8974 (tppp) REVERT: V 51 ASP cc_start: 0.8792 (p0) cc_final: 0.8383 (p0) REVERT: V 60 ASP cc_start: 0.8299 (t0) cc_final: 0.7889 (t0) outliers start: 46 outliers final: 31 residues processed: 370 average time/residue: 1.1667 time to fit residues: 483.1077 Evaluate side-chains 377 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 339 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain X residue 51 ASP Chi-restraints excluded: chain I residue 19 LEU Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 172 LEU Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain J residue 13 ASP Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain K residue 180 ILE Chi-restraints excluded: chain K residue 275 ILE Chi-restraints excluded: chain K residue 283 LEU Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 11 TYR Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 155 ARG Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 97 LYS Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain L residue 28 ARG Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain V residue 2 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 184 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 193 optimal weight: 1.9990 chunk 177 optimal weight: 0.0020 chunk 153 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 94 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 overall best weight: 1.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 ASN ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 134 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 17270 Z= 0.262 Angle : 0.762 17.981 23519 Z= 0.340 Chirality : 0.045 0.217 2557 Planarity : 0.004 0.043 2868 Dihedral : 15.487 146.782 2801 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.59 % Allowed : 25.48 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.18), residues: 1996 helix: 1.45 (0.17), residues: 947 sheet: -1.15 (0.34), residues: 218 loop : -0.42 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP L 190 HIS 0.005 0.001 HIS A 209 PHE 0.017 0.001 PHE M 15 TYR 0.022 0.001 TYR L 102 ARG 0.010 0.001 ARG D 27 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 342 time to evaluate : 1.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 12 TYR cc_start: 0.8932 (p90) cc_final: 0.8684 (p90) REVERT: X 28 LYS cc_start: 0.8494 (mmmm) cc_final: 0.8007 (tttt) REVERT: X 37 MET cc_start: 0.9434 (mmm) cc_final: 0.9173 (mmm) REVERT: X 49 PHE cc_start: 0.8051 (m-80) cc_final: 0.7118 (m-80) REVERT: I 24 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8733 (mp) REVERT: I 82 GLU cc_start: 0.9128 (OUTLIER) cc_final: 0.8435 (mp0) REVERT: K 55 ASP cc_start: 0.8419 (t0) cc_final: 0.8074 (t0) REVERT: K 283 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9030 (tm) REVERT: N 4 GLU cc_start: 0.8540 (tm-30) cc_final: 0.8219 (tm-30) REVERT: B 94 LYS cc_start: 0.8774 (mttt) cc_final: 0.8523 (mttt) REVERT: C 55 ASP cc_start: 0.8317 (t0) cc_final: 0.8008 (t0) REVERT: C 155 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.7837 (ptp-170) REVERT: C 167 SER cc_start: 0.8449 (p) cc_final: 0.8237 (p) REVERT: C 262 MET cc_start: 0.9245 (mtp) cc_final: 0.9027 (mtt) REVERT: D 97 LYS cc_start: 0.7251 (OUTLIER) cc_final: 0.6927 (tmtt) REVERT: D 99 ASP cc_start: 0.6920 (m-30) cc_final: 0.6276 (m-30) REVERT: D 150 LYS cc_start: 0.9465 (ptpp) cc_final: 0.9140 (ptpp) REVERT: H 29 PHE cc_start: 0.7348 (OUTLIER) cc_final: 0.6899 (t80) REVERT: L 90 ARG cc_start: 0.8631 (mmt-90) cc_final: 0.7687 (mpt-90) REVERT: V 13 ARG cc_start: 0.7878 (ptm-80) cc_final: 0.7475 (ptm-80) REVERT: V 25 LYS cc_start: 0.9265 (tppp) cc_final: 0.9039 (tppp) REVERT: V 48 SER cc_start: 0.9541 (t) cc_final: 0.9218 (p) REVERT: V 49 PHE cc_start: 0.7996 (m-80) cc_final: 0.7748 (m-80) REVERT: V 51 ASP cc_start: 0.8840 (p0) cc_final: 0.8424 (p0) REVERT: V 60 ASP cc_start: 0.8292 (t0) cc_final: 0.7876 (t0) outliers start: 43 outliers final: 27 residues processed: 369 average time/residue: 1.1081 time to fit residues: 459.6728 Evaluate side-chains 370 residues out of total 1660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 337 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain X residue 51 ASP Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 172 LEU Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain K residue 180 ILE Chi-restraints excluded: chain K residue 275 ILE Chi-restraints excluded: chain K residue 283 LEU Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 11 TYR Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 155 ARG Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 97 LYS Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain L residue 28 ARG Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain V residue 2 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 141 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 154 optimal weight: 20.0000 chunk 64 optimal weight: 50.0000 chunk 158 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 135 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.086886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.059801 restraints weight = 42891.926| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.29 r_work: 0.2844 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 17270 Z= 0.337 Angle : 0.791 18.557 23519 Z= 0.350 Chirality : 0.046 0.212 2557 Planarity : 0.004 0.037 2868 Dihedral : 15.508 145.052 2801 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.41 % Allowed : 25.96 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.18), residues: 1996 helix: 1.39 (0.16), residues: 947 sheet: -1.94 (0.38), residues: 164 loop : -0.54 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP L 190 HIS 0.007 0.001 HIS A 209 PHE 0.020 0.002 PHE D 81 TYR 0.022 0.002 TYR C 54 ARG 0.010 0.001 ARG D 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7625.05 seconds wall clock time: 133 minutes 19.69 seconds (7999.69 seconds total)