Starting phenix.real_space_refine on Fri Feb 23 03:58:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p61_13214/02_2024/7p61_13214_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p61_13214/02_2024/7p61_13214.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p61_13214/02_2024/7p61_13214.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p61_13214/02_2024/7p61_13214.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p61_13214/02_2024/7p61_13214_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p61_13214/02_2024/7p61_13214_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 Fe 32 7.16 5 P 5 5.49 5 S 265 5.16 5 C 23803 2.51 5 N 6112 2.21 5 O 6472 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F GLU 152": "OE1" <-> "OE2" Residue "F GLU 168": "OE1" <-> "OE2" Residue "F GLU 420": "OE1" <-> "OE2" Residue "E GLU 160": "OE1" <-> "OE2" Residue "G GLU 192": "OE1" <-> "OE2" Residue "G GLU 201": "OE1" <-> "OE2" Residue "G GLU 347": "OE1" <-> "OE2" Residue "G GLU 382": "OE1" <-> "OE2" Residue "G GLU 510": "OE1" <-> "OE2" Residue "G GLU 626": "OE1" <-> "OE2" Residue "G TYR 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 825": "OE1" <-> "OE2" Residue "G GLU 877": "OE1" <-> "OE2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 179": "OE1" <-> "OE2" Residue "C TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 276": "OE1" <-> "OE2" Residue "C PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 482": "OE1" <-> "OE2" Residue "B GLU 23": "OE1" <-> "OE2" Residue "B PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "I GLU 107": "OE1" <-> "OE2" Residue "I GLU 165": "OE1" <-> "OE2" Residue "L GLU 111": "OE1" <-> "OE2" Residue "L GLU 202": "OE1" <-> "OE2" Residue "L GLU 494": "OE1" <-> "OE2" Residue "M GLU 110": "OE1" <-> "OE2" Residue "M PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 364": "OE1" <-> "OE2" Residue "M GLU 407": "OE1" <-> "OE2" Residue "M GLU 464": "OE1" <-> "OE2" Residue "N GLU 96": "OE1" <-> "OE2" Residue "N PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 10": "OE1" <-> "OE2" Residue "H PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 228": "OE1" <-> "OE2" Residue "J GLU 80": "OE1" <-> "OE2" Residue "J GLU 161": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 36690 Number of models: 1 Model: "" Number of chains: 20 Chain: "F" Number of atoms: 3432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3432 Classifications: {'peptide': 442} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 416} Chain: "E" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1220 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 146} Chain: "G" Number of atoms: 7022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7022 Classifications: {'peptide': 905} Link IDs: {'PTRANS': 41, 'TRANS': 863} Chain: "C" Number of atoms: 4606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4606 Classifications: {'peptide': 571} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 536} Chain breaks: 3 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1518 Classifications: {'peptide': 191} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 177} Chain breaks: 3 Chain: "I" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1157 Classifications: {'peptide': 147} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 134} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "L" Number of atoms: 4525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4525 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 18, 'TRANS': 574} Chain breaks: 3 Chain: "M" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3953 Classifications: {'peptide': 504} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 482} Chain: "N" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3630 Classifications: {'peptide': 479} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 458} Chain breaks: 2 Chain: "H" Number of atoms: 2449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2449 Classifications: {'peptide': 312} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 297} Chain breaks: 1 Chain: "A" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 840 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain breaks: 1 Chain: "K" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 760 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Chain: "J" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1326 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 5, 'TRANS': 169} Chain: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 29 Unusual residues: {' CA': 1, 'FES': 1, 'SF4': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "H" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'UQ8': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'UQ8:plan-6': 1, 'UQ8:plan-7': 1, 'UQ8:plan-2': 1, 'UQ8:plan-3': 1, 'UQ8:plan-8': 1, 'UQ8:plan-9': 1} Unresolved non-hydrogen planarities: 29 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2746 SG CYS F 354 58.000 60.060 186.262 1.00 42.83 S ATOM 2766 SG CYS F 357 60.934 59.643 191.244 1.00 43.36 S ATOM 3087 SG CYS F 398 55.147 56.343 190.926 1.00 47.90 S ATOM 2722 SG CYS F 351 60.044 53.849 187.825 1.00 26.05 S ATOM 4079 SG CYS E 92 66.098 50.835 208.196 1.00 63.34 S ATOM 4113 SG CYS E 97 66.059 51.437 211.778 1.00 79.45 S ATOM 4417 SG CYS E 137 59.892 51.003 210.256 1.00 68.11 S ATOM 5501 SG CYS G 114 70.353 66.642 170.358 1.00 31.78 S ATOM 5441 SG CYS G 105 75.450 70.015 173.023 1.00 50.80 S ATOM 5461 SG CYS G 108 76.392 64.376 170.133 1.00 31.29 S ATOM 5836 SG CYS G 153 69.321 57.637 177.949 1.00 39.44 S ATOM 5884 SG CYS G 159 66.868 53.193 173.811 1.00 21.26 S ATOM 6228 SG CYS G 203 69.376 58.432 171.327 1.00 61.45 S ATOM 6453 SG CYS G 230 68.138 50.539 149.627 1.00 37.10 S ATOM 6738 SG CYS G 265 67.377 46.739 154.933 1.00 43.75 S ATOM 6501 SG CYS G 237 62.450 50.242 152.236 1.00 48.43 S ATOM 6477 SG CYS G 233 64.973 44.887 149.265 1.00 56.23 S ATOM 4902 SG CYS G 36 57.091 59.893 176.516 1.00 24.85 S ATOM 4978 SG CYS G 47 58.671 62.966 177.343 1.00 38.74 S ATOM 5004 SG CYS G 50 52.812 64.900 176.532 1.00 60.43 S ATOM 5153 SG CYS G 69 52.567 61.186 175.934 1.00 44.25 S ATOM 17076 SG CYS B 129 83.831 94.080 149.064 1.00 50.33 S ATOM 16699 SG CYS B 64 88.743 98.202 151.003 1.00 77.93 S ATOM 16693 SG CYS B 63 82.655 99.895 151.658 1.00 88.39 S ATOM 17293 SG CYS B 158 84.932 95.073 155.332 1.00100.64 S ATOM 18320 SG CYS I 99 88.373 86.710 157.085 1.00 44.28 S ATOM 18363 SG CYS I 105 86.341 83.319 162.216 1.00 39.73 S ATOM 18078 SG CYS I 70 82.961 82.998 156.632 1.00 32.10 S ATOM 18392 SG CYS I 109 86.636 77.470 168.439 1.00 21.35 S ATOM 18055 SG CYS I 66 85.155 77.080 162.165 1.00 27.29 S ATOM 18015 SG CYS I 60 89.115 72.572 164.619 1.00 30.11 S ATOM 18033 SG CYS I 63 82.761 72.850 166.416 1.00 15.48 S Time building chain proxies: 19.14, per 1000 atoms: 0.52 Number of scatterers: 36690 At special positions: 0 Unit cell: (152.784, 225.993, 241.908, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 32 26.01 Ca 1 19.99 S 265 16.00 P 5 15.00 O 6472 8.00 N 6112 7.00 C 23803 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=0, symmetry=0 Time building additional restraints: 14.61 Conformation dependent library (CDL) restraints added in 6.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 137 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 97 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 92 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 133 " pdb=" FES G1004 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 50 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 69 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 47 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 36 " pdb=" SF4 B 301 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 63 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 129 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 158 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 64 " pdb=" SF4 F 501 " pdb="FE2 SF4 F 501 " - pdb=" SG CYS F 357 " pdb="FE1 SF4 F 501 " - pdb=" SG CYS F 354 " pdb="FE4 SF4 F 501 " - pdb=" SG CYS F 351 " pdb="FE3 SF4 F 501 " - pdb=" SG CYS F 398 " pdb=" SF4 G1001 " pdb="FE3 SF4 G1001 " - pdb=" NE2 HIS G 101 " pdb="FE4 SF4 G1001 " - pdb=" SG CYS G 108 " pdb="FE2 SF4 G1001 " - pdb=" SG CYS G 105 " pdb="FE1 SF4 G1001 " - pdb=" SG CYS G 114 " pdb=" SF4 G1002 " pdb="FE3 SF4 G1002 " - pdb=" SG CYS G 159 " pdb="FE2 SF4 G1002 " - pdb=" SG CYS G 153 " pdb="FE4 SF4 G1002 " - pdb=" SG CYS G 203 " pdb="FE1 SF4 G1002 " - pdb=" SG CYS G 156 " pdb=" SF4 G1003 " pdb="FE3 SF4 G1003 " - pdb=" SG CYS G 237 " pdb="FE1 SF4 G1003 " - pdb=" SG CYS G 230 " pdb="FE4 SF4 G1003 " - pdb=" SG CYS G 233 " pdb="FE2 SF4 G1003 " - pdb=" SG CYS G 265 " pdb=" SF4 I 201 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 105 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 70 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 99 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 102 " pdb=" SF4 I 202 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 66 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 60 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 63 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 109 " Number of angles added : 93 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8554 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 188 helices and 25 sheets defined 52.4% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.81 Creating SS restraints... Processing helix chain 'F' and resid 26 through 31 Processing helix chain 'F' and resid 36 through 44 Processing helix chain 'F' and resid 47 through 57 Processing helix chain 'F' and resid 69 through 74 Processing helix chain 'F' and resid 100 through 106 removed outlier: 4.041A pdb=" N LEU F 104 " --> pdb=" O LYS F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 123 Processing helix chain 'F' and resid 138 through 152 Processing helix chain 'F' and resid 160 through 162 No H-bonds generated for 'chain 'F' and resid 160 through 162' Processing helix chain 'F' and resid 178 through 181 removed outlier: 3.512A pdb=" N GLY F 181 " --> pdb=" O TYR F 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 178 through 181' Processing helix chain 'F' and resid 183 through 190 Processing helix chain 'F' and resid 209 through 211 No H-bonds generated for 'chain 'F' and resid 209 through 211' Processing helix chain 'F' and resid 219 through 231 removed outlier: 3.903A pdb=" N VAL F 225 " --> pdb=" O THR F 221 " (cutoff:3.500A) Proline residue: F 226 - end of helix Processing helix chain 'F' and resid 234 through 237 No H-bonds generated for 'chain 'F' and resid 234 through 237' Processing helix chain 'F' and resid 270 through 276 Processing helix chain 'F' and resid 303 through 306 removed outlier: 4.011A pdb=" N ASP F 306 " --> pdb=" O ALA F 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 303 through 306' Processing helix chain 'F' and resid 311 through 315 Processing helix chain 'F' and resid 335 through 349 Processing helix chain 'F' and resid 355 through 372 Proline residue: F 362 - end of helix Processing helix chain 'F' and resid 381 through 391 Processing helix chain 'F' and resid 400 through 413 Proline residue: F 407 - end of helix Processing helix chain 'F' and resid 416 through 421 Processing helix chain 'E' and resid 16 through 28 removed outlier: 3.605A pdb=" N HIS E 28 " --> pdb=" O HIS E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 47 Processing helix chain 'E' and resid 52 through 62 removed outlier: 4.143A pdb=" N HIS E 56 " --> pdb=" O ASP E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 75 Processing helix chain 'E' and resid 96 through 100 Processing helix chain 'E' and resid 103 through 113 Processing helix chain 'E' and resid 137 through 139 No H-bonds generated for 'chain 'E' and resid 137 through 139' Processing helix chain 'E' and resid 155 through 162 removed outlier: 3.530A pdb=" N ILE E 158 " --> pdb=" O PRO E 155 " (cutoff:3.500A) Proline residue: E 159 - end of helix removed outlier: 3.508A pdb=" N LEU E 162 " --> pdb=" O PRO E 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 155 through 162' Processing helix chain 'G' and resid 21 through 27 Processing helix chain 'G' and resid 84 through 97 Processing helix chain 'G' and resid 111 through 113 No H-bonds generated for 'chain 'G' and resid 111 through 113' Processing helix chain 'G' and resid 115 through 122 Processing helix chain 'G' and resid 150 through 152 No H-bonds generated for 'chain 'G' and resid 150 through 152' Processing helix chain 'G' and resid 158 through 165 Processing helix chain 'G' and resid 196 through 202 removed outlier: 3.720A pdb=" N ILE G 202 " --> pdb=" O LEU G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 214 No H-bonds generated for 'chain 'G' and resid 211 through 214' Processing helix chain 'G' and resid 266 through 270 Processing helix chain 'G' and resid 297 through 310 Processing helix chain 'G' and resid 324 through 333 Processing helix chain 'G' and resid 345 through 360 Processing helix chain 'G' and resid 370 through 373 removed outlier: 3.504A pdb=" N SER G 373 " --> pdb=" O GLU G 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 370 through 373' Processing helix chain 'G' and resid 384 through 387 No H-bonds generated for 'chain 'G' and resid 384 through 387' Processing helix chain 'G' and resid 389 through 410 removed outlier: 4.251A pdb=" N LYS G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ALA G 403 " --> pdb=" O VAL G 399 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN G 410 " --> pdb=" O MET G 406 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 424 Processing helix chain 'G' and resid 453 through 467 Processing helix chain 'G' and resid 479 through 493 removed outlier: 4.157A pdb=" N LYS G 484 " --> pdb=" O GLU G 480 " (cutoff:3.500A) Processing helix chain 'G' and resid 504 through 506 No H-bonds generated for 'chain 'G' and resid 504 through 506' Processing helix chain 'G' and resid 509 through 524 Processing helix chain 'G' and resid 540 through 546 Processing helix chain 'G' and resid 551 through 560 Processing helix chain 'G' and resid 579 through 588 Processing helix chain 'G' and resid 601 through 603 No H-bonds generated for 'chain 'G' and resid 601 through 603' Processing helix chain 'G' and resid 650 through 663 Processing helix chain 'G' and resid 671 through 681 Processing helix chain 'G' and resid 683 through 689 removed outlier: 5.073A pdb=" N GLY G 687 " --> pdb=" O GLU G 684 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE G 688 " --> pdb=" O LEU G 685 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS G 689 " --> pdb=" O ALA G 686 " (cutoff:3.500A) Processing helix chain 'G' and resid 764 through 770 removed outlier: 3.591A pdb=" N TRP G 767 " --> pdb=" O PRO G 764 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASN G 768 " --> pdb=" O GLN G 765 " (cutoff:3.500A) Processing helix chain 'G' and resid 825 through 828 No H-bonds generated for 'chain 'G' and resid 825 through 828' Processing helix chain 'G' and resid 846 through 852 Processing helix chain 'G' and resid 895 through 897 No H-bonds generated for 'chain 'G' and resid 895 through 897' Processing helix chain 'C' and resid 24 through 33 Processing helix chain 'C' and resid 57 through 66 Processing helix chain 'C' and resid 132 through 144 removed outlier: 3.736A pdb=" N ASN C 135 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TRP C 136 " --> pdb=" O ASN C 133 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU C 144 " --> pdb=" O THR C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 193 Processing helix chain 'C' and resid 256 through 260 Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 280 through 295 removed outlier: 3.506A pdb=" N MET C 285 " --> pdb=" O VAL C 282 " (cutoff:3.500A) Proline residue: C 286 - end of helix Processing helix chain 'C' and resid 301 through 328 Processing helix chain 'C' and resid 340 through 353 Processing helix chain 'C' and resid 376 through 384 Processing helix chain 'C' and resid 387 through 400 Processing helix chain 'C' and resid 402 through 408 Processing helix chain 'C' and resid 417 through 420 No H-bonds generated for 'chain 'C' and resid 417 through 420' Processing helix chain 'C' and resid 427 through 431 Processing helix chain 'C' and resid 438 through 441 No H-bonds generated for 'chain 'C' and resid 438 through 441' Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 463 through 486 Processing helix chain 'C' and resid 505 through 510 Processing helix chain 'C' and resid 512 through 522 Processing helix chain 'C' and resid 564 through 570 Processing helix chain 'C' and resid 581 through 590 Processing helix chain 'C' and resid 595 through 599 Processing helix chain 'B' and resid 38 through 52 Processing helix chain 'B' and resid 65 through 69 Processing helix chain 'B' and resid 104 through 116 Proline residue: B 108 - end of helix Processing helix chain 'B' and resid 127 through 131 removed outlier: 3.502A pdb=" N ASN B 131 " --> pdb=" O GLY B 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 127 through 131' Processing helix chain 'B' and resid 145 through 147 No H-bonds generated for 'chain 'B' and resid 145 through 147' Processing helix chain 'B' and resid 162 through 177 Processing helix chain 'B' and resid 200 through 203 No H-bonds generated for 'chain 'B' and resid 200 through 203' Processing helix chain 'B' and resid 205 through 209 Processing helix chain 'I' and resid 65 through 69 Processing helix chain 'I' and resid 104 through 107 No H-bonds generated for 'chain 'I' and resid 104 through 107' Processing helix chain 'I' and resid 128 through 130 No H-bonds generated for 'chain 'I' and resid 128 through 130' Processing helix chain 'I' and resid 134 through 136 No H-bonds generated for 'chain 'I' and resid 134 through 136' Processing helix chain 'L' and resid 4 through 21 Proline residue: L 11 - end of helix Processing helix chain 'L' and resid 27 through 55 removed outlier: 4.201A pdb=" N VAL L 38 " --> pdb=" O GLY L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 106 Processing helix chain 'L' and resid 113 through 132 Processing helix chain 'L' and resid 136 through 154 Processing helix chain 'L' and resid 161 through 191 Processing helix chain 'L' and resid 197 through 207 removed outlier: 4.683A pdb=" N GLU L 202 " --> pdb=" O ARG L 198 " (cutoff:3.500A) Proline residue: L 205 - end of helix Processing helix chain 'L' and resid 216 through 230 Processing helix chain 'L' and resid 239 through 241 No H-bonds generated for 'chain 'L' and resid 239 through 241' Processing helix chain 'L' and resid 247 through 254 Processing helix chain 'L' and resid 259 through 268 removed outlier: 3.900A pdb=" N GLY L 262 " --> pdb=" O VAL L 259 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL L 263 " --> pdb=" O THR L 260 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG L 268 " --> pdb=" O LEU L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 270 through 274 Processing helix chain 'L' and resid 277 through 297 Processing helix chain 'L' and resid 304 through 325 Processing helix chain 'L' and resid 328 through 352 Processing helix chain 'L' and resid 373 through 387 Processing helix chain 'L' and resid 394 through 409 removed outlier: 3.811A pdb=" N ASN L 409 " --> pdb=" O GLY L 405 " (cutoff:3.500A) Processing helix chain 'L' and resid 413 through 437 Processing helix chain 'L' and resid 454 through 463 Processing helix chain 'L' and resid 466 through 470 Processing helix chain 'L' and resid 489 through 512 Processing helix chain 'L' and resid 517 through 523 Processing helix chain 'L' and resid 526 through 536 Processing helix chain 'L' and resid 538 through 549 removed outlier: 6.098A pdb=" N ASP L 542 " --> pdb=" O TRP L 539 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TRP L 543 " --> pdb=" O GLY L 540 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU L 544 " --> pdb=" O PHE L 541 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL L 548 " --> pdb=" O TYR L 545 " (cutoff:3.500A) Processing helix chain 'L' and resid 551 through 559 Processing helix chain 'L' and resid 564 through 583 Proline residue: L 572 - end of helix Processing helix chain 'L' and resid 591 through 611 Processing helix chain 'M' and resid 3 through 19 Proline residue: M 10 - end of helix Processing helix chain 'M' and resid 21 through 23 No H-bonds generated for 'chain 'M' and resid 21 through 23' Processing helix chain 'M' and resid 28 through 49 Processing helix chain 'M' and resid 85 through 104 Processing helix chain 'M' and resid 114 through 132 Processing helix chain 'M' and resid 136 through 156 removed outlier: 4.171A pdb=" N LEU M 147 " --> pdb=" O TRP M 143 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL M 148 " --> pdb=" O GLU M 144 " (cutoff:3.500A) Proline residue: M 149 - end of helix Processing helix chain 'M' and resid 164 through 199 Processing helix chain 'M' and resid 219 through 234 removed outlier: 3.838A pdb=" N LYS M 234 " --> pdb=" O ALA M 230 " (cutoff:3.500A) Processing helix chain 'M' and resid 242 through 249 removed outlier: 4.227A pdb=" N ASP M 246 " --> pdb=" O GLY M 242 " (cutoff:3.500A) Processing helix chain 'M' and resid 256 through 261 Processing helix chain 'M' and resid 266 through 274 Processing helix chain 'M' and resid 280 through 307 Proline residue: M 288 - end of helix Processing helix chain 'M' and resid 311 through 330 Processing helix chain 'M' and resid 335 through 366 Processing helix chain 'M' and resid 384 through 396 Processing helix chain 'M' and resid 402 through 415 Processing helix chain 'M' and resid 419 through 443 Processing helix chain 'M' and resid 462 through 480 Processing helix chain 'M' and resid 483 through 502 removed outlier: 4.893A pdb=" N SER M 491 " --> pdb=" O ASP M 487 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ALA M 492 " --> pdb=" O THR M 488 " (cutoff:3.500A) Processing helix chain 'N' and resid 12 through 30 Processing helix chain 'N' and resid 34 through 57 Processing helix chain 'N' and resid 71 through 97 Proline residue: N 93 - end of helix removed outlier: 4.131A pdb=" N GLY N 97 " --> pdb=" O PRO N 93 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 120 Processing helix chain 'N' and resid 125 through 146 Proline residue: N 138 - end of helix removed outlier: 4.969A pdb=" N ALA N 146 " --> pdb=" O LEU N 142 " (cutoff:3.500A) Processing helix chain 'N' and resid 150 through 180 Processing helix chain 'N' and resid 201 through 217 removed outlier: 4.133A pdb=" N LYS N 217 " --> pdb=" O GLY N 213 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 233 Processing helix chain 'N' and resid 236 through 260 removed outlier: 4.661A pdb=" N SER N 246 " --> pdb=" O LEU N 242 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LYS N 247 " --> pdb=" O ALA N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 262 through 265 removed outlier: 3.608A pdb=" N ASP N 265 " --> pdb=" O PRO N 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 262 through 265' Processing helix chain 'N' and resid 269 through 287 Processing helix chain 'N' and resid 294 through 319 removed outlier: 3.880A pdb=" N ALA N 315 " --> pdb=" O VAL N 311 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU N 316 " --> pdb=" O ALA N 312 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N GLN N 317 " --> pdb=" O LEU N 313 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N THR N 318 " --> pdb=" O ILE N 314 " (cutoff:3.500A) Processing helix chain 'N' and resid 322 through 347 Processing helix chain 'N' and resid 365 through 367 No H-bonds generated for 'chain 'N' and resid 365 through 367' Processing helix chain 'N' and resid 370 through 383 Processing helix chain 'N' and resid 390 through 404 Processing helix chain 'N' and resid 408 through 433 removed outlier: 4.110A pdb=" N TYR N 423 " --> pdb=" O ALA N 419 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N TYR N 424 " --> pdb=" O ILE N 420 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N TYR N 433 " --> pdb=" O ALA N 429 " (cutoff:3.500A) Processing helix chain 'N' and resid 448 through 469 Processing helix chain 'N' and resid 472 through 479 Processing helix chain 'H' and resid 6 through 41 removed outlier: 3.822A pdb=" N LEU H 40 " --> pdb=" O GLU H 36 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLY H 41 " --> pdb=" O ARG H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 68 Processing helix chain 'H' and resid 80 through 98 Proline residue: H 87 - end of helix removed outlier: 4.685A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE H 98 " --> pdb=" O LEU H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 136 removed outlier: 4.233A pdb=" N VAL H 127 " --> pdb=" O ALA H 123 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N TYR H 128 " --> pdb=" O GLY H 124 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ALA H 129 " --> pdb=" O LEU H 125 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL H 130 " --> pdb=" O ALA H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 157 Processing helix chain 'H' and resid 160 through 171 removed outlier: 4.276A pdb=" N VAL H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 182 Processing helix chain 'H' and resid 188 through 191 No H-bonds generated for 'chain 'H' and resid 188 through 191' Processing helix chain 'H' and resid 193 through 206 Processing helix chain 'H' and resid 215 through 218 removed outlier: 4.022A pdb=" N GLU H 218 " --> pdb=" O PRO H 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 215 through 218' Processing helix chain 'H' and resid 232 through 256 Processing helix chain 'H' and resid 267 through 288 Processing helix chain 'H' and resid 294 through 303 Processing helix chain 'H' and resid 306 through 322 Processing helix chain 'A' and resid 9 through 36 Processing helix chain 'A' and resid 67 through 90 removed outlier: 3.970A pdb=" N LEU A 85 " --> pdb=" O GLU A 81 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR A 90 " --> pdb=" O PHE A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 120 Processing helix chain 'K' and resid 4 through 23 Processing helix chain 'K' and resid 28 through 53 Processing helix chain 'K' and resid 57 through 87 Processing helix chain 'J' and resid 2 through 20 Processing helix chain 'J' and resid 25 through 45 Processing helix chain 'J' and resid 49 through 57 Processing helix chain 'J' and resid 63 through 73 Processing helix chain 'J' and resid 86 through 88 No H-bonds generated for 'chain 'J' and resid 86 through 88' Processing helix chain 'J' and resid 90 through 111 removed outlier: 5.198A pdb=" N GLY J 95 " --> pdb=" O GLN J 91 " (cutoff:3.500A) Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 126 through 133 Processing helix chain 'J' and resid 138 through 158 Processing helix chain 'J' and resid 172 through 174 No H-bonds generated for 'chain 'J' and resid 172 through 174' Processing sheet with id= A, first strand: chain 'F' and resid 214 through 218 removed outlier: 6.786A pdb=" N TYR F 86 " --> pdb=" O CYS F 215 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N ASN F 217 " --> pdb=" O TYR F 86 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU F 88 " --> pdb=" O ASN F 217 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ARG F 127 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N CYS F 89 " --> pdb=" O ARG F 127 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N TYR F 129 " --> pdb=" O CYS F 89 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLU F 168 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ILE F 130 " --> pdb=" O GLU F 168 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N PHE F 170 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEU F 132 " --> pdb=" O PHE F 170 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N HIS F 172 " --> pdb=" O LEU F 132 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'F' and resid 247 through 250 Processing sheet with id= C, first strand: chain 'F' and resid 251 through 253 Processing sheet with id= D, first strand: chain 'E' and resid 126 through 131 removed outlier: 6.869A pdb=" N HIS E 87 " --> pdb=" O THR E 127 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N LEU E 129 " --> pdb=" O HIS E 87 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ILE E 89 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR E 131 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N TYR E 91 " --> pdb=" O THR E 131 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'G' and resid 11 through 14 removed outlier: 6.703A pdb=" N THR G 77 " --> pdb=" O HIS G 7 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N PHE G 78 " --> pdb=" O TYR G 55 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'G' and resid 146 through 148 Processing sheet with id= G, first strand: chain 'G' and resid 173 through 175 Processing sheet with id= H, first strand: chain 'G' and resid 224 through 229 removed outlier: 6.451A pdb=" N ARG G 244 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N LEU G 248 " --> pdb=" O ARG G 244 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'G' and resid 284 through 288 Processing sheet with id= J, first strand: chain 'G' and resid 339 through 341 removed outlier: 8.045A pdb=" N TYR G 340 " --> pdb=" O VAL G 314 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N GLY G 316 " --> pdb=" O TYR G 340 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ALA G 565 " --> pdb=" O ILE G 315 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ILE G 317 " --> pdb=" O ALA G 565 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL G 567 " --> pdb=" O ILE G 317 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU G 591 " --> pdb=" O VAL G 566 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N VAL G 568 " --> pdb=" O LEU G 591 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N MET G 593 " --> pdb=" O VAL G 568 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU G 608 " --> pdb=" O VAL G 594 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ASP G 596 " --> pdb=" O LEU G 608 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N LEU G 610 " --> pdb=" O ASP G 596 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'G' and resid 530 through 534 removed outlier: 6.152A pdb=" N ALA G 376 " --> pdb=" O LEU G 499 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ILE G 501 " --> pdb=" O ALA G 376 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU G 378 " --> pdb=" O ILE G 501 " (cutoff:3.500A) removed outlier: 8.704A pdb=" N GLY G 503 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N VAL G 379 " --> pdb=" O PRO G 430 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N PHE G 432 " --> pdb=" O VAL G 379 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N TRP G 447 " --> pdb=" O VAL G 433 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N ASN G 435 " --> pdb=" O TRP G 447 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N TYR G 449 " --> pdb=" O ASN G 435 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 620 through 623 Processing sheet with id= M, first strand: chain 'G' and resid 813 through 816 Processing sheet with id= N, first strand: chain 'G' and resid 841 through 844 removed outlier: 8.283A pdb=" N ILE G 842 " --> pdb=" O THR G 870 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N LEU G 844 " --> pdb=" O PRO G 872 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLU G 874 " --> pdb=" O LEU G 844 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 38 through 41 removed outlier: 4.271A pdb=" N VAL C 49 " --> pdb=" O GLN C 41 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ALA C 116 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE C 103 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N LEU C 74 " --> pdb=" O ILE C 103 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 123 through 125 removed outlier: 6.479A pdb=" N THR C 148 " --> pdb=" O VAL C 124 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'C' and resid 215 through 220 removed outlier: 3.665A pdb=" N ARG C 232 " --> pdb=" O ASP C 248 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP C 244 " --> pdb=" O GLN C 236 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ASP C 238 " --> pdb=" O ILE C 242 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ILE C 242 " --> pdb=" O ASP C 238 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 532 through 538 Processing sheet with id= S, first strand: chain 'B' and resid 23 through 25 removed outlier: 3.919A pdb=" N GLU B 23 " --> pdb=" O LEU B 5 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 95 through 98 removed outlier: 6.343A pdb=" N TRP B 122 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N VAL B 98 " --> pdb=" O TRP B 122 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE B 124 " --> pdb=" O VAL B 98 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'I' and resid 48 through 50 Processing sheet with id= V, first strand: chain 'I' and resid 75 through 81 removed outlier: 4.003A pdb=" N PHE I 91 " --> pdb=" O GLN I 78 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ALA I 80 " --> pdb=" O PRO I 89 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'L' and resid 60 through 63 Processing sheet with id= X, first strand: chain 'L' and resid 66 through 70 removed outlier: 6.895A pdb=" N ILE L 75 " --> pdb=" O TRP L 67 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER L 69 " --> pdb=" O PHE L 73 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N PHE L 73 " --> pdb=" O SER L 69 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'M' and resid 65 through 72 removed outlier: 6.830A pdb=" N ILE M 77 " --> pdb=" O TRP M 71 " (cutoff:3.500A) 1755 hydrogen bonds defined for protein. 5088 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: 12.93 Time building geometry restraints manager: 15.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.42: 15726 1.42 - 1.64: 21389 1.64 - 1.86: 406 1.86 - 2.09: 0 2.09 - 2.31: 92 Bond restraints: 37613 Sorted by residual: bond pdb=" O13 3PE L 802 " pdb=" P 3PE L 802 " ideal model delta sigma weight residual 1.654 1.596 0.058 2.00e-02 2.50e+03 8.29e+00 bond pdb=" O13 3PE L 801 " pdb=" P 3PE L 801 " ideal model delta sigma weight residual 1.654 1.596 0.058 2.00e-02 2.50e+03 8.27e+00 bond pdb=" O3 NAI F 503 " pdb=" PN NAI F 503 " ideal model delta sigma weight residual 1.644 1.592 0.052 2.00e-02 2.50e+03 6.69e+00 bond pdb=" O11 3PE L 801 " pdb=" P 3PE L 801 " ideal model delta sigma weight residual 1.644 1.596 0.048 2.00e-02 2.50e+03 5.78e+00 bond pdb=" O11 3PE L 802 " pdb=" P 3PE L 802 " ideal model delta sigma weight residual 1.644 1.597 0.047 2.00e-02 2.50e+03 5.59e+00 ... (remaining 37608 not shown) Histogram of bond angle deviations from ideal: 70.12 - 83.25: 88 83.25 - 96.38: 1 96.38 - 109.50: 3829 109.50 - 122.63: 43675 122.63 - 135.76: 3531 Bond angle restraints: 51124 Sorted by residual: angle pdb=" CA PRO N 5 " pdb=" N PRO N 5 " pdb=" CD PRO N 5 " ideal model delta sigma weight residual 112.00 104.22 7.78 1.40e+00 5.10e-01 3.09e+01 angle pdb=" CB MET M 136 " pdb=" CG MET M 136 " pdb=" SD MET M 136 " ideal model delta sigma weight residual 112.70 128.68 -15.98 3.00e+00 1.11e-01 2.84e+01 angle pdb=" C PRO N 387 " pdb=" N MET N 388 " pdb=" CA MET N 388 " ideal model delta sigma weight residual 121.54 131.49 -9.95 1.91e+00 2.74e-01 2.71e+01 angle pdb=" C PRO C 153 " pdb=" N ASN C 154 " pdb=" CA ASN C 154 " ideal model delta sigma weight residual 122.46 129.13 -6.67 1.41e+00 5.03e-01 2.24e+01 angle pdb=" C SER A 6 " pdb=" N THR A 7 " pdb=" CA THR A 7 " ideal model delta sigma weight residual 121.54 130.28 -8.74 1.91e+00 2.74e-01 2.09e+01 ... (remaining 51119 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.69: 21396 33.69 - 67.38: 606 67.38 - 101.06: 39 101.06 - 134.75: 1 134.75 - 168.44: 1 Dihedral angle restraints: 22043 sinusoidal: 8677 harmonic: 13366 Sorted by residual: dihedral pdb=" CA CYS B 158 " pdb=" C CYS B 158 " pdb=" N PRO B 159 " pdb=" CA PRO B 159 " ideal model delta harmonic sigma weight residual 180.00 -123.07 -56.93 0 5.00e+00 4.00e-02 1.30e+02 dihedral pdb=" C10 FMN F 502 " pdb=" C1' FMN F 502 " pdb=" N10 FMN F 502 " pdb=" C2' FMN F 502 " ideal model delta sinusoidal sigma weight residual 257.59 89.15 168.44 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" CA GLY I 85 " pdb=" C GLY I 85 " pdb=" N ARG I 86 " pdb=" CA ARG I 86 " ideal model delta harmonic sigma weight residual 180.00 -155.01 -24.99 0 5.00e+00 4.00e-02 2.50e+01 ... (remaining 22040 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.235: 5725 4.235 - 8.470: 0 8.470 - 12.705: 0 12.705 - 16.941: 0 16.941 - 21.176: 28 Chirality restraints: 5753 Sorted by residual: chirality pdb="FE4 SF4 I 202 " pdb=" S1 SF4 I 202 " pdb=" S2 SF4 I 202 " pdb=" S3 SF4 I 202 " both_signs ideal model delta sigma weight residual False 10.55 -10.62 21.18 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE3 SF4 G1001 " pdb=" S1 SF4 G1001 " pdb=" S2 SF4 G1001 " pdb=" S4 SF4 G1001 " both_signs ideal model delta sigma weight residual False -10.55 10.62 -21.17 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4 G1002 " pdb=" S1 SF4 G1002 " pdb=" S2 SF4 G1002 " pdb=" S3 SF4 G1002 " both_signs ideal model delta sigma weight residual False 10.55 -10.61 21.17 2.00e-01 2.50e+01 1.12e+04 ... (remaining 5750 not shown) Planarity restraints: 6421 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 UQ8 H 401 " 0.000 2.00e-02 2.50e+03 5.59e-02 9.39e+01 pdb=" C1M UQ8 H 401 " 0.040 2.00e-02 2.50e+03 pdb=" C2 UQ8 H 401 " -0.038 2.00e-02 2.50e+03 pdb=" C3 UQ8 H 401 " 0.004 2.00e-02 2.50e+03 pdb=" C4 UQ8 H 401 " -0.017 2.00e-02 2.50e+03 pdb=" C5 UQ8 H 401 " -0.013 2.00e-02 2.50e+03 pdb=" C6 UQ8 H 401 " 0.002 2.00e-02 2.50e+03 pdb=" C7 UQ8 H 401 " 0.045 2.00e-02 2.50e+03 pdb=" O2 UQ8 H 401 " -0.103 2.00e-02 2.50e+03 pdb=" O3 UQ8 H 401 " 0.139 2.00e-02 2.50e+03 pdb=" O4 UQ8 H 401 " -0.041 2.00e-02 2.50e+03 pdb=" O5 UQ8 H 401 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN L 62 " -0.068 5.00e-02 4.00e+02 1.05e-01 1.75e+01 pdb=" N PRO L 63 " 0.181 5.00e-02 4.00e+02 pdb=" CA PRO L 63 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO L 63 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 73 " 0.022 2.00e-02 2.50e+03 2.35e-02 1.39e+01 pdb=" CG TRP H 73 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP H 73 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP H 73 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP H 73 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP H 73 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP H 73 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 73 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 73 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP H 73 " -0.007 2.00e-02 2.50e+03 ... (remaining 6418 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 963 2.70 - 3.25: 35972 3.25 - 3.80: 63723 3.80 - 4.35: 82211 4.35 - 4.90: 136206 Nonbonded interactions: 319075 Sorted by model distance: nonbonded pdb=" OG SER E 94 " pdb=" O CYS E 132 " model vdw 2.156 2.440 nonbonded pdb=" O TYR N 159 " pdb=" OG SER N 163 " model vdw 2.200 2.440 nonbonded pdb=" OH TYR A 69 " pdb=" O SER K 74 " model vdw 2.212 2.440 nonbonded pdb=" OG SER G 823 " pdb=" O MET G 888 " model vdw 2.235 2.440 nonbonded pdb=" OH TYR L 318 " pdb=" O GLY L 418 " model vdw 2.257 2.440 ... (remaining 319070 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: 0.390 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: 0.040 Extract box with map and model: 4.030 Check model and map are aligned: 0.520 Set scattering table: 0.330 Process input model: 102.630 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 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 : 0.004 0.088 37613 Z= 0.272 Angle : 0.822 15.978 51124 Z= 0.424 Chirality : 1.475 21.176 5753 Planarity : 0.007 0.105 6421 Dihedral : 15.221 168.439 13489 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.29 % Allowed : 15.52 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.11), residues: 4629 helix: -0.09 (0.09), residues: 2578 sheet: -0.91 (0.29), residues: 315 loop : -1.64 (0.14), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.001 TRP H 73 HIS 0.012 0.001 HIS G 178 PHE 0.052 0.002 PHE H 31 TYR 0.037 0.002 TYR M 435 ARG 0.015 0.001 ARG G 804 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 3830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 599 time to evaluate : 4.480 Fit side-chains revert: symmetry clash REVERT: F 420 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7901 (mm-30) REVERT: G 605 ASN cc_start: 0.8878 (m-40) cc_final: 0.8664 (p0) REVERT: C 62 ASP cc_start: 0.8940 (t0) cc_final: 0.8451 (t70) REVERT: C 215 PHE cc_start: 0.8148 (m-10) cc_final: 0.7784 (p90) REVERT: C 599 ASP cc_start: 0.9240 (m-30) cc_final: 0.9015 (m-30) REVERT: B 92 GLN cc_start: 0.8536 (mp10) cc_final: 0.8242 (mp10) REVERT: B 166 MET cc_start: 0.8716 (tpp) cc_final: 0.8444 (tpp) REVERT: I 176 LYS cc_start: 0.8471 (mttp) cc_final: 0.8106 (mttp) REVERT: L 415 MET cc_start: 0.8151 (ttp) cc_final: 0.7805 (ttp) REVERT: M 5 TRP cc_start: 0.7688 (m100) cc_final: 0.6898 (m-10) REVERT: M 371 MET cc_start: 0.8229 (mtm) cc_final: 0.8022 (mtm) REVERT: M 476 VAL cc_start: 0.8664 (t) cc_final: 0.8266 (m) REVERT: H 10 GLU cc_start: 0.8558 (tp30) cc_final: 0.8316 (tp30) REVERT: H 95 LEU cc_start: 0.8005 (tp) cc_final: 0.7789 (tp) REVERT: H 109 VAL cc_start: 0.8241 (m) cc_final: 0.7722 (p) REVERT: K 32 LEU cc_start: 0.8727 (mt) cc_final: 0.8457 (mt) REVERT: J 24 ASN cc_start: 0.8927 (p0) cc_final: 0.8721 (p0) outliers start: 11 outliers final: 3 residues processed: 602 average time/residue: 0.5034 time to fit residues: 486.9574 Evaluate side-chains 548 residues out of total 3830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 545 time to evaluate : 4.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain L residue 400 ASP Chi-restraints excluded: chain N residue 82 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 390 optimal weight: 2.9990 chunk 350 optimal weight: 0.9990 chunk 194 optimal weight: 4.9990 chunk 119 optimal weight: 9.9990 chunk 236 optimal weight: 0.9990 chunk 187 optimal weight: 10.0000 chunk 362 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 220 optimal weight: 1.9990 chunk 270 optimal weight: 8.9990 chunk 420 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 142 ASN G 180 ASN ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 2 ASN L 78 ASN L 135 ASN ** M 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 138 ASN H 226 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.0864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.252 37613 Z= 0.760 Angle : 2.197 51.134 51124 Z= 1.446 Chirality : 0.441 6.460 5753 Planarity : 0.005 0.103 6421 Dihedral : 6.869 168.615 5214 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.54 % Allowed : 15.31 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: -0.31 (0.12), residues: 4629 helix: 0.75 (0.10), residues: 2573 sheet: -0.84 (0.29), residues: 320 loop : -1.50 (0.14), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 143 HIS 0.007 0.001 HIS L 100 PHE 0.030 0.001 PHE L 341 TYR 0.024 0.001 TYR M 435 ARG 0.006 0.000 ARG K 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 3830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 564 time to evaluate : 3.991 Fit side-chains REVERT: F 287 PHE cc_start: 0.8898 (t80) cc_final: 0.8666 (t80) REVERT: G 98 MET cc_start: 0.8415 (ttm) cc_final: 0.8153 (mmm) REVERT: G 150 MET cc_start: 0.9144 (tpt) cc_final: 0.8823 (tpp) REVERT: G 572 ASP cc_start: 0.9028 (t0) cc_final: 0.8823 (t0) REVERT: C 62 ASP cc_start: 0.8943 (t0) cc_final: 0.8566 (t70) REVERT: C 215 PHE cc_start: 0.8245 (m-10) cc_final: 0.7848 (p90) REVERT: C 585 ILE cc_start: 0.8691 (tt) cc_final: 0.8228 (mt) REVERT: B 2 ASP cc_start: 0.8667 (p0) cc_final: 0.8455 (p0) REVERT: L 221 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8657 (mmt) REVERT: L 415 MET cc_start: 0.7939 (ttp) cc_final: 0.7716 (ttp) REVERT: M 200 THR cc_start: 0.8639 (m) cc_final: 0.8328 (p) REVERT: M 235 MET cc_start: 0.8827 (ttp) cc_final: 0.8572 (ttm) REVERT: M 371 MET cc_start: 0.8336 (mtm) cc_final: 0.8134 (mtm) REVERT: M 476 VAL cc_start: 0.8704 (t) cc_final: 0.8306 (m) REVERT: N 76 TYR cc_start: 0.8686 (m-10) cc_final: 0.8342 (m-10) REVERT: N 81 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8675 (mm) REVERT: H 10 GLU cc_start: 0.8623 (tp30) cc_final: 0.8403 (tp30) REVERT: H 109 VAL cc_start: 0.8260 (m) cc_final: 0.7795 (p) REVERT: H 181 ASN cc_start: 0.8357 (m-40) cc_final: 0.7977 (m-40) REVERT: K 32 LEU cc_start: 0.8748 (mt) cc_final: 0.8480 (mt) REVERT: J 24 ASN cc_start: 0.8852 (p0) cc_final: 0.8631 (p0) REVERT: J 80 GLU cc_start: 0.7103 (mp0) cc_final: 0.6820 (mp0) outliers start: 59 outliers final: 25 residues processed: 600 average time/residue: 0.5224 time to fit residues: 516.9503 Evaluate side-chains 565 residues out of total 3830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 538 time to evaluate : 4.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain G residue 57 ASN Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 799 THR Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 214 MET Chi-restraints excluded: chain L residue 221 MET Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 329 ASP Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain A residue 10 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 233 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 349 optimal weight: 9.9990 chunk 286 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 421 optimal weight: 6.9990 chunk 455 optimal weight: 8.9990 chunk 375 optimal weight: 10.0000 chunk 417 optimal weight: 8.9990 chunk 143 optimal weight: 7.9990 chunk 337 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 110 HIS ** F 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 400 HIS ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 HIS G 180 ASN ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 397 GLN G 465 HIS G 513 GLN ** G 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 607 HIS G 765 GLN ** G 828 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 GLN C 252 HIS ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 GLN ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN L 270 HIS ** L 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 159 HIS N 149 GLN H 226 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.253 37613 Z= 0.909 Angle : 2.253 50.847 51124 Z= 1.468 Chirality : 0.445 6.465 5753 Planarity : 0.006 0.102 6421 Dihedral : 7.085 167.731 5210 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.66 % Allowed : 14.81 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.12), residues: 4629 helix: 0.65 (0.10), residues: 2588 sheet: -0.73 (0.28), residues: 313 loop : -1.32 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP N 408 HIS 0.010 0.002 HIS G 178 PHE 0.046 0.003 PHE I 101 TYR 0.027 0.003 TYR G 340 ARG 0.011 0.001 ARG G 804 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 3830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 522 time to evaluate : 4.224 Fit side-chains REVERT: F 19 ASP cc_start: 0.8787 (p0) cc_final: 0.8500 (m-30) REVERT: G 278 LYS cc_start: 0.9305 (mmmt) cc_final: 0.9085 (mttp) REVERT: G 485 ILE cc_start: 0.9007 (mm) cc_final: 0.8782 (mt) REVERT: G 644 LYS cc_start: 0.8979 (mtmp) cc_final: 0.8693 (mtmm) REVERT: C 62 ASP cc_start: 0.8916 (t0) cc_final: 0.8531 (t0) REVERT: C 215 PHE cc_start: 0.8237 (m-10) cc_final: 0.7852 (p90) REVERT: C 275 ILE cc_start: 0.8382 (pt) cc_final: 0.8057 (mm) REVERT: C 344 GLN cc_start: 0.8538 (mm-40) cc_final: 0.8255 (mm-40) REVERT: C 528 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.8259 (mmt) REVERT: C 585 ILE cc_start: 0.8755 (tt) cc_final: 0.8527 (mt) REVERT: I 171 LYS cc_start: 0.9292 (OUTLIER) cc_final: 0.9073 (mtpp) REVERT: I 174 ASP cc_start: 0.8731 (t0) cc_final: 0.8475 (t0) REVERT: L 88 MET cc_start: 0.8813 (mmm) cc_final: 0.8420 (mmm) REVERT: L 407 MET cc_start: 0.7932 (tpt) cc_final: 0.7546 (tpt) REVERT: M 22 ARG cc_start: 0.6078 (OUTLIER) cc_final: 0.4429 (ptp-170) REVERT: M 229 ILE cc_start: 0.8544 (pt) cc_final: 0.8136 (mt) REVERT: N 81 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8642 (mm) REVERT: N 139 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8576 (mm) REVERT: N 267 GLU cc_start: 0.8326 (mm-30) cc_final: 0.7919 (pp20) REVERT: H 10 GLU cc_start: 0.8665 (tp30) cc_final: 0.8454 (tp30) REVERT: H 63 ASP cc_start: 0.8609 (t0) cc_final: 0.8374 (t0) REVERT: H 138 ASN cc_start: 0.8008 (OUTLIER) cc_final: 0.7657 (p0) REVERT: H 229 TYR cc_start: 0.9156 (m-80) cc_final: 0.8924 (m-80) REVERT: H 278 PHE cc_start: 0.8691 (m-80) cc_final: 0.8463 (m-80) REVERT: J 59 TYR cc_start: 0.9267 (OUTLIER) cc_final: 0.8765 (t80) REVERT: J 80 GLU cc_start: 0.7273 (mp0) cc_final: 0.6982 (mp0) outliers start: 140 outliers final: 75 residues processed: 619 average time/residue: 0.4933 time to fit residues: 497.7731 Evaluate side-chains 574 residues out of total 3830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 492 time to evaluate : 4.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain G residue 57 ASN Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 276 ASN Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 694 ASP Chi-restraints excluded: chain G residue 696 THR Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain G residue 860 VAL Chi-restraints excluded: chain C residue 100 TYR Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 281 CYS Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 171 LYS Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 214 MET Chi-restraints excluded: chain L residue 260 THR Chi-restraints excluded: chain L residue 329 ASP Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 435 ILE Chi-restraints excluded: chain L residue 487 HIS Chi-restraints excluded: chain L residue 542 ASP Chi-restraints excluded: chain M residue 22 ARG Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 187 ILE Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 311 ILE Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 99 ASN Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain N residue 388 MET Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 138 ASN Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 299 SER Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 93 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 416 optimal weight: 3.9990 chunk 316 optimal weight: 1.9990 chunk 218 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 201 optimal weight: 3.9990 chunk 282 optimal weight: 30.0000 chunk 422 optimal weight: 0.6980 chunk 447 optimal weight: 8.9990 chunk 220 optimal weight: 1.9990 chunk 400 optimal weight: 9.9990 chunk 120 optimal weight: 5.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 276 ASN ** G 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 828 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 214 GLN H 226 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.248 37613 Z= 0.771 Angle : 2.204 50.634 51124 Z= 1.448 Chirality : 0.442 6.391 5753 Planarity : 0.004 0.101 6421 Dihedral : 6.629 167.977 5210 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.96 % Allowed : 16.09 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: 0.07 (0.12), residues: 4629 helix: 1.01 (0.10), residues: 2581 sheet: -0.81 (0.28), residues: 323 loop : -1.22 (0.15), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 143 HIS 0.008 0.001 HIS M 80 PHE 0.030 0.001 PHE L 341 TYR 0.023 0.001 TYR M 435 ARG 0.005 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 3830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 524 time to evaluate : 4.211 Fit side-chains revert: symmetry clash REVERT: F 277 TYR cc_start: 0.9336 (m-80) cc_final: 0.8380 (m-80) REVERT: F 434 ASN cc_start: 0.8910 (t0) cc_final: 0.8616 (t0) REVERT: G 98 MET cc_start: 0.8871 (mmm) cc_final: 0.8265 (mmt) REVERT: G 100 ASN cc_start: 0.9101 (OUTLIER) cc_final: 0.8866 (p0) REVERT: G 278 LYS cc_start: 0.9294 (mmmt) cc_final: 0.9069 (mttp) REVERT: G 288 ARG cc_start: 0.9095 (mpp80) cc_final: 0.8840 (ptp90) REVERT: G 485 ILE cc_start: 0.8973 (mm) cc_final: 0.8725 (mt) REVERT: G 644 LYS cc_start: 0.8910 (mtmp) cc_final: 0.8664 (mtmm) REVERT: C 62 ASP cc_start: 0.8853 (t0) cc_final: 0.8448 (t0) REVERT: C 215 PHE cc_start: 0.8205 (m-10) cc_final: 0.7847 (p90) REVERT: C 275 ILE cc_start: 0.8381 (pt) cc_final: 0.8160 (mm) REVERT: C 344 GLN cc_start: 0.8482 (mm-40) cc_final: 0.8205 (mm-40) REVERT: C 585 ILE cc_start: 0.8740 (tt) cc_final: 0.8508 (mt) REVERT: B 2 ASP cc_start: 0.8851 (p0) cc_final: 0.8628 (p0) REVERT: B 126 MET cc_start: 0.9310 (OUTLIER) cc_final: 0.9108 (mmm) REVERT: B 189 ASP cc_start: 0.8598 (t0) cc_final: 0.8332 (t0) REVERT: I 171 LYS cc_start: 0.9272 (mtpt) cc_final: 0.9017 (mmtt) REVERT: L 88 MET cc_start: 0.8753 (mmm) cc_final: 0.8338 (mmm) REVERT: L 407 MET cc_start: 0.7705 (tpt) cc_final: 0.7406 (tpt) REVERT: L 415 MET cc_start: 0.8131 (ttp) cc_final: 0.7827 (ttp) REVERT: M 235 MET cc_start: 0.8798 (ttp) cc_final: 0.8565 (ttm) REVERT: M 303 TRP cc_start: 0.8514 (OUTLIER) cc_final: 0.7919 (m-10) REVERT: M 370 ASP cc_start: 0.8871 (t0) cc_final: 0.8463 (t0) REVERT: N 81 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8673 (mm) REVERT: N 132 ILE cc_start: 0.8556 (pt) cc_final: 0.8353 (mt) REVERT: N 267 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7905 (pp20) REVERT: H 36 GLU cc_start: 0.8718 (tt0) cc_final: 0.8447 (tt0) REVERT: H 63 ASP cc_start: 0.8580 (t0) cc_final: 0.8320 (t0) REVERT: H 257 PHE cc_start: 0.8920 (m-10) cc_final: 0.8712 (m-80) REVERT: A 3 MET cc_start: 0.4699 (OUTLIER) cc_final: 0.4100 (mmm) REVERT: J 59 TYR cc_start: 0.9272 (OUTLIER) cc_final: 0.8637 (t80) outliers start: 113 outliers final: 66 residues processed: 599 average time/residue: 0.4963 time to fit residues: 483.6766 Evaluate side-chains 573 residues out of total 3830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 501 time to evaluate : 4.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 214 THR Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain G residue 100 ASN Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain G residue 276 ASN Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 631 ARG Chi-restraints excluded: chain G residue 694 ASP Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain C residue 100 TYR Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 281 CYS Chi-restraints excluded: chain C residue 358 MET Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 214 MET Chi-restraints excluded: chain L residue 329 ASP Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 400 ASP Chi-restraints excluded: chain L residue 435 ILE Chi-restraints excluded: chain L residue 542 ASP Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 99 ASN Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 171 LEU Chi-restraints excluded: chain N residue 229 ASP Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain N residue 388 MET Chi-restraints excluded: chain N residue 410 LEU Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 93 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 372 optimal weight: 8.9990 chunk 254 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 333 optimal weight: 9.9990 chunk 184 optimal weight: 1.9990 chunk 381 optimal weight: 2.9990 chunk 309 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 228 optimal weight: 4.9990 chunk 401 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 22 GLN ** F 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 GLN ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 605 ASN G 724 HIS ** G 828 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 GLN C 319 HIS ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 214 GLN H 226 HIS ** J 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.248 37613 Z= 0.785 Angle : 2.207 50.648 51124 Z= 1.449 Chirality : 0.442 6.394 5753 Planarity : 0.004 0.096 6421 Dihedral : 6.407 167.730 5210 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.45 % Allowed : 16.25 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: 0.20 (0.12), residues: 4629 helix: 1.10 (0.10), residues: 2590 sheet: -0.77 (0.28), residues: 335 loop : -1.15 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 143 HIS 0.009 0.001 HIS M 80 PHE 0.042 0.002 PHE N 72 TYR 0.021 0.001 TYR M 435 ARG 0.005 0.000 ARG G 269 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 3830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 509 time to evaluate : 4.238 Fit side-chains revert: symmetry clash REVERT: F 277 TYR cc_start: 0.9355 (m-80) cc_final: 0.8410 (m-80) REVERT: F 434 ASN cc_start: 0.8901 (t0) cc_final: 0.8633 (t0) REVERT: E 82 GLN cc_start: 0.9320 (mm-40) cc_final: 0.9110 (mt0) REVERT: G 485 ILE cc_start: 0.8970 (mm) cc_final: 0.8715 (mt) REVERT: G 605 ASN cc_start: 0.8987 (p0) cc_final: 0.8730 (p0) REVERT: G 644 LYS cc_start: 0.8940 (mtmp) cc_final: 0.8711 (mtmm) REVERT: C 62 ASP cc_start: 0.8860 (t0) cc_final: 0.8455 (t0) REVERT: C 215 PHE cc_start: 0.8199 (m-10) cc_final: 0.7855 (p90) REVERT: C 344 GLN cc_start: 0.8512 (mm-40) cc_final: 0.8210 (mm-40) REVERT: C 528 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8105 (mmt) REVERT: C 585 ILE cc_start: 0.8734 (tt) cc_final: 0.8526 (mt) REVERT: B 2 ASP cc_start: 0.8859 (p0) cc_final: 0.8578 (p0) REVERT: B 189 ASP cc_start: 0.8638 (t0) cc_final: 0.8383 (t0) REVERT: I 171 LYS cc_start: 0.9286 (OUTLIER) cc_final: 0.9032 (mmtt) REVERT: L 407 MET cc_start: 0.7834 (tpt) cc_final: 0.7453 (tpt) REVERT: L 415 MET cc_start: 0.8111 (ttp) cc_final: 0.7679 (ttp) REVERT: M 22 ARG cc_start: 0.6156 (OUTLIER) cc_final: 0.4519 (ptp-170) REVERT: M 235 MET cc_start: 0.8792 (ttp) cc_final: 0.8534 (ttm) REVERT: M 303 TRP cc_start: 0.8527 (OUTLIER) cc_final: 0.7867 (m-10) REVERT: M 370 ASP cc_start: 0.8878 (t0) cc_final: 0.8450 (t0) REVERT: N 81 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8697 (mm) REVERT: N 139 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8607 (mm) REVERT: N 267 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7943 (pp20) REVERT: H 63 ASP cc_start: 0.8578 (t0) cc_final: 0.8263 (t0) REVERT: H 138 ASN cc_start: 0.8063 (OUTLIER) cc_final: 0.7759 (p0) REVERT: H 220 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7517 (mm-30) REVERT: A 3 MET cc_start: 0.4732 (OUTLIER) cc_final: 0.4079 (mmm) REVERT: J 59 TYR cc_start: 0.9231 (OUTLIER) cc_final: 0.8600 (t80) outliers start: 132 outliers final: 90 residues processed: 599 average time/residue: 0.5065 time to fit residues: 493.2627 Evaluate side-chains 595 residues out of total 3830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 496 time to evaluate : 4.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 214 THR Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain G residue 57 ASN Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 559 GLU Chi-restraints excluded: chain G residue 631 ARG Chi-restraints excluded: chain G residue 694 ASP Chi-restraints excluded: chain G residue 696 THR Chi-restraints excluded: chain G residue 774 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain C residue 100 TYR Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 281 CYS Chi-restraints excluded: chain C residue 358 MET Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 107 GLU Chi-restraints excluded: chain I residue 171 LYS Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 214 MET Chi-restraints excluded: chain L residue 329 ASP Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 392 VAL Chi-restraints excluded: chain L residue 400 ASP Chi-restraints excluded: chain L residue 435 ILE Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 542 ASP Chi-restraints excluded: chain M residue 22 ARG Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 99 ASN Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 171 LEU Chi-restraints excluded: chain N residue 229 ASP Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain N residue 388 MET Chi-restraints excluded: chain N residue 410 LEU Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 138 ASN Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 93 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 150 optimal weight: 7.9990 chunk 403 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 262 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 447 optimal weight: 1.9990 chunk 371 optimal weight: 4.9990 chunk 207 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 148 optimal weight: 0.9980 chunk 235 optimal weight: 0.6980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 214 GLN H 226 HIS ** J 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.248 37613 Z= 0.763 Angle : 2.196 50.630 51124 Z= 1.445 Chirality : 0.441 6.371 5753 Planarity : 0.004 0.095 6421 Dihedral : 6.237 167.640 5210 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.98 % Allowed : 16.77 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: 0.39 (0.12), residues: 4629 helix: 1.29 (0.10), residues: 2580 sheet: -0.50 (0.28), residues: 316 loop : -1.14 (0.15), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 143 HIS 0.007 0.001 HIS M 80 PHE 0.043 0.001 PHE N 72 TYR 0.024 0.001 TYR M 435 ARG 0.007 0.000 ARG K 87 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 3830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 528 time to evaluate : 4.313 Fit side-chains REVERT: F 277 TYR cc_start: 0.9340 (m-80) cc_final: 0.8336 (m-80) REVERT: F 434 ASN cc_start: 0.8889 (t0) cc_final: 0.8642 (t0) REVERT: E 37 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8421 (mt) REVERT: G 57 ASN cc_start: 0.9040 (OUTLIER) cc_final: 0.8738 (p0) REVERT: G 291 ASP cc_start: 0.8474 (m-30) cc_final: 0.8026 (t0) REVERT: G 485 ILE cc_start: 0.8952 (mm) cc_final: 0.8707 (mt) REVERT: G 605 ASN cc_start: 0.8952 (p0) cc_final: 0.8707 (p0) REVERT: G 644 LYS cc_start: 0.8899 (mtmp) cc_final: 0.8629 (mttp) REVERT: C 62 ASP cc_start: 0.8845 (t0) cc_final: 0.8422 (t0) REVERT: C 215 PHE cc_start: 0.8123 (m-10) cc_final: 0.7796 (p90) REVERT: C 528 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8054 (mmt) REVERT: C 585 ILE cc_start: 0.8725 (tt) cc_final: 0.8512 (mt) REVERT: B 2 ASP cc_start: 0.8820 (p0) cc_final: 0.8509 (p0) REVERT: B 189 ASP cc_start: 0.8528 (t0) cc_final: 0.8307 (t0) REVERT: I 171 LYS cc_start: 0.9294 (mtpt) cc_final: 0.9050 (mmtt) REVERT: L 88 MET cc_start: 0.8743 (mmm) cc_final: 0.8337 (mmm) REVERT: L 326 GLN cc_start: 0.8504 (mp10) cc_final: 0.8210 (mt0) REVERT: L 407 MET cc_start: 0.7899 (tpt) cc_final: 0.7493 (tpt) REVERT: L 415 MET cc_start: 0.8080 (ttp) cc_final: 0.7540 (ttp) REVERT: M 22 ARG cc_start: 0.6065 (OUTLIER) cc_final: 0.4476 (ptp-170) REVERT: M 136 MET cc_start: 0.8971 (mmm) cc_final: 0.8623 (mmp) REVERT: M 235 MET cc_start: 0.8740 (ttp) cc_final: 0.8500 (ttm) REVERT: M 303 TRP cc_start: 0.8523 (OUTLIER) cc_final: 0.7942 (m-10) REVERT: M 370 ASP cc_start: 0.8865 (t0) cc_final: 0.8434 (t0) REVERT: N 74 MET cc_start: 0.8831 (ttm) cc_final: 0.8611 (ttm) REVERT: N 81 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8704 (mm) REVERT: N 139 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8579 (mm) REVERT: N 267 GLU cc_start: 0.8367 (mm-30) cc_final: 0.7950 (pp20) REVERT: H 36 GLU cc_start: 0.8687 (tt0) cc_final: 0.8480 (tt0) REVERT: H 63 ASP cc_start: 0.8530 (t0) cc_final: 0.8219 (t0) REVERT: H 94 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8287 (mm) REVERT: H 109 VAL cc_start: 0.8728 (OUTLIER) cc_final: 0.8421 (p) REVERT: H 220 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7457 (mm-30) REVERT: A 3 MET cc_start: 0.4852 (OUTLIER) cc_final: 0.4033 (mmm) REVERT: J 59 TYR cc_start: 0.9213 (OUTLIER) cc_final: 0.8576 (t80) REVERT: J 85 ARG cc_start: 0.8241 (mmt-90) cc_final: 0.7953 (mmt180) outliers start: 114 outliers final: 67 residues processed: 608 average time/residue: 0.5245 time to fit residues: 517.7663 Evaluate side-chains 586 residues out of total 3830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 508 time to evaluate : 4.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 214 THR Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain G residue 57 ASN Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 559 GLU Chi-restraints excluded: chain G residue 774 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain G residue 860 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 281 CYS Chi-restraints excluded: chain C residue 358 MET Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 214 MET Chi-restraints excluded: chain L residue 329 ASP Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 400 ASP Chi-restraints excluded: chain L residue 435 ILE Chi-restraints excluded: chain L residue 542 ASP Chi-restraints excluded: chain M residue 22 ARG Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 99 ASN Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 171 LEU Chi-restraints excluded: chain N residue 229 ASP Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain N residue 388 MET Chi-restraints excluded: chain N residue 410 LEU Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 69 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 431 optimal weight: 8.9990 chunk 50 optimal weight: 9.9990 chunk 255 optimal weight: 9.9990 chunk 327 optimal weight: 5.9990 chunk 253 optimal weight: 8.9990 chunk 377 optimal weight: 9.9990 chunk 250 optimal weight: 10.0000 chunk 446 optimal weight: 6.9990 chunk 279 optimal weight: 10.0000 chunk 272 optimal weight: 9.9990 chunk 206 optimal weight: 9.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 260 ASN ** G 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 828 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 GLN ** C 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 ASN I 64 ASN L 121 ASN ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 248 HIS M 361 GLN H 214 GLN H 226 HIS ** J 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.244 37613 Z= 0.923 Angle : 2.254 50.772 51124 Z= 1.468 Chirality : 0.446 6.472 5753 Planarity : 0.006 0.101 6421 Dihedral : 6.694 166.820 5210 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.51 % Allowed : 16.90 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % 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: 0.04 (0.12), residues: 4629 helix: 0.90 (0.10), residues: 2588 sheet: -0.64 (0.28), residues: 325 loop : -1.11 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 221 HIS 0.014 0.002 HIS M 80 PHE 0.055 0.003 PHE N 72 TYR 0.028 0.002 TYR C 277 ARG 0.014 0.001 ARG G 269 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 3830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 486 time to evaluate : 4.336 Fit side-chains REVERT: F 387 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8607 (tp) REVERT: F 420 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8293 (mt-10) REVERT: E 37 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.8245 (mt) REVERT: G 98 MET cc_start: 0.8931 (mmm) cc_final: 0.8369 (mmt) REVERT: G 291 ASP cc_start: 0.8574 (m-30) cc_final: 0.8054 (t0) REVERT: G 293 ILE cc_start: 0.9301 (pt) cc_final: 0.9092 (pt) REVERT: G 485 ILE cc_start: 0.9002 (mm) cc_final: 0.8796 (mt) REVERT: G 605 ASN cc_start: 0.8996 (p0) cc_final: 0.8691 (p0) REVERT: G 644 LYS cc_start: 0.9003 (mtmp) cc_final: 0.8773 (mtmm) REVERT: G 811 LYS cc_start: 0.9220 (OUTLIER) cc_final: 0.8833 (ttmm) REVERT: C 62 ASP cc_start: 0.8898 (t0) cc_final: 0.8532 (t0) REVERT: C 215 PHE cc_start: 0.8194 (m-10) cc_final: 0.7852 (p90) REVERT: C 403 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8132 (tp) REVERT: C 528 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.8373 (mmt) REVERT: B 2 ASP cc_start: 0.8785 (p0) cc_final: 0.8556 (p0) REVERT: B 189 ASP cc_start: 0.8629 (t0) cc_final: 0.8381 (t0) REVERT: L 88 MET cc_start: 0.8822 (mmm) cc_final: 0.8419 (mmm) REVERT: L 326 GLN cc_start: 0.8705 (mp10) cc_final: 0.8358 (mt0) REVERT: M 22 ARG cc_start: 0.6207 (OUTLIER) cc_final: 0.4563 (ptp-170) REVERT: M 187 ILE cc_start: 0.8966 (pt) cc_final: 0.8674 (mt) REVERT: M 303 TRP cc_start: 0.8601 (OUTLIER) cc_final: 0.7705 (m-10) REVERT: M 370 ASP cc_start: 0.8865 (t0) cc_final: 0.8457 (t0) REVERT: M 466 PHE cc_start: 0.8732 (m-80) cc_final: 0.8059 (t80) REVERT: N 53 TRP cc_start: 0.8184 (t60) cc_final: 0.7860 (t-100) REVERT: N 74 MET cc_start: 0.8881 (ttm) cc_final: 0.8679 (ttm) REVERT: N 81 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8732 (mm) REVERT: H 63 ASP cc_start: 0.8686 (t0) cc_final: 0.8351 (t0) REVERT: H 109 VAL cc_start: 0.8905 (OUTLIER) cc_final: 0.8610 (p) REVERT: H 138 ASN cc_start: 0.8117 (OUTLIER) cc_final: 0.7748 (p0) REVERT: H 220 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7712 (mm-30) REVERT: A 3 MET cc_start: 0.4903 (OUTLIER) cc_final: 0.3945 (mmm) REVERT: J 59 TYR cc_start: 0.9263 (OUTLIER) cc_final: 0.8774 (t80) REVERT: J 80 GLU cc_start: 0.7404 (mp0) cc_final: 0.7176 (mp0) outliers start: 134 outliers final: 89 residues processed: 580 average time/residue: 0.5087 time to fit residues: 481.5150 Evaluate side-chains 569 residues out of total 3830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 468 time to evaluate : 4.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 214 THR Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 559 GLU Chi-restraints excluded: chain G residue 631 ARG Chi-restraints excluded: chain G residue 696 THR Chi-restraints excluded: chain G residue 811 LYS Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain G residue 860 VAL Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain C residue 100 TYR Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 281 CYS Chi-restraints excluded: chain C residue 358 MET Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 214 MET Chi-restraints excluded: chain L residue 260 THR Chi-restraints excluded: chain L residue 329 ASP Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 380 LEU Chi-restraints excluded: chain L residue 400 ASP Chi-restraints excluded: chain L residue 435 ILE Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 487 HIS Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 542 ASP Chi-restraints excluded: chain L residue 571 ILE Chi-restraints excluded: chain M residue 22 ARG Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 99 ASN Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain N residue 410 LEU Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 138 ASN Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 93 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 276 optimal weight: 0.8980 chunk 178 optimal weight: 4.9990 chunk 266 optimal weight: 0.4980 chunk 134 optimal weight: 0.5980 chunk 87 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 283 optimal weight: 7.9990 chunk 304 optimal weight: 8.9990 chunk 220 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 350 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 238 ASN ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 276 ASN ** G 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 828 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 214 GLN H 219 GLN H 226 HIS ** K 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.248 37613 Z= 0.764 Angle : 2.200 50.663 51124 Z= 1.447 Chirality : 0.440 6.356 5753 Planarity : 0.004 0.097 6421 Dihedral : 6.311 167.300 5210 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.67 % Allowed : 17.92 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: 0.42 (0.12), residues: 4629 helix: 1.26 (0.10), residues: 2580 sheet: -0.45 (0.28), residues: 316 loop : -1.06 (0.15), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 143 HIS 0.006 0.001 HIS M 80 PHE 0.045 0.001 PHE N 72 TYR 0.026 0.001 TYR M 435 ARG 0.007 0.000 ARG K 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 3830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 510 time to evaluate : 4.679 Fit side-chains REVERT: F 277 TYR cc_start: 0.9325 (m-80) cc_final: 0.8395 (m-80) REVERT: F 285 LEU cc_start: 0.8062 (mt) cc_final: 0.7828 (mp) REVERT: F 420 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8251 (mt-10) REVERT: F 434 ASN cc_start: 0.8938 (t0) cc_final: 0.8726 (t0) REVERT: E 37 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8378 (mt) REVERT: G 20 ASN cc_start: 0.7741 (t0) cc_final: 0.7415 (m-40) REVERT: G 150 MET cc_start: 0.9163 (tpt) cc_final: 0.8810 (tpp) REVERT: G 291 ASP cc_start: 0.8445 (m-30) cc_final: 0.8003 (t0) REVERT: G 293 ILE cc_start: 0.9333 (pt) cc_final: 0.9019 (pt) REVERT: G 485 ILE cc_start: 0.8945 (mm) cc_final: 0.8707 (mt) REVERT: G 605 ASN cc_start: 0.8922 (p0) cc_final: 0.8674 (p0) REVERT: G 644 LYS cc_start: 0.8912 (mtmp) cc_final: 0.8695 (mttp) REVERT: C 62 ASP cc_start: 0.8809 (t0) cc_final: 0.8418 (t0) REVERT: C 215 PHE cc_start: 0.8141 (m-10) cc_final: 0.7830 (p90) REVERT: C 528 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8123 (mmt) REVERT: B 2 ASP cc_start: 0.8825 (p0) cc_final: 0.8495 (p0) REVERT: B 189 ASP cc_start: 0.8510 (t0) cc_final: 0.8299 (t0) REVERT: L 88 MET cc_start: 0.8684 (mmm) cc_final: 0.8444 (mmm) REVERT: L 326 GLN cc_start: 0.8602 (mp10) cc_final: 0.8354 (mt0) REVERT: L 415 MET cc_start: 0.8240 (ttp) cc_final: 0.7727 (ttp) REVERT: M 22 ARG cc_start: 0.6133 (OUTLIER) cc_final: 0.4522 (ptp-170) REVERT: M 235 MET cc_start: 0.8738 (ttp) cc_final: 0.8498 (ttm) REVERT: M 303 TRP cc_start: 0.8564 (OUTLIER) cc_final: 0.7836 (m-10) REVERT: M 370 ASP cc_start: 0.8876 (t0) cc_final: 0.8431 (t0) REVERT: N 74 MET cc_start: 0.8827 (ttm) cc_final: 0.8609 (ttm) REVERT: N 81 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8684 (mm) REVERT: N 103 ASP cc_start: 0.8792 (m-30) cc_final: 0.8581 (m-30) REVERT: N 223 PHE cc_start: 0.9227 (OUTLIER) cc_final: 0.8290 (m-80) REVERT: N 267 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8092 (pp20) REVERT: H 36 GLU cc_start: 0.8760 (tt0) cc_final: 0.8551 (tt0) REVERT: H 63 ASP cc_start: 0.8599 (t0) cc_final: 0.8275 (t0) REVERT: H 94 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8438 (mm) REVERT: H 109 VAL cc_start: 0.8823 (OUTLIER) cc_final: 0.8529 (p) REVERT: A 3 MET cc_start: 0.5001 (OUTLIER) cc_final: 0.3998 (mmm) REVERT: A 8 GLU cc_start: 0.8278 (tm-30) cc_final: 0.8042 (tm-30) REVERT: J 59 TYR cc_start: 0.9220 (OUTLIER) cc_final: 0.8571 (t80) REVERT: J 80 GLU cc_start: 0.7363 (mp0) cc_final: 0.7114 (mp0) outliers start: 102 outliers final: 66 residues processed: 584 average time/residue: 0.5058 time to fit residues: 484.1770 Evaluate side-chains 566 residues out of total 3830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 490 time to evaluate : 4.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 214 THR Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain G residue 276 ASN Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 559 GLU Chi-restraints excluded: chain G residue 774 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain G residue 860 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 281 CYS Chi-restraints excluded: chain C residue 358 MET Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 214 MET Chi-restraints excluded: chain L residue 329 ASP Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 400 ASP Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 542 ASP Chi-restraints excluded: chain M residue 22 ARG Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 145 MET Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 99 ASN Chi-restraints excluded: chain N residue 171 LEU Chi-restraints excluded: chain N residue 223 PHE Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain N residue 410 LEU Chi-restraints excluded: chain N residue 482 MET Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 93 TRP Chi-restraints excluded: chain J residue 152 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 405 optimal weight: 7.9990 chunk 427 optimal weight: 0.8980 chunk 390 optimal weight: 5.9990 chunk 415 optimal weight: 8.9990 chunk 250 optimal weight: 0.9980 chunk 181 optimal weight: 8.9990 chunk 326 optimal weight: 10.0000 chunk 127 optimal weight: 0.9980 chunk 375 optimal weight: 8.9990 chunk 393 optimal weight: 9.9990 chunk 414 optimal weight: 0.4980 overall best weight: 1.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 238 ASN ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 GLN ** G 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 828 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 GLN ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 226 HIS ** J 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.246 37613 Z= 0.766 Angle : 2.203 50.628 51124 Z= 1.447 Chirality : 0.441 6.372 5753 Planarity : 0.004 0.094 6421 Dihedral : 6.213 167.198 5210 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.28 % Allowed : 18.50 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.12), residues: 4629 helix: 1.34 (0.10), residues: 2578 sheet: -0.58 (0.28), residues: 325 loop : -1.00 (0.15), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 143 HIS 0.007 0.001 HIS M 80 PHE 0.050 0.001 PHE N 72 TYR 0.024 0.001 TYR M 435 ARG 0.007 0.000 ARG K 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 3830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 496 time to evaluate : 4.271 Fit side-chains REVERT: F 277 TYR cc_start: 0.9337 (m-80) cc_final: 0.8388 (m-80) REVERT: F 285 LEU cc_start: 0.7998 (mt) cc_final: 0.7752 (mp) REVERT: F 387 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8523 (tp) REVERT: F 420 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8243 (mt-10) REVERT: E 37 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8412 (mt) REVERT: G 20 ASN cc_start: 0.7780 (t0) cc_final: 0.7474 (m-40) REVERT: G 98 MET cc_start: 0.8759 (mmm) cc_final: 0.8373 (mmm) REVERT: G 291 ASP cc_start: 0.8424 (m-30) cc_final: 0.7975 (t0) REVERT: G 293 ILE cc_start: 0.9347 (OUTLIER) cc_final: 0.9114 (pt) REVERT: G 485 ILE cc_start: 0.8951 (mm) cc_final: 0.8724 (mt) REVERT: G 605 ASN cc_start: 0.8907 (p0) cc_final: 0.8661 (p0) REVERT: G 644 LYS cc_start: 0.8936 (mtmp) cc_final: 0.8674 (mttp) REVERT: G 811 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8877 (ttmm) REVERT: C 62 ASP cc_start: 0.8821 (t0) cc_final: 0.8421 (t0) REVERT: C 215 PHE cc_start: 0.8123 (m-10) cc_final: 0.7829 (p90) REVERT: C 528 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.8135 (mmt) REVERT: B 2 ASP cc_start: 0.8861 (p0) cc_final: 0.8515 (p0) REVERT: M 22 ARG cc_start: 0.6130 (OUTLIER) cc_final: 0.4522 (ptp-170) REVERT: M 303 TRP cc_start: 0.8569 (OUTLIER) cc_final: 0.7828 (m-10) REVERT: M 370 ASP cc_start: 0.8889 (t0) cc_final: 0.8445 (t0) REVERT: N 81 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8702 (mm) REVERT: N 223 PHE cc_start: 0.9218 (OUTLIER) cc_final: 0.7528 (m-80) REVERT: N 267 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8089 (pp20) REVERT: H 36 GLU cc_start: 0.8758 (tt0) cc_final: 0.8532 (tt0) REVERT: H 63 ASP cc_start: 0.8602 (t0) cc_final: 0.8282 (t0) REVERT: H 94 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8407 (mm) REVERT: H 109 VAL cc_start: 0.8818 (OUTLIER) cc_final: 0.8532 (p) REVERT: A 3 MET cc_start: 0.5021 (OUTLIER) cc_final: 0.3976 (mmm) REVERT: A 8 GLU cc_start: 0.8229 (tm-30) cc_final: 0.8001 (tm-30) REVERT: J 80 GLU cc_start: 0.7488 (mp0) cc_final: 0.7208 (mp0) outliers start: 87 outliers final: 69 residues processed: 558 average time/residue: 0.5089 time to fit residues: 462.6311 Evaluate side-chains 576 residues out of total 3830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 495 time to evaluate : 4.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 214 THR Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain G residue 293 ILE Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 559 GLU Chi-restraints excluded: chain G residue 774 VAL Chi-restraints excluded: chain G residue 811 LYS Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain G residue 860 VAL Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 281 CYS Chi-restraints excluded: chain C residue 358 MET Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 77 PHE Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 214 MET Chi-restraints excluded: chain L residue 329 ASP Chi-restraints excluded: chain L residue 400 ASP Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 542 ASP Chi-restraints excluded: chain M residue 22 ARG Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 99 ASN Chi-restraints excluded: chain N residue 171 LEU Chi-restraints excluded: chain N residue 223 PHE Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain N residue 410 LEU Chi-restraints excluded: chain N residue 482 MET Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 93 TRP Chi-restraints excluded: chain J residue 152 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 273 optimal weight: 0.9990 chunk 439 optimal weight: 0.9990 chunk 268 optimal weight: 10.0000 chunk 208 optimal weight: 0.2980 chunk 305 optimal weight: 7.9990 chunk 461 optimal weight: 2.9990 chunk 424 optimal weight: 1.9990 chunk 367 optimal weight: 20.0000 chunk 38 optimal weight: 0.4980 chunk 283 optimal weight: 3.9990 chunk 225 optimal weight: 3.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 434 ASN ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 490 GLN ** G 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 219 GLN H 226 HIS ** K 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.247 37613 Z= 0.761 Angle : 2.197 50.644 51124 Z= 1.445 Chirality : 0.441 6.361 5753 Planarity : 0.004 0.093 6421 Dihedral : 6.059 166.957 5210 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.09 % Allowed : 18.63 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: 0.62 (0.13), residues: 4629 helix: 1.45 (0.10), residues: 2569 sheet: -0.60 (0.28), residues: 327 loop : -0.95 (0.15), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 143 HIS 0.007 0.001 HIS M 80 PHE 0.045 0.001 PHE N 72 TYR 0.025 0.001 TYR M 435 ARG 0.007 0.000 ARG K 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 3830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 522 time to evaluate : 4.623 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 277 TYR cc_start: 0.9330 (m-80) cc_final: 0.8364 (m-80) REVERT: F 285 LEU cc_start: 0.7907 (mt) cc_final: 0.7665 (mp) REVERT: F 387 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8512 (tp) REVERT: F 420 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8189 (mt-10) REVERT: E 37 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8430 (mt) REVERT: G 150 MET cc_start: 0.9170 (tpt) cc_final: 0.8836 (tpp) REVERT: G 293 ILE cc_start: 0.9333 (OUTLIER) cc_final: 0.9125 (pt) REVERT: G 485 ILE cc_start: 0.8943 (mm) cc_final: 0.8702 (mt) REVERT: G 605 ASN cc_start: 0.8870 (p0) cc_final: 0.8653 (p0) REVERT: G 644 LYS cc_start: 0.8880 (mtmp) cc_final: 0.8613 (mttp) REVERT: C 62 ASP cc_start: 0.8816 (t0) cc_final: 0.8392 (t0) REVERT: C 215 PHE cc_start: 0.8115 (m-10) cc_final: 0.7826 (p90) REVERT: B 2 ASP cc_start: 0.8868 (p0) cc_final: 0.8539 (p0) REVERT: M 303 TRP cc_start: 0.8551 (OUTLIER) cc_final: 0.7872 (m-10) REVERT: M 370 ASP cc_start: 0.8880 (t0) cc_final: 0.8449 (t0) REVERT: N 81 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8693 (mm) REVERT: N 223 PHE cc_start: 0.9199 (OUTLIER) cc_final: 0.7463 (m-80) REVERT: N 267 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8068 (pp20) REVERT: H 36 GLU cc_start: 0.8736 (tt0) cc_final: 0.8520 (tt0) REVERT: H 63 ASP cc_start: 0.8669 (t0) cc_final: 0.8330 (t0) REVERT: H 94 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8245 (mm) REVERT: H 109 VAL cc_start: 0.8689 (OUTLIER) cc_final: 0.8405 (p) REVERT: H 278 PHE cc_start: 0.8621 (m-80) cc_final: 0.8406 (m-80) REVERT: A 8 GLU cc_start: 0.8230 (tm-30) cc_final: 0.8017 (tm-30) REVERT: J 80 GLU cc_start: 0.7492 (mp0) cc_final: 0.7218 (mp0) outliers start: 80 outliers final: 63 residues processed: 576 average time/residue: 0.5076 time to fit residues: 475.8661 Evaluate side-chains 577 residues out of total 3830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 506 time to evaluate : 4.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 214 THR Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 434 ASN Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain G residue 293 ILE Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 559 GLU Chi-restraints excluded: chain G residue 728 GLN Chi-restraints excluded: chain G residue 774 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain G residue 860 VAL Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 281 CYS Chi-restraints excluded: chain C residue 358 MET Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 77 PHE Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 214 MET Chi-restraints excluded: chain L residue 329 ASP Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 400 ASP Chi-restraints excluded: chain L residue 542 ASP Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 99 ASN Chi-restraints excluded: chain N residue 223 PHE Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain N residue 410 LEU Chi-restraints excluded: chain N residue 482 MET Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 210 HIS Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 93 TRP Chi-restraints excluded: chain J residue 152 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 291 optimal weight: 7.9990 chunk 391 optimal weight: 0.0170 chunk 112 optimal weight: 6.9990 chunk 338 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 367 optimal weight: 20.0000 chunk 153 optimal weight: 8.9990 chunk 377 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 overall best weight: 4.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 GLN ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 828 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 GLN ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 226 HIS ** J 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.077019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.063805 restraints weight = 62550.055| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 1.22 r_work: 0.2729 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.244 37613 Z= 0.811 Angle : 2.221 50.691 51124 Z= 1.454 Chirality : 0.443 6.414 5753 Planarity : 0.005 0.096 6421 Dihedral : 6.249 167.293 5210 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.25 % Allowed : 18.68 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: 0.51 (0.12), residues: 4629 helix: 1.32 (0.10), residues: 2573 sheet: -0.51 (0.28), residues: 324 loop : -0.94 (0.15), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP N 53 HIS 0.010 0.001 HIS M 80 PHE 0.027 0.002 PHE L 341 TYR 0.033 0.002 TYR C 277 ARG 0.008 0.000 ARG F 358 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9407.99 seconds wall clock time: 170 minutes 16.36 seconds (10216.36 seconds total)