Starting phenix.real_space_refine (version: dev) on Wed Dec 14 17:49:54 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nhp_12336/12_2022/7nhp_12336_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nhp_12336/12_2022/7nhp_12336.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nhp_12336/12_2022/7nhp_12336.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nhp_12336/12_2022/7nhp_12336.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nhp_12336/12_2022/7nhp_12336_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nhp_12336/12_2022/7nhp_12336_updated.pdb" } resolution = 2.72 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ASP 61": "OD1" <-> "OD2" Residue "A ASP 103": "OD1" <-> "OD2" Residue "A TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 132": "OE1" <-> "OE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 170": "OD1" <-> "OD2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 308": "OD1" <-> "OD2" Residue "A GLU 329": "OE1" <-> "OE2" Residue "A ASP 342": "OD1" <-> "OD2" Residue "B GLU 41": "OE1" <-> "OE2" Residue "B GLU 83": "OE1" <-> "OE2" Residue "B ASP 87": "OD1" <-> "OD2" Residue "B PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 119": "OD1" <-> "OD2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B GLU 184": "OE1" <-> "OE2" Residue "B ASP 188": "OD1" <-> "OD2" Residue "B PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 220": "NH1" <-> "NH2" Residue "B PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 276": "OD1" <-> "OD2" Residue "B PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 283": "OE1" <-> "OE2" Residue "B GLU 307": "OE1" <-> "OE2" Residue "B TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 313": "OD1" <-> "OD2" Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 428": "OE1" <-> "OE2" Residue "B PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 431": "OE1" <-> "OE2" Residue "B ASP 433": "OD1" <-> "OD2" Residue "B PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 492": "OE1" <-> "OE2" Residue "B TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 17": "OE1" <-> "OE2" Residue "C PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 95": "OD1" <-> "OD2" Residue "C PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 123": "NH1" <-> "NH2" Residue "C GLU 129": "OE1" <-> "OE2" Residue "C TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 141": "OD1" <-> "OD2" Residue "C PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 183": "OD1" <-> "OD2" Residue "C PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 288": "OE1" <-> "OE2" Residue "C GLU 296": "OE1" <-> "OE2" Residue "C PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 309": "OD1" <-> "OD2" Residue "C TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 348": "OD1" <-> "OD2" Residue "C ASP 364": "OD1" <-> "OD2" Residue "C GLU 382": "OE1" <-> "OE2" Residue "C PHE 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 437": "NH1" <-> "NH2" Residue "C GLU 444": "OE1" <-> "OE2" Residue "D ASP 19": "OD1" <-> "OD2" Residue "D ASP 20": "OD1" <-> "OD2" Residue "D ASP 25": "OD1" <-> "OD2" Residue "D PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 96": "OE1" <-> "OE2" Residue "D GLU 131": "OE1" <-> "OE2" Residue "D PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 227": "OE1" <-> "OE2" Residue "D PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 302": "OE1" <-> "OE2" Residue "D GLU 307": "OE1" <-> "OE2" Residue "D ASP 308": "OD1" <-> "OD2" Residue "D GLU 312": "OE1" <-> "OE2" Residue "D PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 343": "OE1" <-> "OE2" Residue "E PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 12": "OD1" <-> "OD2" Residue "E TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 45": "OD1" <-> "OD2" Residue "E TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E ASP 68": "OD1" <-> "OD2" Residue "E GLU 77": "OE1" <-> "OE2" Residue "E PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 9": "OE1" <-> "OE2" Residue "F TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 45": "NH1" <-> "NH2" Residue "H TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 47": "OE1" <-> "OE2" Residue "H TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 13": "OE1" <-> "OE2" Residue "K ASP 19": "OD1" <-> "OD2" Residue "K ASP 23": "OD1" <-> "OD2" Residue "L PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 2": "OE1" <-> "OE2" Residue "M PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 30": "OE1" <-> "OE2" Residue "T GLU 25": "OE1" <-> "OE2" Residue "X PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ARG 43": "NH1" <-> "NH2" Residue "Z PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 32": "OD1" <-> "OD2" Residue "Z ASP 34": "OD1" <-> "OD2" Residue "Z PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 111": "OE1" <-> "OE2" Residue "1 GLU 125": "OE1" <-> "OE2" Residue "1 GLU 131": "OE1" <-> "OE2" Residue "2 GLU 15": "OE1" <-> "OE2" Residue "2 GLU 16": "OE1" <-> "OE2" Residue "2 GLU 62": "OE1" <-> "OE2" Residue "2 ASP 67": "OD1" <-> "OD2" Residue "2 TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 6": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 21839 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 2627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2627 Classifications: {'peptide': 335} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 319} Chain: "B" Number of atoms: 3909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3909 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 32, 'TRANS': 463} Chain: "C" Number of atoms: 3345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3345 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 22, 'TRANS': 409} Chain: "D" Number of atoms: 2717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2717 Classifications: {'peptide': 341} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 15, 'TRANS': 323} Chain: "E" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 635 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 71} Chain: "F" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 307 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 34} Chain: "H" Number of atoms: 511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 511 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain: "I" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 211 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Chain: "K" Number of atoms: 293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 293 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 32} Chain: "L" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 304 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "M" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 267 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "T" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 241 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 2, 'TRANS': 25} Chain: "X" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 254 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "y" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 208 Classifications: {'peptide': 28} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "Z" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 463 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "1" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 893 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "2" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 897 Classifications: {'peptide': 112} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 106} Chain: "3" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 419 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 52} Chain: "A" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 415 Unusual residues: {' CL': 1, ' MN': 1, 'BCR': 1, 'CLA': 4, 'LHG': 1, 'PHO': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 1160 Unusual residues: {'BCR': 3, 'CLA': 16} Classifications: {'undetermined': 19} Link IDs: {None: 18} Chain: "C" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 1075 Unusual residues: {'BCR': 3, 'CLA': 13, 'LMG': 2} Classifications: {'undetermined': 18} Link IDs: {None: 17} Chain: "D" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 510 Unusual residues: {' FE': 1, 'BCR': 1, 'CLA': 2, 'LMG': 4, 'PHO': 1, 'PL9': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 55 Unusual residues: {'LMG': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.30, per 1000 atoms: 0.56 Number of scatterers: 21839 At special positions: 0 Unit cell: (132.98, 106.82, 143.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Fe 2 26.01 Mn 1 24.99 Cl 1 17.00 S 74 16.00 P 1 15.00 Mg 35 11.99 O 3481 8.00 N 3200 7.00 C 15044 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=19, symmetry=0 Number of additional bonds: simple=19, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.41 Conformation dependent library (CDL) restraints added in 3.0 seconds 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4254 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 89 helices and 9 sheets defined 54.5% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 13 through 21 Processing helix chain 'A' and resid 34 through 54 Proline residue: A 39 - end of helix Processing helix chain 'A' and resid 102 through 107 Processing helix chain 'A' and resid 110 through 136 removed outlier: 3.660A pdb=" N LEU A 114 " --> pdb=" O GLY A 110 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 158 removed outlier: 4.364A pdb=" N ALA A 149 " --> pdb=" O VAL A 145 " (cutoff:3.500A) Proline residue: A 150 - end of helix Processing helix chain 'A' and resid 160 through 165 Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 176 through 190 removed outlier: 3.554A pdb=" N PHE A 180 " --> pdb=" O ILE A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 222 Processing helix chain 'A' and resid 256 through 262 removed outlier: 5.091A pdb=" N GLN A 261 " --> pdb=" O ARG A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 295 removed outlier: 4.138A pdb=" N HIS A 272 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE A 273 " --> pdb=" O SER A 270 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 275 " --> pdb=" O HIS A 272 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA A 276 " --> pdb=" O PHE A 273 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N TRP A 278 " --> pdb=" O LEU A 275 " (cutoff:3.500A) Proline residue: A 279 - end of helix removed outlier: 3.656A pdb=" N THR A 286 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE A 290 " --> pdb=" O ALA A 287 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET A 293 " --> pdb=" O ILE A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 332 removed outlier: 3.583A pdb=" N MET A 331 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS A 332 " --> pdb=" O MET A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 11 removed outlier: 4.037A pdb=" N VAL B 11 " --> pdb=" O VAL B 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 8 through 11' Processing helix chain 'B' and resid 16 through 43 Processing helix chain 'B' and resid 63 through 67 Processing helix chain 'B' and resid 93 through 116 Processing helix chain 'B' and resid 135 through 156 Processing helix chain 'B' and resid 195 through 218 removed outlier: 3.603A pdb=" N VAL B 199 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE B 217 " --> pdb=" O GLY B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 228 Processing helix chain 'B' and resid 234 through 258 removed outlier: 3.787A pdb=" N LEU B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER B 239 " --> pdb=" O GLU B 235 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 276 Processing helix chain 'B' and resid 279 through 293 Processing helix chain 'B' and resid 298 through 304 removed outlier: 3.510A pdb=" N ALA B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 313 removed outlier: 3.543A pdb=" N TYR B 312 " --> pdb=" O LYS B 308 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASP B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 330 through 334 removed outlier: 3.902A pdb=" N ASP B 334 " --> pdb=" O ASN B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 423 Processing helix chain 'B' and resid 447 through 474 removed outlier: 3.655A pdb=" N LEU B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU B 474 " --> pdb=" O GLY B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 479 No H-bonds generated for 'chain 'B' and resid 476 through 479' Processing helix chain 'C' and resid 26 through 30 Processing helix chain 'C' and resid 34 through 62 removed outlier: 3.683A pdb=" N HIS C 62 " --> pdb=" O PHE C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 83 removed outlier: 3.967A pdb=" N LEU C 83 " --> pdb=" O HIS C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 122 removed outlier: 4.052A pdb=" N ALA C 111 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL C 112 " --> pdb=" O ILE C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 168 removed outlier: 4.013A pdb=" N LEU C 163 " --> pdb=" O GLY C 159 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL C 164 " --> pdb=" O ALA C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 197 No H-bonds generated for 'chain 'C' and resid 194 through 197' Processing helix chain 'C' and resid 200 through 202 No H-bonds generated for 'chain 'C' and resid 200 through 202' Processing helix chain 'C' and resid 218 through 241 removed outlier: 3.738A pdb=" N ILE C 240 " --> pdb=" O GLY C 236 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU C 241 " --> pdb=" O ILE C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 251 Processing helix chain 'C' and resid 256 through 280 removed outlier: 4.076A pdb=" N LEU C 260 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA C 266 " --> pdb=" O TYR C 262 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N MET C 269 " --> pdb=" O GLY C 265 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE C 272 " --> pdb=" O SER C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 311 removed outlier: 4.184A pdb=" N SER C 298 " --> pdb=" O GLY C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 357 No H-bonds generated for 'chain 'C' and resid 355 through 357' Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 374 through 386 removed outlier: 3.657A pdb=" N THR C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N HIS C 386 " --> pdb=" O GLU C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 441 Processing helix chain 'D' and resid 14 through 23 Processing helix chain 'D' and resid 31 through 51 removed outlier: 3.778A pdb=" N ILE D 35 " --> pdb=" O GLY D 31 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU D 36 " --> pdb=" O TRP D 32 " (cutoff:3.500A) Proline residue: D 39 - end of helix Processing helix chain 'D' and resid 101 through 106 Processing helix chain 'D' and resid 109 through 136 Processing helix chain 'D' and resid 141 through 156 removed outlier: 4.550A pdb=" N ALA D 148 " --> pdb=" O ILE D 144 " (cutoff:3.500A) Proline residue: D 149 - end of helix Processing helix chain 'D' and resid 161 through 163 No H-bonds generated for 'chain 'D' and resid 161 through 163' Processing helix chain 'D' and resid 167 through 169 No H-bonds generated for 'chain 'D' and resid 167 through 169' Processing helix chain 'D' and resid 175 through 188 removed outlier: 3.563A pdb=" N PHE D 181 " --> pdb=" O ALA D 177 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU D 183 " --> pdb=" O PHE D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 193 No H-bonds generated for 'chain 'D' and resid 191 through 193' Processing helix chain 'D' and resid 195 through 219 removed outlier: 3.669A pdb=" N GLU D 219 " --> pdb=" O GLY D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 238 No H-bonds generated for 'chain 'D' and resid 236 through 238' Processing helix chain 'D' and resid 246 through 256 removed outlier: 4.187A pdb=" N GLN D 255 " --> pdb=" O ARG D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 291 removed outlier: 3.600A pdb=" N LEU D 272 " --> pdb=" O HIS D 268 " (cutoff:3.500A) Proline residue: D 275 - end of helix removed outlier: 4.308A pdb=" N LEU D 291 " --> pdb=" O VAL D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 307 Processing helix chain 'D' and resid 314 through 333 removed outlier: 3.784A pdb=" N ALA D 327 " --> pdb=" O GLU D 323 " (cutoff:3.500A) Proline residue: D 331 - end of helix Processing helix chain 'D' and resid 335 through 337 No H-bonds generated for 'chain 'D' and resid 335 through 337' Processing helix chain 'D' and resid 349 through 351 No H-bonds generated for 'chain 'D' and resid 349 through 351' Processing helix chain 'E' and resid 10 through 14 Processing helix chain 'E' and resid 17 through 39 removed outlier: 3.964A pdb=" N ILE E 22 " --> pdb=" O ARG E 18 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ILE E 25 " --> pdb=" O VAL E 21 " (cutoff:3.500A) Proline residue: E 28 - end of helix Processing helix chain 'E' and resid 42 through 46 Processing helix chain 'E' and resid 72 through 81 Processing helix chain 'F' and resid 18 through 24 Processing helix chain 'F' and resid 28 through 42 removed outlier: 3.551A pdb=" N ALA F 39 " --> pdb=" O GLY F 35 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N PHE F 42 " --> pdb=" O ALA F 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 10 Processing helix chain 'H' and resid 12 through 14 No H-bonds generated for 'chain 'H' and resid 12 through 14' Processing helix chain 'H' and resid 28 through 49 removed outlier: 3.639A pdb=" N VAL H 33 " --> pdb=" O PRO H 29 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR H 49 " --> pdb=" O ILE H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'I' and resid 2 through 22 Processing helix chain 'K' and resid 16 through 22 Proline residue: K 20 - end of helix Processing helix chain 'K' and resid 25 through 42 Proline residue: K 29 - end of helix removed outlier: 3.523A pdb=" N PHE K 37 " --> pdb=" O ALA K 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 35 removed outlier: 4.241A pdb=" N SER L 33 " --> pdb=" O LEU L 29 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N TYR L 34 " --> pdb=" O LEU L 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 30 removed outlier: 3.968A pdb=" N ILE M 9 " --> pdb=" O GLN M 5 " (cutoff:3.500A) Proline residue: M 18 - end of helix Processing helix chain 'T' and resid 2 through 22 Processing helix chain 'X' and resid 5 through 32 Processing helix chain 'y' and resid 23 through 41 removed outlier: 4.313A pdb=" N GLY y 32 " --> pdb=" O ILE y 28 " (cutoff:3.500A) Proline residue: y 33 - end of helix removed outlier: 4.145A pdb=" N ILE y 36 " --> pdb=" O GLY y 32 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU y 39 " --> pdb=" O ILE y 35 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL y 41 " --> pdb=" O PHE y 37 " (cutoff:3.500A) Processing helix chain 'Z' and resid 3 through 28 removed outlier: 4.192A pdb=" N ILE Z 21 " --> pdb=" O PHE Z 17 " (cutoff:3.500A) Proline residue: Z 24 - end of helix Processing helix chain 'Z' and resid 33 through 59 removed outlier: 4.362A pdb=" N GLN Z 38 " --> pdb=" O ASP Z 34 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU Z 39 " --> pdb=" O ARG Z 35 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N PHE Z 59 " --> pdb=" O GLY Z 55 " (cutoff:3.500A) Processing helix chain '1' and resid 33 through 48 Processing helix chain '1' and resid 57 through 75 removed outlier: 3.640A pdb=" N ALA 1 62 " --> pdb=" O LYS 1 58 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU 1 63 " --> pdb=" O ALA 1 59 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU 1 74 " --> pdb=" O ASP 1 70 " (cutoff:3.500A) Processing helix chain '1' and resid 80 through 83 Processing helix chain '1' and resid 86 through 103 removed outlier: 3.841A pdb=" N THR 1 92 " --> pdb=" O MET 1 88 " (cutoff:3.500A) Processing helix chain '1' and resid 111 through 133 removed outlier: 4.077A pdb=" N LYS 1 133 " --> pdb=" O ASP 1 129 " (cutoff:3.500A) Processing helix chain '2' and resid 42 through 45 No H-bonds generated for 'chain '2' and resid 42 through 45' Processing helix chain '2' and resid 89 through 106 Processing helix chain '3' and resid 28 through 55 removed outlier: 3.953A pdb=" N LEU 3 37 " --> pdb=" O ARG 3 33 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 223 through 228 removed outlier: 6.954A pdb=" N GLU A 242 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N GLU A 226 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N GLY A 240 " --> pdb=" O GLU A 226 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 166 through 168 Processing sheet with id= C, first strand: chain 'B' and resid 343 through 347 Processing sheet with id= D, first strand: chain 'B' and resid 336 through 340 removed outlier: 6.509A pdb=" N GLU B 431 " --> pdb=" O GLN B 338 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 369 through 371 Processing sheet with id= F, first strand: chain 'C' and resid 173 through 175 Processing sheet with id= G, first strand: chain 'C' and resid 329 through 331 Processing sheet with id= H, first strand: chain '2' and resid 5 through 8 Processing sheet with id= I, first strand: chain '2' and resid 20 through 25 removed outlier: 6.913A pdb=" N LYS 2 71 " --> pdb=" O VAL 2 78 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE 2 80 " --> pdb=" O ASN 2 69 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ASN 2 69 " --> pdb=" O ILE 2 80 " (cutoff:3.500A) 877 hydrogen bonds defined for protein. 2502 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.10 Time building geometry restraints manager: 10.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.36: 6393 1.36 - 1.55: 15651 1.55 - 1.74: 382 1.74 - 1.93: 132 1.93 - 2.12: 144 Bond restraints: 22702 Sorted by residual: bond pdb=" C5 BCR K 101 " pdb=" C6 BCR K 101 " ideal model delta sigma weight residual 1.347 1.172 0.175 2.00e-02 2.50e+03 7.63e+01 bond pdb=" C5 BCR H 101 " pdb=" C6 BCR H 101 " ideal model delta sigma weight residual 1.347 1.182 0.165 2.00e-02 2.50e+03 6.78e+01 bond pdb=" C33 BCR H 101 " pdb=" C5 BCR H 101 " ideal model delta sigma weight residual 1.503 1.360 0.143 2.00e-02 2.50e+03 5.09e+01 bond pdb=" C1 BCR H 101 " pdb=" C6 BCR H 101 " ideal model delta sigma weight residual 1.532 1.393 0.139 2.00e-02 2.50e+03 4.80e+01 bond pdb=" C33 BCR K 101 " pdb=" C5 BCR K 101 " ideal model delta sigma weight residual 1.503 1.364 0.139 2.00e-02 2.50e+03 4.80e+01 ... (remaining 22697 not shown) Histogram of bond angle deviations from ideal: 83.04 - 102.14: 342 102.14 - 121.25: 23609 121.25 - 140.35: 7261 140.35 - 159.45: 27 159.45 - 178.55: 72 Bond angle restraints: 31311 Sorted by residual: angle pdb=" CB MET C 145 " pdb=" CG MET C 145 " pdb=" SD MET C 145 " ideal model delta sigma weight residual 112.70 136.40 -23.70 3.00e+00 1.11e-01 6.24e+01 angle pdb=" C4A CLA B 601 " pdb=" C3A CLA B 601 " pdb=" CMA CLA B 601 " ideal model delta sigma weight residual 112.13 88.70 23.43 3.00e+00 1.11e-01 6.10e+01 angle pdb=" C1A CLA B 601 " pdb=" C2A CLA B 601 " pdb=" CAA CLA B 601 " ideal model delta sigma weight residual 110.32 131.81 -21.49 3.00e+00 1.11e-01 5.13e+01 angle pdb=" C2A CLA B 608 " pdb=" C3A CLA B 608 " pdb=" CMA CLA B 608 " ideal model delta sigma weight residual 112.13 133.26 -21.13 3.00e+00 1.11e-01 4.96e+01 angle pdb=" C3D CLA B 616 " pdb=" CAD CLA B 616 " pdb=" CBD CLA B 616 " ideal model delta sigma weight residual 107.10 86.74 20.36 3.00e+00 1.11e-01 4.61e+01 ... (remaining 31306 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.66: 10986 24.66 - 49.31: 668 49.31 - 73.97: 162 73.97 - 98.63: 65 98.63 - 123.29: 11 Dihedral angle restraints: 11892 sinusoidal: 5234 harmonic: 6658 Sorted by residual: dihedral pdb=" CA ARG 2 27 " pdb=" C ARG 2 27 " pdb=" N ASP 2 28 " pdb=" CA ASP 2 28 " ideal model delta harmonic sigma weight residual 180.00 -132.91 -47.09 0 5.00e+00 4.00e-02 8.87e+01 dihedral pdb=" CA LEU A 343 " pdb=" C LEU A 343 " pdb=" N ALA A 344 " pdb=" CA ALA A 344 " ideal model delta harmonic sigma weight residual 0.00 35.78 -35.78 0 5.00e+00 4.00e-02 5.12e+01 dihedral pdb=" CA GLY K 44 " pdb=" C GLY K 44 " pdb=" N PHE K 45 " pdb=" CA PHE K 45 " ideal model delta harmonic sigma weight residual 180.00 146.58 33.42 0 5.00e+00 4.00e-02 4.47e+01 ... (remaining 11889 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.620: 2984 0.620 - 1.240: 18 1.240 - 1.860: 21 1.860 - 2.480: 12 2.480 - 3.099: 14 Chirality restraints: 3049 Sorted by residual: chirality pdb=" C8 PHO D 407 " pdb=" C10 PHO D 407 " pdb=" C7 PHO D 407 " pdb=" C9 PHO D 407 " both_signs ideal model delta sigma weight residual False 2.59 -0.51 3.10 2.00e-01 2.50e+01 2.40e+02 chirality pdb=" C8 CLA B 608 " pdb=" C10 CLA B 608 " pdb=" C7 CLA B 608 " pdb=" C9 CLA B 608 " both_signs ideal model delta sigma weight residual False 2.59 -0.50 3.09 2.00e-01 2.50e+01 2.39e+02 chirality pdb=" C8 CLA C 505 " pdb=" C10 CLA C 505 " pdb=" C7 CLA C 505 " pdb=" C9 CLA C 505 " both_signs ideal model delta sigma weight residual False 2.59 -0.42 3.02 2.00e-01 2.50e+01 2.28e+02 ... (remaining 3046 not shown) Planarity restraints: 3951 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 BCR H 101 " 0.121 2.00e-02 2.50e+03 1.13e-01 1.60e+02 pdb=" C11 BCR H 101 " -0.117 2.00e-02 2.50e+03 pdb=" C34 BCR H 101 " -0.022 2.00e-02 2.50e+03 pdb=" C8 BCR H 101 " -0.123 2.00e-02 2.50e+03 pdb=" C9 BCR H 101 " 0.141 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 BCR K 101 " 0.117 2.00e-02 2.50e+03 1.12e-01 1.56e+02 pdb=" C11 BCR K 101 " -0.115 2.00e-02 2.50e+03 pdb=" C34 BCR K 101 " -0.022 2.00e-02 2.50e+03 pdb=" C8 BCR K 101 " -0.122 2.00e-02 2.50e+03 pdb=" C9 BCR K 101 " 0.142 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A CLA B 601 " -0.067 2.00e-02 2.50e+03 8.77e-02 1.15e+02 pdb=" C2A CLA B 601 " 0.130 2.00e-02 2.50e+03 pdb=" C4A CLA B 601 " -0.041 2.00e-02 2.50e+03 pdb=" CHA CLA B 601 " -0.010 2.00e-02 2.50e+03 pdb=" NA CLA B 601 " -0.113 2.00e-02 2.50e+03 pdb="MG CLA B 601 " 0.101 2.00e-02 2.50e+03 ... (remaining 3948 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 39 2.52 - 3.11: 14984 3.11 - 3.71: 32028 3.71 - 4.30: 48991 4.30 - 4.90: 78841 Nonbonded interactions: 174883 Sorted by model distance: nonbonded pdb=" NE2 HIS A 215 " pdb="FE FE D 401 " model vdw 1.924 2.340 nonbonded pdb=" NE2 HIS D 214 " pdb="FE FE D 401 " model vdw 1.947 2.340 nonbonded pdb=" OD2 ASP C 309 " pdb=" OH TYR C 328 " model vdw 2.079 2.440 nonbonded pdb=" O PHE 1 33 " pdb=" OG1 THR 1 37 " model vdw 2.187 2.440 nonbonded pdb=" NH1 ARG C 29 " pdb=" NH1 ARG K 46 " model vdw 2.194 3.200 ... (remaining 174878 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 9 Type Number sf(0) Gaussians Mn 1 7.51 5 Fe 2 7.16 5 P 1 5.49 5 Mg 35 5.21 5 S 74 5.16 5 Cl 1 4.86 5 C 15044 2.51 5 N 3200 2.21 5 O 3481 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.650 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: 6.030 Check model and map are aligned: 0.290 Convert atoms to be neutral: 0.160 Process input model: 54.570 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 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 : 0.012 0.175 22702 Z= 0.708 Angle : 2.192 23.701 31311 Z= 0.940 Chirality : 0.295 3.099 3049 Planarity : 0.015 0.113 3951 Dihedral : 18.458 123.286 7638 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.83 % Favored : 93.82 % Rotamer Outliers : 1.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.15), residues: 2314 helix: -1.27 (0.12), residues: 1296 sheet: -0.22 (0.65), residues: 63 loop : -2.44 (0.17), residues: 955 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 854 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 828 time to evaluate : 2.343 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: symmetry clash outliers start: 26 outliers final: 16 residues processed: 840 average time/residue: 1.0290 time to fit residues: 1011.7435 Evaluate side-chains 606 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 590 time to evaluate : 2.032 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 8 residues processed: 10 average time/residue: 0.4222 time to fit residues: 8.5530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 190 optimal weight: 0.9980 chunk 171 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 131 optimal weight: 0.2980 chunk 205 optimal weight: 8.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN A 199 GLN ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 HIS B 179 GLN B 281 GLN B 318 ASN B 490 GLN C 189 ASN C 282 ASN C 386 HIS D 322 ASN E 58 GLN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 GLN M 4 ASN y 45 ASN ** Z 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 58 ASN 1 95 ASN 1 106 ASN 3 22 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.079 22702 Z= 0.218 Angle : 0.807 13.820 31311 Z= 0.372 Chirality : 0.047 0.378 3049 Planarity : 0.006 0.057 3951 Dihedral : 16.999 107.573 3580 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.28 % Favored : 96.59 % Rotamer Outliers : 5.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.81 (0.16), residues: 2314 helix: 0.29 (0.14), residues: 1298 sheet: -0.18 (0.65), residues: 63 loop : -1.71 (0.18), residues: 953 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 607 time to evaluate : 1.972 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: symmetry clash outliers start: 106 outliers final: 35 residues processed: 646 average time/residue: 1.0413 time to fit residues: 787.7780 Evaluate side-chains 548 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 513 time to evaluate : 2.249 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 17 residues processed: 19 average time/residue: 0.4470 time to fit residues: 14.7636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 114 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 170 optimal weight: 0.5980 chunk 139 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 205 optimal weight: 10.0000 chunk 222 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 203 optimal weight: 9.9990 chunk 70 optimal weight: 0.8980 chunk 164 optimal weight: 3.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS A 187 GLN A 199 GLN B 318 ASN C 120 HIS C 376 GLN D 164 GLN D 186 GLN D 322 ASN L 6 ASN M 4 ASN Z 38 GLN 1 56 ASN 1 106 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 22702 Z= 0.273 Angle : 0.721 13.078 31311 Z= 0.341 Chirality : 0.045 0.221 3049 Planarity : 0.005 0.049 3951 Dihedral : 15.571 106.846 3580 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.54 % Favored : 96.37 % Rotamer Outliers : 6.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.07 (0.17), residues: 2314 helix: 0.87 (0.14), residues: 1291 sheet: 0.50 (0.65), residues: 65 loop : -1.35 (0.19), residues: 958 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 555 time to evaluate : 2.140 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 outliers start: 116 outliers final: 55 residues processed: 604 average time/residue: 1.0822 time to fit residues: 766.4030 Evaluate side-chains 578 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 523 time to evaluate : 2.255 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 30 residues processed: 27 average time/residue: 0.3902 time to fit residues: 18.3015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 203 optimal weight: 2.9990 chunk 154 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 98 optimal weight: 6.9990 chunk 138 optimal weight: 1.9990 chunk 206 optimal weight: 9.9990 chunk 218 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 195 optimal weight: 0.2980 chunk 58 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN B 374 ASN C 189 ASN C 299 GLN C 376 GLN C 386 HIS D 186 GLN D 322 ASN D 332 GLN E 58 GLN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 ASN Z 38 GLN 1 56 ASN 1 106 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 22702 Z= 0.222 Angle : 0.657 12.300 31311 Z= 0.314 Chirality : 0.043 0.231 3049 Planarity : 0.005 0.055 3951 Dihedral : 14.777 105.604 3580 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.11 % Favored : 96.85 % Rotamer Outliers : 6.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.17), residues: 2314 helix: 1.19 (0.15), residues: 1292 sheet: 0.06 (0.62), residues: 75 loop : -1.09 (0.19), residues: 947 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 560 time to evaluate : 2.169 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 outliers start: 116 outliers final: 60 residues processed: 612 average time/residue: 1.0633 time to fit residues: 761.6469 Evaluate side-chains 593 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 533 time to evaluate : 2.121 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 36 residues processed: 28 average time/residue: 0.4411 time to fit residues: 20.0740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 181 optimal weight: 0.7980 chunk 124 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 162 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 186 optimal weight: 1.9990 chunk 151 optimal weight: 0.0770 chunk 0 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 chunk 196 optimal weight: 8.9990 chunk 55 optimal weight: 0.2980 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN B 282 GLN B 490 GLN C 189 ASN C 386 HIS C 432 HIS ** D 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 GLN D 322 ASN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 ASN 1 56 ASN 1 106 ASN 2 74 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 22702 Z= 0.186 Angle : 0.650 13.499 31311 Z= 0.309 Chirality : 0.042 0.227 3049 Planarity : 0.005 0.043 3951 Dihedral : 14.392 101.768 3580 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.50 % Favored : 96.46 % Rotamer Outliers : 5.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.55 (0.18), residues: 2314 helix: 1.35 (0.15), residues: 1293 sheet: 0.10 (0.60), residues: 82 loop : -1.00 (0.20), residues: 939 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 557 time to evaluate : 2.204 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 outliers start: 111 outliers final: 56 residues processed: 604 average time/residue: 1.0525 time to fit residues: 752.9769 Evaluate side-chains 584 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 528 time to evaluate : 2.178 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 32 residues processed: 27 average time/residue: 0.3918 time to fit residues: 18.7102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 73 optimal weight: 7.9990 chunk 196 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 128 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 218 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 101 optimal weight: 0.1980 chunk 18 optimal weight: 0.5980 chunk 72 optimal weight: 6.9990 chunk 114 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 282 GLN B 374 ASN C 189 ASN ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 386 HIS ** D 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 GLN F 8 GLN L 6 ASN Z 31 GLN 1 56 ASN 1 106 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.5040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 22702 Z= 0.187 Angle : 0.642 12.700 31311 Z= 0.306 Chirality : 0.042 0.232 3049 Planarity : 0.004 0.040 3951 Dihedral : 14.094 95.086 3580 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.07 % Favored : 96.89 % Rotamer Outliers : 5.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.66 (0.18), residues: 2314 helix: 1.43 (0.15), residues: 1288 sheet: 0.09 (0.59), residues: 82 loop : -0.92 (0.20), residues: 944 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 541 time to evaluate : 2.250 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: symmetry clash outliers start: 101 outliers final: 56 residues processed: 589 average time/residue: 1.0224 time to fit residues: 710.1792 Evaluate side-chains 567 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 511 time to evaluate : 2.375 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 32 residues processed: 25 average time/residue: 0.4710 time to fit residues: 19.0610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 210 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 124 optimal weight: 0.0270 chunk 159 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 chunk 184 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 217 optimal weight: 7.9990 chunk 136 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 overall best weight: 1.1842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 282 GLN C 386 HIS ** D 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 GLN L 6 ASN ** Z 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 56 ASN 1 106 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.5211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 22702 Z= 0.208 Angle : 0.660 12.961 31311 Z= 0.315 Chirality : 0.043 0.230 3049 Planarity : 0.005 0.067 3951 Dihedral : 13.812 89.842 3580 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.41 % Favored : 96.54 % Rotamer Outliers : 4.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.72 (0.18), residues: 2314 helix: 1.47 (0.15), residues: 1286 sheet: -0.03 (0.59), residues: 85 loop : -0.86 (0.20), residues: 943 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 534 time to evaluate : 2.439 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 outliers start: 92 outliers final: 52 residues processed: 581 average time/residue: 1.0394 time to fit residues: 708.2442 Evaluate side-chains 576 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 524 time to evaluate : 2.058 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 33 residues processed: 20 average time/residue: 0.4146 time to fit residues: 14.6092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 134 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 138 optimal weight: 0.1980 chunk 148 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 171 optimal weight: 0.6980 chunk 198 optimal weight: 5.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN B 374 ASN C 189 ASN ** D 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 GLN L 6 ASN ** Z 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 56 ASN 1 106 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.5365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 22702 Z= 0.220 Angle : 0.676 14.556 31311 Z= 0.322 Chirality : 0.043 0.230 3049 Planarity : 0.005 0.046 3951 Dihedral : 13.564 89.993 3580 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.24 % Favored : 96.72 % Rotamer Outliers : 4.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.79 (0.18), residues: 2314 helix: 1.50 (0.15), residues: 1287 sheet: 0.12 (0.61), residues: 85 loop : -0.80 (0.20), residues: 942 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 535 time to evaluate : 2.077 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 outliers start: 80 outliers final: 52 residues processed: 581 average time/residue: 1.0622 time to fit residues: 727.5422 Evaluate side-chains 581 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 529 time to evaluate : 2.057 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 35 residues processed: 18 average time/residue: 0.5052 time to fit residues: 14.8290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 208 optimal weight: 8.9990 chunk 190 optimal weight: 0.8980 chunk 202 optimal weight: 30.0000 chunk 122 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 159 optimal weight: 20.0000 chunk 62 optimal weight: 0.6980 chunk 183 optimal weight: 2.9990 chunk 191 optimal weight: 0.0020 chunk 133 optimal weight: 0.4980 chunk 214 optimal weight: 10.0000 overall best weight: 1.0190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN A 303 ASN B 282 GLN ** D 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 ASN ** Z 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 56 ASN 1 106 ASN 3 22 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.5486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 22702 Z= 0.207 Angle : 0.685 13.803 31311 Z= 0.326 Chirality : 0.043 0.224 3049 Planarity : 0.005 0.047 3951 Dihedral : 13.385 89.127 3580 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.41 % Favored : 96.54 % Rotamer Outliers : 3.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.82 (0.18), residues: 2314 helix: 1.50 (0.15), residues: 1289 sheet: 0.02 (0.68), residues: 70 loop : -0.72 (0.20), residues: 955 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 537 time to evaluate : 2.305 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 outliers start: 63 outliers final: 41 residues processed: 577 average time/residue: 1.0543 time to fit residues: 715.0632 Evaluate side-chains 563 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 522 time to evaluate : 2.354 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 33 residues processed: 9 average time/residue: 0.4884 time to fit residues: 8.9994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 131 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 chunk 149 optimal weight: 4.9990 chunk 225 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 chunk 179 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 138 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 190 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 ASN ** Z 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 56 ASN 1 106 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.5556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 22702 Z= 0.230 Angle : 0.702 12.609 31311 Z= 0.335 Chirality : 0.043 0.229 3049 Planarity : 0.005 0.050 3951 Dihedral : 13.289 87.264 3580 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.46 % Favored : 96.50 % Rotamer Outliers : 3.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.84 (0.18), residues: 2314 helix: 1.52 (0.15), residues: 1283 sheet: 0.09 (0.69), residues: 70 loop : -0.70 (0.20), residues: 961 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 525 time to evaluate : 1.977 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: symmetry clash outliers start: 58 outliers final: 44 residues processed: 563 average time/residue: 1.0698 time to fit residues: 710.8862 Evaluate side-chains 557 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 513 time to evaluate : 2.070 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 32 residues processed: 15 average time/residue: 0.6114 time to fit residues: 14.7877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 54 optimal weight: 0.9980 chunk 165 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 179 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 184 optimal weight: 2.9990 chunk 22 optimal weight: 0.0770 chunk 33 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 overall best weight: 1.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 ASN L 6 ASN ** Z 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 56 ASN 1 106 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.128730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.092294 restraints weight = 35983.500| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.71 r_work: 0.2982 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.5636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 22702 Z= 0.236 Angle : 0.707 12.631 31311 Z= 0.338 Chirality : 0.044 0.226 3049 Planarity : 0.005 0.071 3951 Dihedral : 13.234 85.349 3580 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.50 % Favored : 96.46 % Rotamer Outliers : 2.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.81 (0.18), residues: 2314 helix: 1.48 (0.15), residues: 1283 sheet: -0.01 (0.67), residues: 70 loop : -0.69 (0.20), residues: 961 =============================================================================== Job complete usr+sys time: 10320.94 seconds wall clock time: 181 minutes 58.90 seconds (10918.90 seconds total)