Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 21:09:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nhq_12337/04_2023/7nhq_12337_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nhq_12337/04_2023/7nhq_12337.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nhq_12337/04_2023/7nhq_12337.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nhq_12337/04_2023/7nhq_12337.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nhq_12337/04_2023/7nhq_12337_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nhq_12337/04_2023/7nhq_12337_updated.pdb" } resolution = 2.68 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 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 71 5.16 5 Cl 1 4.86 5 C 14488 2.51 5 N 3039 2.21 5 O 3308 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 15": "OE1" <-> "OE2" Residue "A PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 104": "OE1" <-> "OE2" Residue "A TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 132": "OE1" <-> "OE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 229": "OE1" <-> "OE2" Residue "A TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 244": "OE1" <-> "OE2" Residue "A TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 262": "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 GLU 333": "OE1" <-> "OE2" Residue "A PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 342": "OD1" <-> "OD2" Residue "B TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 119": "OD1" <-> "OD2" Residue "B GLU 121": "OE1" <-> "OE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 170": "OD1" <-> "OD2" Residue "B GLU 184": "OE1" <-> "OE2" Residue "B ASP 188": "OD1" <-> "OD2" Residue "B ARG 220": "NH1" <-> "NH2" Residue "B TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 235": "OE1" <-> "OE2" Residue "B PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 276": "OD1" <-> "OD2" Residue "B GLU 299": "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 GLU 353": "OE1" <-> "OE2" Residue "B PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 380": "OD1" <-> "OD2" Residue "B PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 405": "OE1" <-> "OE2" Residue "B ASP 413": "OD1" <-> "OD2" Residue "B GLU 428": "OE1" <-> "OE2" Residue "B GLU 431": "OE1" <-> "OE2" Residue "B GLU 435": "OE1" <-> "OE2" Residue "B PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 464": "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 PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 123": "NH1" <-> "NH2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C GLU 129": "OE1" <-> "OE2" Residue "C GLU 130": "OE1" <-> "OE2" Residue "C ASP 138": "OD1" <-> "OD2" Residue "C ASP 175": "OD1" <-> "OD2" Residue "C PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 309": "OD1" <-> "OD2" Residue "C GLU 336": "OE1" <-> "OE2" Residue "C PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 377": "OE1" <-> "OE2" Residue "C ARG 437": "NH1" <-> "NH2" Residue "D ASP 16": "OD1" <-> "OD2" Residue "D PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 96": "OE1" <-> "OE2" Residue "D PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 131": "OE1" <-> "OE2" Residue "D PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 168": "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 PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 308": "OD1" <-> "OD2" Residue "D GLU 312": "OE1" <-> "OE2" Residue "D GLU 323": "OE1" <-> "OE2" Residue "D PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 344": "OE1" <-> "OE2" Residue "E PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E ASP 68": "OD1" <-> "OD2" Residue "E PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 45": "NH1" <-> "NH2" Residue "H ASP 9": "OD1" <-> "OD2" 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 GLU 2": "OE1" <-> "OE2" Residue "K GLU 13": "OE1" <-> "OE2" Residue "K TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 19": "OD1" <-> "OD2" Residue "L GLU 2": "OE1" <-> "OE2" Residue "L PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 2": "OE1" <-> "OE2" Residue "M PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ARG 43": "NH1" <-> "NH2" Residue "Z ASP 32": "OD1" <-> "OD2" Residue "Z PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z LEU 46": "CD1" <-> "CD2" Residue "Z PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 16": "OE1" <-> "OE2" Residue "2 GLU 46": "OE1" <-> "OE2" Residue "2 GLU 50": "OE1" <-> "OE2" Residue "2 TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 81": "OE1" <-> "OE2" Residue "2 PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 7": "OE1" <-> "OE2" Residue "3 PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 17": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 20946 Number of models: 1 Model: "" Number of chains: 27 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: "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: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 286 Unusual residues: {' CL': 1, ' FE': 1, ' MN': 1, 'BCR': 1, 'CLA': 2, 'LHG': 1, 'PHO': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} 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: 489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 489 Unusual residues: {'CLA': 4, 'LMG': 2, 'PHO': 1, 'PL9': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} 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: "F" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 95 Unusual residues: {'BCR': 1, 'LMG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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} Chain: "3" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 55 Unusual residues: {'LMG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.31, per 1000 atoms: 0.54 Number of scatterers: 20946 At special positions: 0 Unit cell: (132.98, 109, 141.7, 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 71 16.00 P 1 15.00 Mg 35 11.99 O 3308 8.00 N 3039 7.00 C 14488 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=26, symmetry=0 Number of additional bonds: simple=26, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.54 Conformation dependent library (CDL) restraints added in 2.7 seconds 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4034 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 84 helices and 9 sheets defined 54.2% alpha, 3.5% 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 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 102 through 107 Processing helix chain 'A' and resid 110 through 136 Processing helix chain 'A' and resid 143 through 158 removed outlier: 4.336A 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 176 through 190 removed outlier: 3.753A pdb=" N GLU A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 222 Processing helix chain 'A' and resid 249 through 254 Processing helix chain 'A' and resid 256 through 262 Processing helix chain 'A' and resid 268 through 295 removed outlier: 3.901A pdb=" N HIS A 272 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N TRP A 278 " --> pdb=" O LEU A 275 " (cutoff:3.500A) Proline residue: A 279 - end of helix removed outlier: 3.623A pdb=" N THR A 286 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE A 290 " --> pdb=" O ALA A 287 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N MET A 293 " --> pdb=" O ILE A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 332 removed outlier: 3.664A pdb=" N MET A 331 " --> pdb=" O GLY A 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 43 Processing helix chain 'B' and resid 63 through 69 removed outlier: 4.134A pdb=" N LEU B 69 " --> pdb=" O PHE B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 116 Processing helix chain 'B' and resid 135 through 155 Processing helix chain 'B' and resid 195 through 218 removed outlier: 3.502A pdb=" N ILE B 217 " --> pdb=" O GLY B 213 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 218 " --> pdb=" O LEU B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 229 Processing helix chain 'B' and resid 234 through 258 removed outlier: 3.632A pdb=" N LEU B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER B 239 " --> pdb=" O GLU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 276 Processing helix chain 'B' and resid 279 through 295 Processing helix chain 'B' and resid 298 through 304 Processing helix chain 'B' and resid 307 through 312 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: 3.838A pdb=" N ASP B 334 " --> pdb=" O ASN B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 426 removed outlier: 5.210A pdb=" N PHE B 426 " --> pdb=" O ARG B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 474 removed outlier: 3.646A pdb=" N PHE B 464 " --> pdb=" O LEU B 460 " (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 removed outlier: 3.536A pdb=" N LEU C 30 " --> pdb=" O ASN C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 62 removed outlier: 3.651A pdb=" N LEU C 47 " --> pdb=" O ALA C 43 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N HIS C 62 " --> pdb=" O PHE C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 71 No H-bonds generated for 'chain 'C' and resid 69 through 71' Processing helix chain 'C' and resid 77 through 83 removed outlier: 3.680A pdb=" N LEU C 83 " --> pdb=" O HIS C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 122 removed outlier: 3.953A pdb=" N ALA C 111 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL C 112 " --> pdb=" O ILE C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 168 removed outlier: 3.616A pdb=" N ILE C 154 " --> pdb=" O GLY C 150 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL C 155 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU C 163 " --> pdb=" O GLY C 159 " (cutoff:3.500A) removed outlier: 3.921A 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 240 Processing helix chain 'C' and resid 246 through 251 Processing helix chain 'C' and resid 257 through 280 removed outlier: 3.762A pdb=" N MET C 269 " --> pdb=" O GLY C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 312 removed outlier: 3.746A pdb=" N SER C 298 " --> pdb=" O GLY C 294 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS C 311 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU C 312 " --> pdb=" O ARG C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 345 Processing helix chain 'C' and resid 352 through 357 Proline residue: C 356 - end of helix No H-bonds generated for 'chain 'C' and resid 352 through 357' Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 374 through 386 removed outlier: 4.353A pdb=" N THR C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N HIS C 386 " --> pdb=" O GLU C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 443 Processing helix chain 'D' and resid 14 through 22 Processing helix chain 'D' and resid 31 through 54 removed outlier: 3.695A pdb=" N ILE D 35 " --> pdb=" O GLY D 31 " (cutoff:3.500A) removed outlier: 4.140A 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 67 through 69 No H-bonds generated for 'chain 'D' and resid 67 through 69' Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'D' and resid 101 through 106 Processing helix chain 'D' and resid 109 through 136 removed outlier: 3.698A pdb=" N PHE D 113 " --> pdb=" O GLY D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 157 removed outlier: 3.670A pdb=" N SER D 147 " --> pdb=" O ALA D 143 " (cutoff:3.500A) removed outlier: 4.328A 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 159 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 189 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 220 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: 4.035A pdb=" N GLN D 255 " --> pdb=" O ARG D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 291 removed outlier: 3.666A pdb=" N LEU D 272 " --> pdb=" O HIS D 268 " (cutoff:3.500A) Proline residue: D 275 - end of helix removed outlier: 4.322A 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 Proline residue: D 331 - end of helix 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 17 through 39 removed outlier: 5.061A pdb=" N ILE E 25 " --> pdb=" O VAL E 21 " (cutoff:3.500A) Proline residue: E 28 - end of helix removed outlier: 4.066A pdb=" N VAL E 38 " --> pdb=" O GLY E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 46 No H-bonds generated for 'chain 'E' and resid 43 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 27 through 42 removed outlier: 3.530A pdb=" N ALA F 39 " --> pdb=" O GLY F 35 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN F 41 " --> pdb=" O ILE F 37 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE F 42 " --> pdb=" O ALA F 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 15 Proline residue: H 13 - end of helix Processing helix chain 'H' and resid 28 through 49 Processing helix chain 'I' and resid 2 through 23 removed outlier: 3.524A pdb=" N PHE I 15 " --> pdb=" O VAL I 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 24 No H-bonds generated for 'chain 'K' and resid 22 through 24' Processing helix chain 'K' and resid 28 through 42 removed outlier: 3.707A pdb=" N LEU K 33 " --> pdb=" O PRO K 29 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA K 34 " --> pdb=" O VAL K 30 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLN K 40 " --> pdb=" O ALA K 36 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 35 removed outlier: 4.527A pdb=" N SER L 33 " --> pdb=" O LEU L 29 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N TYR L 34 " --> pdb=" O LEU L 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 32 Proline residue: M 18 - end of helix removed outlier: 3.894A pdb=" N SER M 31 " --> pdb=" O VAL M 27 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN M 32 " --> pdb=" O GLN M 28 " (cutoff:3.500A) Processing helix chain 'T' and resid 2 through 22 Processing helix chain 'X' and resid 5 through 34 Processing helix chain 'y' and resid 23 through 41 removed outlier: 3.654A pdb=" N GLY y 29 " --> pdb=" O ILE y 25 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLY y 32 " --> pdb=" O ILE y 28 " (cutoff:3.500A) Proline residue: y 33 - end of helix removed outlier: 3.918A pdb=" N ILE y 36 " --> pdb=" O GLY y 32 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU y 39 " --> pdb=" O ILE y 35 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA y 40 " --> pdb=" O ILE y 36 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL y 41 " --> pdb=" O PHE y 37 " (cutoff:3.500A) Processing helix chain 'Z' and resid 4 through 28 removed outlier: 3.602A 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 60 removed outlier: 4.264A pdb=" N LEU Z 52 " --> pdb=" O ILE Z 48 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE Z 59 " --> pdb=" O GLY Z 55 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE Z 60 " --> pdb=" O VAL Z 56 " (cutoff:3.500A) Processing helix chain '2' and resid 89 through 105 Processing helix chain '3' and resid 28 through 54 removed outlier: 3.575A 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 227 removed outlier: 7.065A pdb=" N GLU A 242 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N GLU A 226 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 7.064A 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: 7.029A 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 26 removed outlier: 3.660A pdb=" N ASP 2 20 " --> pdb=" O TYR 2 37 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N SER 2 31 " --> pdb=" O ALA 2 26 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LYS 2 71 " --> pdb=" O VAL 2 78 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ILE 2 80 " --> pdb=" O ASN 2 69 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ASN 2 69 " --> pdb=" O ILE 2 80 " (cutoff:3.500A) 840 hydrogen bonds defined for protein. 2430 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: 5.36 Time building geometry restraints manager: 9.08 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: 6111 1.36 - 1.55: 15085 1.55 - 1.74: 327 1.74 - 1.93: 128 1.93 - 2.12: 144 Bond restraints: 21795 Sorted by residual: bond pdb=" C5 BCR H 101 " pdb=" C6 BCR H 101 " ideal model delta sigma weight residual 1.347 1.173 0.174 2.00e-02 2.50e+03 7.58e+01 bond pdb=" C3D CLA C 510 " pdb=" CAD CLA C 510 " ideal model delta sigma weight residual 1.454 1.605 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" C5 BCR K 101 " pdb=" C6 BCR K 101 " ideal model delta sigma weight residual 1.347 1.196 0.151 2.00e-02 2.50e+03 5.66e+01 bond pdb=" C3D CLA C 507 " pdb=" CAD CLA C 507 " ideal model delta sigma weight residual 1.454 1.590 -0.136 2.00e-02 2.50e+03 4.64e+01 bond pdb=" C1 BCR H 101 " pdb=" C6 BCR H 101 " ideal model delta sigma weight residual 1.532 1.397 0.135 2.00e-02 2.50e+03 4.53e+01 ... (remaining 21790 not shown) Histogram of bond angle deviations from ideal: 84.67 - 103.58: 626 103.58 - 122.49: 24990 122.49 - 141.40: 4382 141.40 - 160.31: 19 160.31 - 179.22: 72 Bond angle restraints: 30089 Sorted by residual: angle pdb=" CA GLU 3 7 " pdb=" CB GLU 3 7 " pdb=" CG GLU 3 7 " ideal model delta sigma weight residual 114.10 133.98 -19.88 2.00e+00 2.50e-01 9.88e+01 angle pdb=" CB GLU 3 7 " pdb=" CG GLU 3 7 " pdb=" CD GLU 3 7 " ideal model delta sigma weight residual 112.60 128.97 -16.37 1.70e+00 3.46e-01 9.27e+01 angle pdb=" C3A CLA C 513 " pdb=" C2A CLA C 513 " pdb=" CAA CLA C 513 " ideal model delta sigma weight residual 112.02 139.43 -27.41 3.00e+00 1.11e-01 8.35e+01 angle pdb=" C3A CLA B 616 " pdb=" C2A CLA B 616 " pdb=" CAA CLA B 616 " ideal model delta sigma weight residual 112.02 137.34 -25.32 3.00e+00 1.11e-01 7.12e+01 angle pdb=" C2A CLA B 604 " pdb=" C3A CLA B 604 " pdb=" CMA CLA B 604 " ideal model delta sigma weight residual 112.13 137.22 -25.09 3.00e+00 1.11e-01 6.99e+01 ... (remaining 30084 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.07: 10456 26.07 - 52.14: 643 52.14 - 78.21: 138 78.21 - 104.28: 69 104.28 - 130.35: 12 Dihedral angle restraints: 11318 sinusoidal: 4995 harmonic: 6323 Sorted by residual: dihedral pdb=" CA ASN y 45 " pdb=" C ASN y 45 " pdb=" N LEU y 46 " pdb=" CA LEU y 46 " ideal model delta harmonic sigma weight residual 180.00 136.30 43.70 0 5.00e+00 4.00e-02 7.64e+01 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 -139.62 -40.38 0 5.00e+00 4.00e-02 6.52e+01 dihedral pdb=" CA ARG D 233 " pdb=" C ARG D 233 " pdb=" N ALA D 234 " pdb=" CA ALA D 234 " ideal model delta harmonic sigma weight residual 0.00 40.32 -40.32 0 5.00e+00 4.00e-02 6.50e+01 ... (remaining 11315 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.884: 2836 0.884 - 1.768: 19 1.768 - 2.652: 28 2.652 - 3.536: 25 3.536 - 4.420: 6 Chirality restraints: 2914 Sorted by residual: chirality pdb=" C2A CLA B 601 " pdb=" C1A CLA B 601 " pdb=" C3A CLA B 601 " pdb=" CAA CLA B 601 " both_signs ideal model delta sigma weight residual False 2.84 -1.58 4.42 2.00e-01 2.50e+01 4.89e+02 chirality pdb=" C2A CLA B 609 " pdb=" C1A CLA B 609 " pdb=" C3A CLA B 609 " pdb=" CAA CLA B 609 " both_signs ideal model delta sigma weight residual False 2.84 -1.53 4.37 2.00e-01 2.50e+01 4.78e+02 chirality pdb=" C2A CLA B 614 " pdb=" C1A CLA B 614 " pdb=" C3A CLA B 614 " pdb=" CAA CLA B 614 " both_signs ideal model delta sigma weight residual False 2.84 -1.44 4.28 2.00e-01 2.50e+01 4.57e+02 ... (remaining 2911 not shown) Planarity restraints: 3788 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C20 BCR K 101 " 0.087 2.00e-02 2.50e+03 1.59e-01 3.15e+02 pdb=" C21 BCR K 101 " -0.218 2.00e-02 2.50e+03 pdb=" C22 BCR K 101 " 0.248 2.00e-02 2.50e+03 pdb=" C23 BCR K 101 " -0.023 2.00e-02 2.50e+03 pdb=" C37 BCR K 101 " -0.094 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C20 BCR H 101 " -0.084 2.00e-02 2.50e+03 1.56e-01 3.04e+02 pdb=" C21 BCR H 101 " 0.213 2.00e-02 2.50e+03 pdb=" C22 BCR H 101 " -0.245 2.00e-02 2.50e+03 pdb=" C23 BCR H 101 " 0.024 2.00e-02 2.50e+03 pdb=" C37 BCR H 101 " 0.092 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 BCR C 518 " 0.112 2.00e-02 2.50e+03 1.15e-01 1.32e+02 pdb=" C7 BCR C 518 " -0.102 2.00e-02 2.50e+03 pdb=" C8 BCR C 518 " -0.127 2.00e-02 2.50e+03 pdb=" C9 BCR C 518 " 0.118 2.00e-02 2.50e+03 ... (remaining 3785 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 10 2.41 - 3.03: 11118 3.03 - 3.66: 29963 3.66 - 4.28: 48044 4.28 - 4.90: 78327 Nonbonded interactions: 167462 Sorted by model distance: nonbonded pdb=" NE2 HIS A 215 " pdb="FE FE A 401 " model vdw 1.790 2.340 nonbonded pdb=" NE2 HIS D 214 " pdb="FE FE A 401 " model vdw 1.950 2.340 nonbonded pdb=" NE2 HIS A 272 " pdb="FE FE A 401 " model vdw 2.216 2.340 nonbonded pdb=" O TYR C 200 " pdb=" O TRP C 211 " model vdw 2.358 3.040 nonbonded pdb=" O THR 2 85 " pdb=" NH1 ARG 2 87 " model vdw 2.360 2.520 ... (remaining 167457 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 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: 0.900 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: 0.010 Extract box with map and model: 5.860 Check model and map are aligned: 0.310 Set scattering table: 0.170 Process input model: 50.450 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 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 0.174 21795 Z= 0.714 Angle : 2.313 27.411 30089 Z= 0.977 Chirality : 0.414 4.420 2914 Planarity : 0.017 0.159 3788 Dihedral : 19.449 130.346 7284 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.13 % Favored : 94.55 % Rotamer Outliers : 1.77 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: -2.58 (0.15), residues: 2203 helix: -1.31 (0.13), residues: 1219 sheet: -0.64 (0.58), residues: 77 loop : -2.26 (0.17), residues: 907 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 784 time to evaluate : 2.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 13 residues processed: 804 average time/residue: 1.0321 time to fit residues: 972.4409 Evaluate side-chains 573 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 560 time to evaluate : 2.109 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 10 residues processed: 5 average time/residue: 0.6345 time to fit residues: 6.7503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 181 optimal weight: 0.9990 chunk 162 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 109 optimal weight: 0.8980 chunk 87 optimal weight: 0.0070 chunk 168 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 195 optimal weight: 5.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 187 GLN A 298 ASN A 332 HIS B 179 GLN B 233 ASN B 274 GLN C 120 HIS C 143 ASN C 281 ASN D 129 GLN D 164 GLN D 186 GLN ** D 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 GLN D 318 ASN H 15 ASN H 50 ASN L 8 GLN 2 45 GLN 2 76 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.076 21795 Z= 0.239 Angle : 0.931 15.605 30089 Z= 0.403 Chirality : 0.063 0.920 2914 Planarity : 0.007 0.044 3788 Dihedral : 18.378 108.132 3455 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.86 % Favored : 97.05 % Rotamer Outliers : 5.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.96 (0.17), residues: 2203 helix: 0.09 (0.14), residues: 1231 sheet: -0.83 (0.64), residues: 58 loop : -1.57 (0.19), residues: 914 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 573 time to evaluate : 2.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 91 outliers final: 36 residues processed: 613 average time/residue: 1.0413 time to fit residues: 750.1276 Evaluate side-chains 561 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 525 time to evaluate : 2.164 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 17 residues processed: 20 average time/residue: 0.3952 time to fit residues: 14.3925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 108 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 162 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 195 optimal weight: 10.0000 chunk 211 optimal weight: 3.9990 chunk 174 optimal weight: 0.9990 chunk 193 optimal weight: 0.9980 chunk 66 optimal weight: 8.9990 chunk 156 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN B 14 ASN B 318 ASN B 338 GLN ** C 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 GLN D 301 GLN D 318 ASN H 50 ASN ** M 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.115 21795 Z= 0.366 Angle : 0.870 14.235 30089 Z= 0.389 Chirality : 0.057 0.673 2914 Planarity : 0.006 0.050 3788 Dihedral : 16.880 109.960 3455 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.36 % Favored : 96.60 % Rotamer Outliers : 6.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: -0.20 (0.17), residues: 2203 helix: 0.59 (0.15), residues: 1233 sheet: 0.52 (0.74), residues: 48 loop : -1.12 (0.20), residues: 922 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 552 time to evaluate : 2.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 116 outliers final: 54 residues processed: 607 average time/residue: 1.0415 time to fit residues: 736.0761 Evaluate side-chains 564 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 510 time to evaluate : 2.120 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 27 residues processed: 28 average time/residue: 0.3559 time to fit residues: 17.6009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 193 optimal weight: 0.9990 chunk 147 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 196 optimal weight: 7.9990 chunk 207 optimal weight: 7.9990 chunk 102 optimal weight: 0.7980 chunk 186 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN B 289 GLN C 299 GLN D 129 GLN D 186 GLN D 301 GLN K 40 GLN ** 2 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 21795 Z= 0.197 Angle : 0.721 12.268 30089 Z= 0.327 Chirality : 0.047 0.412 2914 Planarity : 0.005 0.045 3788 Dihedral : 16.127 103.508 3455 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer Outliers : 5.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: 0.27 (0.18), residues: 2203 helix: 0.97 (0.15), residues: 1228 sheet: 0.47 (0.73), residues: 48 loop : -0.88 (0.20), residues: 927 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 529 time to evaluate : 2.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 105 outliers final: 58 residues processed: 582 average time/residue: 1.0407 time to fit residues: 709.4070 Evaluate side-chains 565 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 507 time to evaluate : 2.088 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 33 residues processed: 26 average time/residue: 0.4283 time to fit residues: 18.3013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 173 optimal weight: 3.9990 chunk 117 optimal weight: 10.0000 chunk 3 optimal weight: 0.7980 chunk 154 optimal weight: 0.6980 chunk 85 optimal weight: 6.9990 chunk 177 optimal weight: 0.0070 chunk 143 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 186 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 overall best weight: 1.2200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN D 129 GLN D 186 GLN ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 GLN D 322 ASN F 41 GLN H 15 ASN H 50 ASN K 40 GLN Z 58 ASN ** 2 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.4868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 21795 Z= 0.219 Angle : 0.706 12.040 30089 Z= 0.325 Chirality : 0.046 0.343 2914 Planarity : 0.005 0.051 3788 Dihedral : 15.419 89.077 3455 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer Outliers : 5.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.53 (0.18), residues: 2203 helix: 1.14 (0.15), residues: 1228 sheet: 0.48 (0.65), residues: 62 loop : -0.70 (0.21), residues: 913 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 520 time to evaluate : 2.237 Fit side-chains 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: 61 residues processed: 573 average time/residue: 1.0810 time to fit residues: 726.6687 Evaluate side-chains 566 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 505 time to evaluate : 2.198 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 36 residues processed: 27 average time/residue: 0.4274 time to fit residues: 19.2451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 69 optimal weight: 5.9990 chunk 187 optimal weight: 4.9990 chunk 41 optimal weight: 0.0970 chunk 122 optimal weight: 4.9990 chunk 51 optimal weight: 0.0470 chunk 208 optimal weight: 10.0000 chunk 172 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 overall best weight: 1.2080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 GLN ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 GLN F 41 GLN H 50 ASN K 40 GLN ** 2 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 22 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.5085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.070 21795 Z= 0.219 Angle : 0.697 11.914 30089 Z= 0.322 Chirality : 0.045 0.320 2914 Planarity : 0.005 0.043 3788 Dihedral : 15.021 88.321 3455 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer Outliers : 4.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % 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: 0.70 (0.18), residues: 2203 helix: 1.30 (0.15), residues: 1217 sheet: 0.08 (0.64), residues: 65 loop : -0.60 (0.21), residues: 921 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 510 time to evaluate : 2.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 89 outliers final: 60 residues processed: 558 average time/residue: 1.0790 time to fit residues: 703.9015 Evaluate side-chains 558 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 498 time to evaluate : 1.937 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 38 residues processed: 26 average time/residue: 0.5653 time to fit residues: 21.5640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 200 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 117 optimal weight: 9.9990 chunk 175 optimal weight: 3.9990 chunk 116 optimal weight: 0.5980 chunk 207 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 199 GLN A 322 ASN C 299 GLN D 129 GLN D 186 GLN ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 ASN F 41 GLN ** H 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 GLN Z 58 ASN ** 2 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.5327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 21795 Z= 0.299 Angle : 0.737 13.489 30089 Z= 0.340 Chirality : 0.047 0.304 2914 Planarity : 0.005 0.040 3788 Dihedral : 14.811 88.301 3455 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer Outliers : 5.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % 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: 0.73 (0.18), residues: 2203 helix: 1.29 (0.15), residues: 1215 sheet: 0.38 (0.65), residues: 60 loop : -0.55 (0.21), residues: 928 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 503 time to evaluate : 2.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 94 outliers final: 57 residues processed: 553 average time/residue: 1.0819 time to fit residues: 704.0460 Evaluate side-chains 552 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 495 time to evaluate : 2.308 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 36 residues processed: 23 average time/residue: 0.4570 time to fit residues: 17.8805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 128 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 40 optimal weight: 0.0040 chunk 131 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 chunk 188 optimal weight: 1.9990 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN D 106 GLN D 129 GLN D 186 GLN ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 GLN D 322 ASN F 41 GLN H 50 ASN Z 58 ASN ** 2 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 22 GLN ** 3 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.5470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 21795 Z= 0.250 Angle : 0.719 12.952 30089 Z= 0.333 Chirality : 0.045 0.291 2914 Planarity : 0.005 0.114 3788 Dihedral : 14.678 86.855 3455 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer Outliers : 4.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % 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: 0.77 (0.18), residues: 2203 helix: 1.30 (0.15), residues: 1220 sheet: 0.36 (0.65), residues: 60 loop : -0.49 (0.21), residues: 923 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 499 time to evaluate : 2.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 48 residues processed: 545 average time/residue: 1.0719 time to fit residues: 686.0923 Evaluate side-chains 536 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 488 time to evaluate : 2.203 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 38 residues processed: 12 average time/residue: 0.5158 time to fit residues: 11.2858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 198 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 193 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 84 optimal weight: 0.0970 chunk 151 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 182 optimal weight: 0.9990 chunk 192 optimal weight: 9.9990 chunk 126 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 98 GLN D 106 GLN D 129 GLN ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 GLN ** D 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 GLN ** 2 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.5598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 21795 Z= 0.195 Angle : 0.707 11.840 30089 Z= 0.329 Chirality : 0.044 0.264 2914 Planarity : 0.005 0.066 3788 Dihedral : 14.436 85.557 3455 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.36 % Favored : 96.60 % Rotamer Outliers : 3.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % 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: 0.87 (0.18), residues: 2203 helix: 1.37 (0.15), residues: 1215 sheet: 0.38 (0.65), residues: 60 loop : -0.42 (0.21), residues: 928 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 515 time to evaluate : 2.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 45 residues processed: 559 average time/residue: 1.0825 time to fit residues: 717.0135 Evaluate side-chains 542 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 497 time to evaluate : 2.240 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 35 residues processed: 11 average time/residue: 0.5250 time to fit residues: 10.5739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 204 optimal weight: 10.0000 chunk 124 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 chunk 141 optimal weight: 0.6980 chunk 214 optimal weight: 5.9990 chunk 197 optimal weight: 7.9990 chunk 170 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 135 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 HIS D 98 GLN D 106 GLN D 129 GLN D 186 GLN ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 ASN F 41 GLN ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.5685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 21795 Z= 0.212 Angle : 0.714 11.964 30089 Z= 0.332 Chirality : 0.045 0.265 2914 Planarity : 0.005 0.058 3788 Dihedral : 14.275 82.362 3455 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 2.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % 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: 0.88 (0.18), residues: 2203 helix: 1.37 (0.15), residues: 1220 sheet: 0.28 (0.65), residues: 60 loop : -0.40 (0.21), residues: 923 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 499 time to evaluate : 2.297 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: 50 outliers final: 36 residues processed: 539 average time/residue: 1.0780 time to fit residues: 681.9804 Evaluate side-chains 523 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 487 time to evaluate : 2.045 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 34 residues processed: 3 average time/residue: 0.2537 time to fit residues: 3.9652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 181 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 157 optimal weight: 0.2980 chunk 25 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 170 optimal weight: 4.9990 chunk 71 optimal weight: 0.0010 chunk 175 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 31 optimal weight: 0.1980 chunk 149 optimal weight: 2.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 HIS C 79 HIS D 98 GLN D 106 GLN D 129 GLN ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 GLN L 37 ASN Z 58 ASN ** 2 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.131505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.098365 restraints weight = 34047.794| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.59 r_work: 0.3029 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.5760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 21795 Z= 0.180 Angle : 0.697 11.850 30089 Z= 0.326 Chirality : 0.043 0.261 2914 Planarity : 0.004 0.054 3788 Dihedral : 14.066 84.397 3455 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 2.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % 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: 0.92 (0.18), residues: 2203 helix: 1.41 (0.15), residues: 1223 sheet: -0.13 (0.62), residues: 67 loop : -0.37 (0.21), residues: 913 =============================================================================== Job complete usr+sys time: 10091.85 seconds wall clock time: 178 minutes 58.11 seconds (10738.11 seconds total)