Starting phenix.real_space_refine on Fri Feb 23 08:42:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7l_13239/02_2024/7p7l_13239_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7l_13239/02_2024/7p7l_13239.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7l_13239/02_2024/7p7l_13239.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7l_13239/02_2024/7p7l_13239.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7l_13239/02_2024/7p7l_13239_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7l_13239/02_2024/7p7l_13239_updated.pdb" } resolution = 3.0 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= 0.004 sd= 0.017 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 16 5.49 5 S 266 5.16 5 C 24527 2.51 5 N 6162 2.21 5 O 6583 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 283": "OD1" <-> "OD2" Residue "E GLU 23": "OE1" <-> "OE2" Residue "E TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 12": "OE1" <-> "OE2" Residue "G GLU 84": "OE1" <-> "OE2" Residue "G PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 332": "OE1" <-> "OE2" Residue "G GLU 336": "OE1" <-> "OE2" Residue "G GLU 684": "OE1" <-> "OE2" Residue "G GLU 789": "OE1" <-> "OE2" Residue "G TYR 864": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 877": "OE1" <-> "OE2" Residue "G ASP 904": "OD1" <-> "OD2" Residue "C PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 382": "OE1" <-> "OE2" Residue "C GLU 472": "OE1" <-> "OE2" Residue "C TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 202": "OE1" <-> "OE2" Residue "I ASP 53": "OD1" <-> "OD2" Residue "I ASP 159": "OD1" <-> "OD2" Residue "H GLU 71": "OE1" <-> "OE2" Residue "H ASP 79": "OD1" <-> "OD2" Residue "H PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 81": "OE1" <-> "OE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "L PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 84": "OD1" <-> "OD2" Residue "M TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 370": "OD1" <-> "OD2" Residue "M GLU 407": "OE1" <-> "OE2" Residue "N ASP 62": "OD1" <-> "OD2" Residue "N ASP 70": "OD1" <-> "OD2" Residue "N ASP 183": "OD1" <-> "OD2" Residue "N GLU 200": "OE1" <-> "OE2" Residue "N PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 229": "OD1" <-> "OD2" Residue "N GLU 324": "OE1" <-> "OE2" Residue "N TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 36": "OE1" <-> "OE2" Residue "K PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 55": "OE1" <-> "OE2" Residue "J PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 120": "OD1" <-> "OD2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 37587 Number of models: 1 Model: "" Number of chains: 24 Chain: "F" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3407 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 413} 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: {'PCIS': 1, 'PTRANS': 8, '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: 4705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4705 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 547} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1568 Classifications: {'peptide': 198} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 185} Chain breaks: 2 Chain: "I" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1436 Classifications: {'peptide': 180} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 166} Chain: "H" Number of atoms: 2444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2444 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 296} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 800 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 1, 'TRANS': 99} Chain breaks: 1 Chain: "L" Number of atoms: 4498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4498 Classifications: {'peptide': 589} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 570} Chain breaks: 2 Chain: "M" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3953 Classifications: {'peptide': 504} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 482} Chain: "N" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3630 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 459} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 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: 1214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1214 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 156} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'SF4': 1, 'UQ8': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'UQ8:plan-6': 1, 'UQ8:plan-7': 1, 'UQ8:plan-8': 1, 'UQ8:plan-9': 1, 'UQ8:plan-2': 1} Unresolved non-hydrogen planarities: 24 Chain: "I" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'3PE': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 161 Unusual residues: {'3PE': 3, 'LFA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "A" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "L" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 249 Unusual residues: {'3PE': 5, 'LFA': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 26 Chain: "M" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 173 Unusual residues: {'3PE': 3, 'LFA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "N" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'LFA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2721 SG CYS F 354 73.598 60.094 192.702 1.00 81.30 S ATOM 2741 SG CYS F 357 77.444 59.772 196.893 1.00112.84 S ATOM 2697 SG CYS F 351 75.896 53.793 194.168 1.00160.05 S ATOM 4054 SG CYS E 92 85.692 50.893 213.156 1.00150.77 S ATOM 4088 SG CYS E 97 86.327 51.892 216.566 1.00137.26 S ATOM 5476 SG CYS G 114 83.830 65.896 174.866 1.00 22.18 S ATOM 5416 SG CYS G 105 89.114 69.604 176.256 1.00 22.78 S ATOM 5436 SG CYS G 108 89.729 63.600 173.866 1.00 27.41 S ATOM 5830 SG CYS G 156 77.963 58.252 180.051 1.00 74.70 S ATOM 5811 SG CYS G 153 83.864 57.075 182.836 1.00 21.40 S ATOM 5859 SG CYS G 159 80.938 52.485 179.366 1.00 21.77 S ATOM 6203 SG CYS G 203 82.998 57.642 176.241 1.00 19.87 S ATOM 6428 SG CYS G 230 79.235 49.329 155.062 1.00 31.37 S ATOM 6713 SG CYS G 265 79.286 45.578 160.449 1.00 35.22 S ATOM 6476 SG CYS G 237 73.964 49.082 158.326 1.00 18.03 S ATOM 6452 SG CYS G 233 76.068 43.634 155.347 1.00 36.75 S ATOM 4877 SG CYS G 36 71.566 59.377 182.749 1.00 29.66 S ATOM 4953 SG CYS G 47 73.332 62.642 183.013 1.00 50.07 S ATOM 4979 SG CYS G 50 67.591 64.581 183.079 1.00 38.67 S ATOM 5128 SG CYS G 69 66.998 60.946 183.016 1.00 44.68 S ATOM 17200 SG CYS B 129 94.079 92.874 150.497 1.00 30.04 S ATOM 16697 SG CYS B 64 99.391 96.540 151.965 1.00 33.49 S ATOM 16691 SG CYS B 63 93.938 98.721 153.950 1.00 36.23 S ATOM 17417 SG CYS B 158 96.028 92.883 156.287 1.00 42.48 S ATOM 18748 SG CYS I 102 94.800 87.072 162.464 1.00 15.72 S ATOM 18723 SG CYS I 99 100.168 85.666 158.686 1.00 46.21 S ATOM 18766 SG CYS I 105 98.840 82.439 164.172 1.00 39.22 S ATOM 18481 SG CYS I 70 94.878 81.737 159.068 1.00 18.70 S ATOM 18795 SG CYS I 109 99.840 76.893 170.485 1.00 20.26 S ATOM 18458 SG CYS I 66 97.732 76.187 164.399 1.00 17.39 S ATOM 18418 SG CYS I 60 101.786 71.817 166.593 1.00 17.60 S ATOM 18436 SG CYS I 63 95.605 72.420 169.208 1.00 25.20 S Time building chain proxies: 20.03, per 1000 atoms: 0.53 Number of scatterers: 37587 At special positions: 0 Unit cell: (157.94, 214.12, 245.92, 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 266 16.00 P 16 15.00 O 6583 8.00 N 6162 7.00 C 24527 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: 14.10 Conformation dependent library (CDL) restraints added in 6.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 92 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 97 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 133 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 137 " pdb=" FES G1004 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 50 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 47 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 69 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 36 " pdb=" SF4 B 301 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 158 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 129 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 63 " 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="FE1 SF4 G1001 " - pdb=" SG CYS G 114 " pdb="FE2 SF4 G1001 " - pdb=" SG CYS G 105 " 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="FE4 SF4 G1003 " - pdb=" SG CYS G 233 " pdb="FE1 SF4 G1003 " - pdb=" SG CYS G 230 " pdb="FE3 SF4 G1003 " - pdb=" SG CYS G 237 " 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="FE1 SF4 I 202 " - pdb=" SG CYS I 109 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 63 " Number of angles added : 93 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8602 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 193 helices and 25 sheets defined 54.0% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.05 Creating SS restraints... Processing helix chain 'F' and resid 26 through 31 Processing helix chain 'F' and resid 37 through 44 Processing helix chain 'F' and resid 47 through 57 Processing helix chain 'F' and resid 69 through 75 Processing helix chain 'F' and resid 100 through 105 Processing helix chain 'F' and resid 110 through 123 Processing helix chain 'F' and resid 137 through 152 Processing helix 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 230 Proline residue: F 226 - end of helix Processing helix chain 'F' and resid 233 through 237 Processing helix chain 'F' and resid 270 through 274 removed outlier: 3.548A pdb=" N ILE F 273 " --> pdb=" O ALA F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 296 No H-bonds generated for 'chain 'F' and resid 294 through 296' Processing helix chain 'F' and resid 302 through 304 No H-bonds generated for 'chain 'F' and resid 302 through 304' Processing helix chain 'F' and resid 312 through 315 No H-bonds generated for 'chain 'F' and resid 312 through 315' Processing helix chain 'F' and resid 335 through 348 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 414 Proline residue: F 407 - end of helix Processing helix chain 'F' and resid 416 through 422 removed outlier: 3.747A pdb=" N ALA F 421 " --> pdb=" O GLU F 417 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLY F 422 " --> pdb=" O GLU F 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 26 Processing helix chain 'E' and resid 32 through 47 removed outlier: 4.624A pdb=" N ILE E 37 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU E 38 " --> pdb=" O ALA E 35 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG E 47 " --> pdb=" O GLN E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 62 removed outlier: 4.019A 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 95 through 99 Processing helix chain 'E' and resid 102 through 113 Processing helix chain 'E' and resid 158 through 164 removed outlier: 4.182A pdb=" N ARG E 164 " --> pdb=" O GLU E 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 27 Processing helix chain 'G' and resid 84 through 97 Processing helix chain 'G' and resid 105 through 107 No H-bonds generated for 'chain 'G' and resid 105 through 107' 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 Processing helix chain 'G' and resid 211 through 215 Processing helix chain 'G' and resid 266 through 270 Processing helix chain 'G' and resid 272 through 274 No H-bonds generated for 'chain 'G' and resid 272 through 274' Processing helix chain 'G' and resid 297 through 309 Processing helix chain 'G' and resid 324 through 334 Processing helix chain 'G' and resid 345 through 360 Processing helix 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: 4.356A pdb=" N LYS G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ALA G 403 " --> pdb=" O VAL G 399 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN G 410 " --> pdb=" O MET G 406 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 423 Processing helix chain 'G' and resid 453 through 467 Processing helix chain 'G' and resid 479 through 494 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 615 through 617 No H-bonds generated for 'chain 'G' and resid 615 through 617' Processing helix chain 'G' and resid 638 through 640 No H-bonds generated for 'chain 'G' and resid 638 through 640' 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 690 removed outlier: 5.084A pdb=" N GLY G 687 " --> pdb=" O GLU G 684 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS G 689 " --> pdb=" O ALA G 686 " (cutoff:3.500A) Processing helix chain 'G' and resid 764 through 767 removed outlier: 3.638A pdb=" N TRP G 767 " --> pdb=" O PRO G 764 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 764 through 767' Processing helix chain 'G' and resid 825 through 829 Processing helix chain 'G' and resid 831 through 833 No H-bonds generated for 'chain 'G' and resid 831 through 833' 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 54 through 65 removed outlier: 4.618A pdb=" N LEU C 58 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 145 removed outlier: 3.695A pdb=" N ASN C 135 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N TRP C 136 " --> pdb=" O ASN C 133 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP C 142 " --> pdb=" O ARG C 139 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU C 144 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N PHE C 145 " --> pdb=" O TRP C 142 " (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 281 through 295 Proline residue: C 286 - end of helix Processing helix chain 'C' and resid 301 through 330 Processing helix chain 'C' and resid 335 through 354 Processing helix chain 'C' and resid 376 through 397 Proline residue: C 388 - end of helix Processing helix chain 'C' and resid 402 through 408 Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 427 through 432 removed outlier: 4.042A pdb=" N THR C 432 " --> pdb=" O GLY C 428 " (cutoff:3.500A) 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 521 Processing helix chain 'C' and resid 564 through 571 Processing helix chain 'C' and resid 573 through 575 No H-bonds generated for 'chain 'C' and resid 573 through 575' Processing helix chain 'C' and resid 581 through 590 Processing helix chain 'C' and resid 595 through 599 Processing helix chain 'B' and resid 37 through 52 Processing helix chain 'B' and resid 63 through 71 Processing helix chain 'B' and resid 78 through 81 Processing helix chain 'B' and resid 104 through 116 Proline residue: B 108 - end of helix Processing helix chain 'B' and resid 128 through 132 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 178 removed outlier: 4.063A pdb=" N LYS B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 208 removed outlier: 4.608A pdb=" N GLY B 206 " --> pdb=" O GLU B 202 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N GLU B 207 " --> pdb=" O ARG B 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 24 Processing helix chain 'I' and resid 65 through 69 Processing helix chain 'I' and resid 104 through 108 Processing helix chain 'I' and resid 127 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 'I' and resid 150 through 152 No H-bonds generated for 'chain 'I' and resid 150 through 152' Processing helix chain 'H' and resid 6 through 43 Processing helix chain 'H' and resid 54 through 56 No H-bonds generated for 'chain 'H' and resid 54 through 56' Processing helix chain 'H' and resid 59 through 68 Processing helix chain 'H' and resid 80 through 100 Proline residue: H 87 - end of helix removed outlier: 4.592A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 136 Processing helix chain 'H' and resid 140 through 171 removed outlier: 4.991A pdb=" N PHE H 159 " --> pdb=" O SER H 155 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N GLY H 161 " --> pdb=" O GLU H 157 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LEU H 162 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLY H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 4.778A 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 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 305 through 322 Processing helix chain 'A' and resid 8 through 36 Processing helix chain 'A' and resid 66 through 119 removed outlier: 3.622A pdb=" N THR A 90 " --> pdb=" O PHE A 86 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N SER A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 92 " --> pdb=" O TRP A 88 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ARG A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLU A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TRP A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N VAL A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 21 removed outlier: 3.656A pdb=" N THR L 7 " --> pdb=" O LEU L 4 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N LEU L 10 " --> pdb=" O THR L 7 " (cutoff:3.500A) Proline residue: L 11 - end of helix removed outlier: 3.501A pdb=" N PHE L 20 " --> pdb=" O LEU L 17 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER L 21 " --> pdb=" O LEU L 18 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 55 Processing helix chain 'L' and resid 83 through 104 Processing helix chain 'L' and resid 113 through 132 Processing helix chain 'L' and resid 136 through 156 removed outlier: 3.547A pdb=" N GLY L 155 " --> pdb=" O TYR L 151 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N PHE L 156 " --> pdb=" O LEU L 152 " (cutoff:3.500A) Processing helix chain 'L' and resid 161 through 192 Processing helix chain 'L' and resid 197 through 204 Processing helix chain 'L' and resid 213 through 229 Processing helix chain 'L' and resid 239 through 244 removed outlier: 5.024A pdb=" N ALA L 244 " --> pdb=" O ALA L 240 " (cutoff:3.500A) Processing helix chain 'L' and resid 247 through 255 Processing helix chain 'L' and resid 260 through 268 Processing helix chain 'L' and resid 270 through 274 Processing helix chain 'L' and resid 277 through 298 Processing helix chain 'L' and resid 304 through 324 Processing helix chain 'L' and resid 328 through 351 Processing helix chain 'L' and resid 373 through 387 Processing helix chain 'L' and resid 394 through 409 Processing helix chain 'L' and resid 412 through 437 Processing helix chain 'L' and resid 455 through 464 Processing helix chain 'L' and resid 466 through 470 Processing helix chain 'L' and resid 487 through 512 Processing helix chain 'L' and resid 518 through 524 Processing helix chain 'L' and resid 526 through 536 Processing helix chain 'L' and resid 541 through 560 removed outlier: 5.100A pdb=" N LYS L 551 " --> pdb=" O LYS L 547 " (cutoff:3.500A) Proline residue: L 552 - end of helix Processing helix chain 'L' and resid 564 through 586 Proline residue: L 572 - end of helix removed outlier: 4.160A pdb=" N SER L 586 " --> pdb=" O GLY L 582 " (cutoff:3.500A) 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 27 through 50 Processing helix chain 'M' and resid 85 through 104 Processing helix chain 'M' and resid 113 through 132 Processing helix chain 'M' and resid 136 through 156 removed outlier: 4.686A pdb=" N LEU M 147 " --> pdb=" O TRP M 143 " (cutoff:3.500A) removed outlier: 4.202A 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 233 Processing helix chain 'M' and resid 242 through 249 Processing helix chain 'M' and resid 256 through 260 Processing helix chain 'M' and resid 266 through 273 Processing helix chain 'M' and resid 275 through 278 No H-bonds generated for 'chain 'M' and resid 275 through 278' Processing helix chain 'M' and resid 280 through 306 Proline residue: M 288 - end of helix Processing helix chain 'M' and resid 311 through 332 removed outlier: 3.706A pdb=" N TYR M 331 " --> pdb=" O LEU M 327 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR M 332 " --> pdb=" O ILE M 328 " (cutoff:3.500A) Processing helix chain 'M' and resid 335 through 366 Processing helix chain 'M' and resid 377 through 379 No H-bonds generated for 'chain 'M' and resid 377 through 379' Processing helix chain 'M' and resid 384 through 395 Processing helix chain 'M' and resid 402 through 417 Processing helix chain 'M' and resid 419 through 443 Processing helix chain 'M' and resid 452 through 454 No H-bonds generated for 'chain 'M' and resid 452 through 454' Processing helix chain 'M' and resid 462 through 480 Processing helix chain 'M' and resid 483 through 488 Processing helix chain 'M' and resid 490 through 501 Processing helix chain 'N' and resid 5 through 10 Processing helix chain 'N' and resid 12 through 30 Processing helix chain 'N' and resid 34 through 58 removed outlier: 4.495A pdb=" N TRP N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N PHE N 54 " --> pdb=" O VAL N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 71 through 97 Proline residue: N 93 - end of helix removed outlier: 4.202A 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 143 Proline residue: N 138 - end of helix Processing helix chain 'N' and resid 150 through 181 Processing helix chain 'N' and resid 186 through 188 No H-bonds generated for 'chain 'N' and resid 186 through 188' Processing helix chain 'N' and resid 201 through 217 Processing helix chain 'N' and resid 227 through 233 Processing helix chain 'N' and resid 236 through 260 removed outlier: 4.358A pdb=" N SER N 246 " --> pdb=" O LEU N 242 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LYS N 247 " --> pdb=" O ALA N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 267 through 288 removed outlier: 3.854A pdb=" N ALA N 288 " --> pdb=" O GLY N 284 " (cutoff:3.500A) Processing helix chain 'N' and resid 294 through 314 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 432 Processing helix chain 'N' and resid 448 through 469 Processing helix chain 'N' and resid 472 through 479 Processing helix chain 'K' and resid 4 through 24 Processing helix chain 'K' and resid 28 through 52 Processing helix chain 'K' and resid 57 through 87 Processing helix chain 'J' and resid 2 through 21 removed outlier: 3.581A pdb=" N THR J 21 " --> pdb=" O LEU J 17 " (cutoff:3.500A) 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 74 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 113 removed outlier: 5.738A pdb=" N GLY J 95 " --> pdb=" O GLN J 91 " (cutoff:3.500A) Proline residue: J 96 - end of helix removed outlier: 3.797A pdb=" N GLY J 113 " --> pdb=" O TYR J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 133 Processing helix chain 'J' and resid 138 through 158 Processing sheet with id= A, first strand: chain 'F' and resid 213 through 218 removed outlier: 6.593A pdb=" N ARG F 127 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N CYS F 89 " --> pdb=" O ARG F 127 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N TYR F 129 " --> pdb=" O CYS F 89 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ALA F 91 " --> pdb=" O TYR F 129 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N PHE F 131 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N GLU F 168 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ILE F 130 " --> pdb=" O GLU F 168 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N PHE F 170 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LEU F 132 " --> pdb=" O PHE F 170 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N HIS F 172 " --> pdb=" O LEU F 132 " (cutoff:3.500A) 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 removed outlier: 3.561A pdb=" N ALA F 328 " --> pdb=" O SER F 253 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'E' and resid 87 through 92 Processing sheet with id= E, first strand: chain 'E' and resid 143 through 145 Processing sheet with id= F, first strand: chain 'G' and resid 11 through 14 removed outlier: 6.614A pdb=" N THR G 77 " --> pdb=" O HIS G 7 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N PHE G 78 " --> pdb=" O TYR G 55 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'G' and resid 146 through 148 Processing sheet with id= H, first strand: chain 'G' and resid 173 through 175 Processing sheet with id= I, first strand: chain 'G' and resid 224 through 229 removed outlier: 6.443A pdb=" N ARG G 244 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N LEU G 248 " --> pdb=" O ARG G 244 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 285 through 288 Processing sheet with id= K, first strand: chain 'G' and resid 314 through 317 removed outlier: 6.475A pdb=" N ALA G 565 " --> pdb=" O ILE G 315 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ILE G 317 " --> pdb=" O ALA G 565 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL G 567 " --> pdb=" O ILE G 317 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU G 591 " --> pdb=" O VAL G 566 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N VAL G 568 " --> pdb=" O LEU G 591 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N MET G 593 " --> pdb=" O VAL G 568 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU G 608 " --> pdb=" O VAL G 594 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ASP G 596 " --> pdb=" O LEU G 608 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N LEU G 610 " --> pdb=" O ASP G 596 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'G' and resid 530 through 534 removed outlier: 6.361A pdb=" N ALA G 376 " --> pdb=" O LEU G 499 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ILE G 501 " --> pdb=" O ALA G 376 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU G 378 " --> pdb=" O ILE G 501 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N GLY G 503 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N LEU G 380 " --> pdb=" O GLY G 503 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N VAL G 379 " --> pdb=" O PRO G 430 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N PHE G 432 " --> pdb=" O VAL G 379 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N TRP G 447 " --> pdb=" O VAL G 433 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ASN G 435 " --> pdb=" O TRP G 447 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N TYR G 449 " --> pdb=" O ASN G 435 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 620 through 623 Processing sheet with id= N, first strand: chain 'G' and resid 883 through 886 removed outlier: 7.629A pdb=" N VAL G 884 " --> pdb=" O LYS G 811 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ARG G 813 " --> pdb=" O VAL G 884 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU G 886 " --> pdb=" O ARG G 813 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ALA G 815 " --> pdb=" O LEU G 886 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLU G 903 " --> pdb=" O SER G 863 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER G 863 " --> pdb=" O GLU G 903 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LEU G 905 " --> pdb=" O SER G 861 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N SER G 861 " --> pdb=" O LEU G 905 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N GLU G 907 " --> pdb=" O ARG G 859 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N ARG G 859 " --> pdb=" O GLU G 907 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 38 through 41 removed outlier: 4.242A pdb=" N VAL C 49 " --> pdb=" O GLN C 41 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA C 116 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE C 103 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 5.624A 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: 6.452A 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 219 removed outlier: 3.651A pdb=" N ASP C 244 " --> pdb=" O GLN C 236 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ASP C 238 " --> pdb=" O ILE C 242 " (cutoff:3.500A) removed outlier: 5.591A 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 3 through 6 Processing sheet with id= T, first strand: chain 'B' and resid 95 through 99 removed outlier: 6.497A pdb=" N TRP B 122 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL B 98 " --> pdb=" O TRP B 122 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE B 124 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL B 153 " --> pdb=" O SER B 125 " (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: 3.510A pdb=" N GLN I 78 " --> pdb=" O PHE I 91 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE I 91 " --> pdb=" O GLN I 78 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ALA I 80 " --> pdb=" O PRO I 89 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'L' and resid 68 through 70 Processing sheet with id= X, first strand: chain 'L' and resid 60 through 66 removed outlier: 6.979A pdb=" N PHE L 77 " --> pdb=" O LEU L 64 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'M' and resid 65 through 72 removed outlier: 6.800A pdb=" N ILE M 77 " --> pdb=" O TRP M 71 " (cutoff:3.500A) 1837 hydrogen bonds defined for protein. 5322 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: 12.66 Time building geometry restraints manager: 15.31 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: 15885 1.42 - 1.64: 22121 1.64 - 1.86: 408 1.86 - 2.09: 0 2.09 - 2.31: 92 Bond restraints: 38506 Sorted by residual: bond pdb=" O13 3PE L 801 " pdb=" P 3PE L 801 " ideal model delta sigma weight residual 1.654 1.594 0.060 2.00e-02 2.50e+03 9.00e+00 bond pdb=" O13 3PE L 804 " pdb=" P 3PE L 804 " ideal model delta sigma weight residual 1.654 1.594 0.060 2.00e-02 2.50e+03 8.99e+00 bond pdb=" O13 3PE H 604 " pdb=" P 3PE H 604 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.77e+00 bond pdb=" O13 3PE M1202 " pdb=" P 3PE M1202 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.69e+00 bond pdb=" O13 3PE C 701 " pdb=" P 3PE C 701 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.68e+00 ... (remaining 38501 not shown) Histogram of bond angle deviations from ideal: 69.53 - 82.85: 88 82.85 - 96.17: 1 96.17 - 109.50: 3980 109.50 - 122.82: 45262 122.82 - 136.14: 2821 Bond angle restraints: 52152 Sorted by residual: angle pdb=" N THR N 64 " pdb=" CA THR N 64 " pdb=" C THR N 64 " ideal model delta sigma weight residual 109.81 95.15 14.66 2.21e+00 2.05e-01 4.40e+01 angle pdb=" CA PRO J 90 " pdb=" N PRO J 90 " pdb=" CD PRO J 90 " ideal model delta sigma weight residual 112.00 104.13 7.87 1.40e+00 5.10e-01 3.16e+01 angle pdb=" CA GLN G 310 " pdb=" CB GLN G 310 " pdb=" CG GLN G 310 " ideal model delta sigma weight residual 114.10 124.42 -10.32 2.00e+00 2.50e-01 2.66e+01 angle pdb=" CA LEU L 491 " pdb=" CB LEU L 491 " pdb=" CG LEU L 491 " ideal model delta sigma weight residual 116.30 133.87 -17.57 3.50e+00 8.16e-02 2.52e+01 angle pdb=" C MET E 26 " pdb=" N HIS E 27 " pdb=" CA HIS E 27 " ideal model delta sigma weight residual 121.94 112.35 9.59 2.00e+00 2.50e-01 2.30e+01 ... (remaining 52147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.26: 22100 35.26 - 70.53: 637 70.53 - 105.79: 32 105.79 - 141.05: 8 141.05 - 176.31: 1 Dihedral angle restraints: 22778 sinusoidal: 9328 harmonic: 13450 Sorted by residual: dihedral pdb=" CA VAL N 63 " pdb=" C VAL N 63 " pdb=" N THR N 64 " pdb=" CA THR N 64 " ideal model delta harmonic sigma weight residual 180.00 133.17 46.83 0 5.00e+00 4.00e-02 8.77e+01 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 81.28 176.31 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" CA THR N 64 " pdb=" C THR N 64 " pdb=" N PRO N 65 " pdb=" CA PRO N 65 " ideal model delta harmonic sigma weight residual 180.00 149.68 30.32 0 5.00e+00 4.00e-02 3.68e+01 ... (remaining 22775 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.236: 5762 4.236 - 8.472: 0 8.472 - 12.708: 0 12.708 - 16.943: 0 16.943 - 21.179: 28 Chirality restraints: 5790 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="FE2 SF4 B 301 " pdb=" S1 SF4 B 301 " pdb=" S3 SF4 B 301 " pdb=" S4 SF4 B 301 " 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 F 501 " pdb=" S1 SF4 F 501 " pdb=" S2 SF4 F 501 " pdb=" S3 SF4 F 501 " 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 5787 not shown) Planarity restraints: 6490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 UQ8 B 302 " -0.037 2.00e-02 2.50e+03 7.68e-02 1.77e+02 pdb=" C1M UQ8 B 302 " -0.154 2.00e-02 2.50e+03 pdb=" C2 UQ8 B 302 " 0.051 2.00e-02 2.50e+03 pdb=" C3 UQ8 B 302 " -0.010 2.00e-02 2.50e+03 pdb=" C4 UQ8 B 302 " -0.004 2.00e-02 2.50e+03 pdb=" C5 UQ8 B 302 " 0.021 2.00e-02 2.50e+03 pdb=" C6 UQ8 B 302 " 0.023 2.00e-02 2.50e+03 pdb=" C7 UQ8 B 302 " 0.030 2.00e-02 2.50e+03 pdb=" O2 UQ8 B 302 " 0.173 2.00e-02 2.50e+03 pdb=" O3 UQ8 B 302 " -0.092 2.00e-02 2.50e+03 pdb=" O4 UQ8 B 302 " -0.038 2.00e-02 2.50e+03 pdb=" O5 UQ8 B 302 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS J 89 " 0.095 5.00e-02 4.00e+02 1.39e-01 3.07e+01 pdb=" N PRO J 90 " -0.239 5.00e-02 4.00e+02 pdb=" CA PRO J 90 " 0.074 5.00e-02 4.00e+02 pdb=" CD PRO J 90 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL N 63 " -0.020 2.00e-02 2.50e+03 4.09e-02 1.67e+01 pdb=" C VAL N 63 " 0.071 2.00e-02 2.50e+03 pdb=" O VAL N 63 " -0.026 2.00e-02 2.50e+03 pdb=" N THR N 64 " -0.024 2.00e-02 2.50e+03 ... (remaining 6487 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3087 2.74 - 3.28: 36884 3.28 - 3.82: 68169 3.82 - 4.36: 82612 4.36 - 4.90: 140307 Nonbonded interactions: 331059 Sorted by model distance: nonbonded pdb=" OE1 GLU H 36 " pdb=" OH TYR H 242 " model vdw 2.203 2.440 nonbonded pdb=" OH TYR A 69 " pdb=" O SER K 74 " model vdw 2.221 2.440 nonbonded pdb=" O ILE N 386 " pdb=" OG1 THR N 389 " model vdw 2.239 2.440 nonbonded pdb=" OD2 ASP G 731 " pdb=" OG1 THR G 734 " model vdw 2.259 2.440 nonbonded pdb=" N THR N 64 " pdb=" O THR N 64 " model vdw 2.267 2.496 ... (remaining 331054 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: 0.360 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: 0.060 Extract box with map and model: 4.510 Check model and map are aligned: 0.590 Set scattering table: 0.370 Process input model: 101.580 Find NCS groups from input model: 1.320 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:10.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 38506 Z= 0.355 Angle : 0.789 17.568 52152 Z= 0.395 Chirality : 1.469 21.179 5790 Planarity : 0.006 0.139 6490 Dihedral : 15.514 176.313 14176 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.46 % Favored : 97.51 % Rotamer: Outliers : 1.30 % Allowed : 16.05 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.46 % 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: -0.49 (0.11), residues: 4668 helix: 0.29 (0.09), residues: 2705 sheet: -0.76 (0.28), residues: 312 loop : -1.12 (0.14), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP H 54 HIS 0.012 0.001 HIS E 27 PHE 0.043 0.002 PHE H 282 TYR 0.032 0.002 TYR L 428 ARG 0.026 0.001 ARG C 374 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 434 time to evaluate : 4.479 Fit side-chains REVERT: G 877 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8560 (tp30) REVERT: G 904 ASP cc_start: 0.8298 (t0) cc_final: 0.8047 (t0) REVERT: C 193 GLU cc_start: 0.5130 (OUTLIER) cc_final: 0.3984 (mp0) REVERT: C 488 MET cc_start: 0.6123 (OUTLIER) cc_final: 0.5612 (tpt) REVERT: I 27 LYS cc_start: 0.8882 (ttpt) cc_final: 0.8639 (tttp) REVERT: H 286 ARG cc_start: 0.8505 (ttt180) cc_final: 0.8295 (ttt180) REVERT: L 72 ASP cc_start: 0.8111 (t0) cc_final: 0.7841 (t0) REVERT: L 258 MET cc_start: 0.8692 (mmm) cc_final: 0.8416 (tpp) REVERT: L 490 MET cc_start: 0.8391 (ttm) cc_final: 0.8000 (ttp) REVERT: M 466 PHE cc_start: 0.8186 (m-10) cc_final: 0.7192 (p90) REVERT: N 30 TRP cc_start: 0.8773 (t-100) cc_final: 0.7798 (t60) REVERT: J 115 ASN cc_start: 0.8798 (t0) cc_final: 0.8591 (t0) outliers start: 50 outliers final: 33 residues processed: 469 average time/residue: 1.5086 time to fit residues: 859.0811 Evaluate side-chains 459 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 424 time to evaluate : 4.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 351 CYS Chi-restraints excluded: chain F residue 357 CYS Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 336 GLU Chi-restraints excluded: chain G residue 475 ASP Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 905 LEU Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 193 GLU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 489 SER Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 14 LEU Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 401 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 393 optimal weight: 6.9990 chunk 353 optimal weight: 7.9990 chunk 195 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 238 optimal weight: 8.9990 chunk 188 optimal weight: 8.9990 chunk 365 optimal weight: 0.9990 chunk 141 optimal weight: 10.0000 chunk 222 optimal weight: 20.0000 chunk 271 optimal weight: 3.9990 chunk 423 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 238 ASN F 425 GLN ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 517 ASN ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 323 GLN ** L 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.0821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.271 38506 Z= 0.792 Angle : 2.190 51.042 52152 Z= 1.438 Chirality : 0.439 6.637 5790 Planarity : 0.005 0.083 6490 Dihedral : 10.924 178.315 5923 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.49 % Favored : 97.49 % Rotamer: Outliers : 2.92 % Allowed : 14.43 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 4668 helix: 0.98 (0.10), residues: 2680 sheet: -0.85 (0.27), residues: 324 loop : -0.78 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 143 HIS 0.006 0.001 HIS N 124 PHE 0.031 0.002 PHE L 341 TYR 0.020 0.002 TYR L 428 ARG 0.010 0.001 ARG G 727 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 439 time to evaluate : 4.796 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 143 MET cc_start: 0.7966 (ttp) cc_final: 0.7681 (ttp) REVERT: E 145 ILE cc_start: 0.6986 (OUTLIER) cc_final: 0.6711 (tt) REVERT: G 56 GLN cc_start: 0.8403 (mp10) cc_final: 0.8189 (mp10) REVERT: G 85 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8295 (tp30) REVERT: G 129 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8519 (ptm-80) REVERT: G 792 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8601 (mp0) REVERT: G 877 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8278 (tp30) REVERT: G 904 ASP cc_start: 0.8236 (t0) cc_final: 0.7922 (t0) REVERT: C 193 GLU cc_start: 0.5341 (OUTLIER) cc_final: 0.4130 (mp0) REVERT: I 27 LYS cc_start: 0.9056 (ttpt) cc_final: 0.8362 (tptp) REVERT: I 83 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8780 (ptpt) REVERT: I 153 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.6927 (mtt) REVERT: H 64 MET cc_start: 0.6896 (OUTLIER) cc_final: 0.6652 (mmm) REVERT: H 122 MET cc_start: 0.8862 (mmm) cc_final: 0.8592 (mmp) REVERT: L 72 ASP cc_start: 0.8060 (t0) cc_final: 0.7790 (t0) REVERT: L 198 ARG cc_start: 0.8731 (mtm110) cc_final: 0.8467 (ttp-110) REVERT: L 258 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8480 (tpp) REVERT: L 318 TYR cc_start: 0.8371 (OUTLIER) cc_final: 0.7220 (t80) REVERT: L 490 MET cc_start: 0.8367 (ttm) cc_final: 0.8031 (ttp) REVERT: L 491 LEU cc_start: 0.8903 (mm) cc_final: 0.8688 (mm) REVERT: M 303 TRP cc_start: 0.9052 (OUTLIER) cc_final: 0.8420 (m-10) REVERT: M 466 PHE cc_start: 0.8300 (m-10) cc_final: 0.7298 (p90) REVERT: N 30 TRP cc_start: 0.8797 (t-100) cc_final: 0.7840 (t60) REVERT: N 485 MET cc_start: 0.2324 (mmt) cc_final: 0.1949 (mmp) REVERT: K 46 PHE cc_start: 0.8749 (OUTLIER) cc_final: 0.8228 (t80) REVERT: J 69 PHE cc_start: 0.8978 (OUTLIER) cc_final: 0.8774 (t80) REVERT: J 162 GLU cc_start: 0.5818 (OUTLIER) cc_final: 0.5088 (tp30) outliers start: 112 outliers final: 44 residues processed: 496 average time/residue: 1.5161 time to fit residues: 912.1447 Evaluate side-chains 482 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 425 time to evaluate : 3.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 89 CYS Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 129 ARG Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 643 SER Chi-restraints excluded: chain G residue 796 ASP Chi-restraints excluded: chain G residue 799 THR Chi-restraints excluded: chain G residue 828 GLN Chi-restraints excluded: chain G residue 905 LEU Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 193 GLU Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain I residue 83 LYS Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 64 MET Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 200 MET Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 258 MET Chi-restraints excluded: chain L residue 313 MET Chi-restraints excluded: chain L residue 318 TYR Chi-restraints excluded: chain L residue 351 SER Chi-restraints excluded: chain L residue 457 LEU Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 14 LEU Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 431 SER Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 162 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 235 optimal weight: 0.9990 chunk 131 optimal weight: 8.9990 chunk 352 optimal weight: 7.9990 chunk 288 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 423 optimal weight: 1.9990 chunk 457 optimal weight: 3.9990 chunk 377 optimal weight: 3.9990 chunk 420 optimal weight: 1.9990 chunk 144 optimal weight: 6.9990 chunk 340 optimal weight: 10.0000 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 425 GLN ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 GLN C 162 GLN ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 323 GLN ** L 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 GLN ** L 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 115 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.0889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.246 38506 Z= 0.740 Angle : 2.163 50.699 52152 Z= 1.426 Chirality : 0.441 6.397 5790 Planarity : 0.004 0.065 6490 Dihedral : 10.185 177.854 5891 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.21 % Favored : 97.77 % Rotamer: Outliers : 2.74 % Allowed : 14.93 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.78 (0.12), residues: 4668 helix: 1.44 (0.10), residues: 2656 sheet: -0.69 (0.28), residues: 319 loop : -0.67 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 143 HIS 0.006 0.001 HIS F 172 PHE 0.030 0.001 PHE L 341 TYR 0.025 0.001 TYR M 435 ARG 0.009 0.000 ARG C 374 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 444 time to evaluate : 4.184 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 103 LEU cc_start: 0.8982 (tm) cc_final: 0.8636 (mp) REVERT: E 143 MET cc_start: 0.8014 (ttp) cc_final: 0.7756 (ttp) REVERT: G 56 GLN cc_start: 0.8419 (mp10) cc_final: 0.8018 (mp10) REVERT: G 85 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8280 (tp30) REVERT: G 129 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.8287 (ptm-80) REVERT: G 215 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8512 (tm-30) REVERT: G 877 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8226 (tp30) REVERT: G 904 ASP cc_start: 0.8233 (t0) cc_final: 0.7844 (t0) REVERT: C 488 MET cc_start: 0.6433 (OUTLIER) cc_final: 0.6097 (mmp) REVERT: I 27 LYS cc_start: 0.8969 (ttpt) cc_final: 0.8309 (tptp) REVERT: I 153 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.6888 (mtt) REVERT: H 64 MET cc_start: 0.6913 (OUTLIER) cc_final: 0.6700 (mmm) REVERT: H 122 MET cc_start: 0.8778 (mmm) cc_final: 0.8463 (mmp) REVERT: L 72 ASP cc_start: 0.8123 (t0) cc_final: 0.7865 (t0) REVERT: L 139 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.8706 (ttp) REVERT: L 318 TYR cc_start: 0.8400 (OUTLIER) cc_final: 0.7228 (t80) REVERT: L 490 MET cc_start: 0.8369 (ttm) cc_final: 0.8031 (ttp) REVERT: L 491 LEU cc_start: 0.8985 (mm) cc_final: 0.8709 (mm) REVERT: M 303 TRP cc_start: 0.9021 (OUTLIER) cc_final: 0.8340 (m-10) REVERT: M 464 GLU cc_start: 0.7988 (pt0) cc_final: 0.7549 (pt0) REVERT: M 466 PHE cc_start: 0.8204 (m-10) cc_final: 0.7196 (p90) REVERT: N 30 TRP cc_start: 0.8766 (t-100) cc_final: 0.7801 (t60) REVERT: N 150 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8768 (ttmt) REVERT: N 485 MET cc_start: 0.2437 (mmt) cc_final: 0.2131 (mmp) REVERT: K 46 PHE cc_start: 0.8713 (OUTLIER) cc_final: 0.8121 (t80) REVERT: J 85 ARG cc_start: 0.7965 (mtt90) cc_final: 0.7681 (mtt90) REVERT: J 115 ASN cc_start: 0.8792 (t0) cc_final: 0.8578 (t0) outliers start: 105 outliers final: 41 residues processed: 503 average time/residue: 1.5056 time to fit residues: 922.5853 Evaluate side-chains 477 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 425 time to evaluate : 4.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 89 CYS Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 129 ARG Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 215 GLU Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 643 SER Chi-restraints excluded: chain G residue 694 ASP Chi-restraints excluded: chain G residue 796 ASP Chi-restraints excluded: chain G residue 799 THR Chi-restraints excluded: chain G residue 905 LEU Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 64 MET Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 230 SER Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 318 TYR Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain L residue 457 LEU Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 159 HIS Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 150 LYS Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 46 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 418 optimal weight: 9.9990 chunk 318 optimal weight: 9.9990 chunk 220 optimal weight: 9.9990 chunk 46 optimal weight: 20.0000 chunk 202 optimal weight: 0.9980 chunk 284 optimal weight: 10.0000 chunk 425 optimal weight: 8.9990 chunk 450 optimal weight: 9.9990 chunk 222 optimal weight: 0.0010 chunk 403 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 overall best weight: 3.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 377 GLN F 425 GLN ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 GLN C 162 GLN ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 323 GLN ** L 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 409 ASN ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.243 38506 Z= 0.762 Angle : 2.172 50.626 52152 Z= 1.429 Chirality : 0.443 6.424 5790 Planarity : 0.004 0.061 6490 Dihedral : 10.089 178.615 5878 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.49 % Favored : 97.49 % Rotamer: Outliers : 3.23 % Allowed : 14.90 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.87 (0.12), residues: 4668 helix: 1.48 (0.10), residues: 2659 sheet: -0.64 (0.28), residues: 319 loop : -0.57 (0.15), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP L 143 HIS 0.005 0.001 HIS N 124 PHE 0.028 0.002 PHE L 341 TYR 0.020 0.002 TYR L 428 ARG 0.009 0.000 ARG C 374 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 437 time to evaluate : 4.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 335 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.8401 (mmp) REVERT: E 46 GLN cc_start: 0.8250 (mm110) cc_final: 0.8017 (mm-40) REVERT: E 100 ASN cc_start: 0.8656 (m-40) cc_final: 0.8446 (m-40) REVERT: E 143 MET cc_start: 0.7976 (ttp) cc_final: 0.7740 (ttp) REVERT: G 56 GLN cc_start: 0.8452 (mp10) cc_final: 0.8080 (mp10) REVERT: G 85 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8318 (tp30) REVERT: G 215 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8675 (tm-30) REVERT: G 714 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.7715 (ptt-90) REVERT: G 877 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8285 (tp30) REVERT: G 904 ASP cc_start: 0.8328 (t0) cc_final: 0.7905 (t0) REVERT: I 1 MET cc_start: 0.6035 (pmm) cc_final: 0.5721 (pmm) REVERT: I 27 LYS cc_start: 0.9089 (ttpt) cc_final: 0.8366 (tptp) REVERT: I 153 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.6908 (mtt) REVERT: H 64 MET cc_start: 0.6927 (OUTLIER) cc_final: 0.6720 (mmm) REVERT: H 122 MET cc_start: 0.8851 (mmm) cc_final: 0.8613 (mmp) REVERT: L 72 ASP cc_start: 0.8112 (t0) cc_final: 0.7862 (t0) REVERT: L 139 MET cc_start: 0.9143 (OUTLIER) cc_final: 0.8699 (ttp) REVERT: L 198 ARG cc_start: 0.8753 (mtm110) cc_final: 0.8461 (ttp-110) REVERT: L 318 TYR cc_start: 0.8373 (OUTLIER) cc_final: 0.7221 (t80) REVERT: L 490 MET cc_start: 0.8463 (ttm) cc_final: 0.8060 (ttp) REVERT: L 491 LEU cc_start: 0.9030 (mm) cc_final: 0.8656 (mm) REVERT: M 303 TRP cc_start: 0.9017 (OUTLIER) cc_final: 0.8409 (m-10) REVERT: M 371 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8177 (mmt) REVERT: N 30 TRP cc_start: 0.8788 (t-100) cc_final: 0.7828 (t60) REVERT: N 485 MET cc_start: 0.2633 (mmt) cc_final: 0.2377 (mmp) REVERT: K 46 PHE cc_start: 0.8754 (OUTLIER) cc_final: 0.8178 (t80) REVERT: J 85 ARG cc_start: 0.8107 (mtt90) cc_final: 0.7820 (mtt90) outliers start: 124 outliers final: 60 residues processed: 510 average time/residue: 1.4950 time to fit residues: 927.3470 Evaluate side-chains 501 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 430 time to evaluate : 4.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 89 CYS Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 357 CYS Chi-restraints excluded: chain E residue 26 MET Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 129 ARG Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 215 GLU Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 593 MET Chi-restraints excluded: chain G residue 617 GLU Chi-restraints excluded: chain G residue 643 SER Chi-restraints excluded: chain G residue 694 ASP Chi-restraints excluded: chain G residue 714 ARG Chi-restraints excluded: chain G residue 796 ASP Chi-restraints excluded: chain G residue 799 THR Chi-restraints excluded: chain G residue 905 LEU Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 64 MET Chi-restraints excluded: chain H residue 273 LEU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 230 SER Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 313 MET Chi-restraints excluded: chain L residue 318 TYR Chi-restraints excluded: chain L residue 351 SER Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain L residue 457 LEU Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 159 HIS Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 14 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 431 SER Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 65 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 375 optimal weight: 9.9990 chunk 255 optimal weight: 0.7980 chunk 6 optimal weight: 30.0000 chunk 335 optimal weight: 10.0000 chunk 185 optimal weight: 5.9990 chunk 384 optimal weight: 5.9990 chunk 311 optimal weight: 10.0000 chunk 0 optimal weight: 90.0000 chunk 230 optimal weight: 5.9990 chunk 404 optimal weight: 9.9990 chunk 113 optimal weight: 6.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 425 GLN ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 598 GLN C 162 GLN ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 323 GLN ** L 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 GLN L 121 ASN N 57 GLN J 115 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.243 38506 Z= 0.792 Angle : 2.183 50.626 52152 Z= 1.433 Chirality : 0.444 6.448 5790 Planarity : 0.004 0.061 6490 Dihedral : 10.307 179.668 5878 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.46 % Favored : 97.51 % Rotamer: Outliers : 3.41 % Allowed : 14.64 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.75 (0.12), residues: 4668 helix: 1.36 (0.10), residues: 2662 sheet: -0.65 (0.28), residues: 319 loop : -0.59 (0.15), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP L 143 HIS 0.006 0.001 HIS N 124 PHE 0.030 0.002 PHE A 36 TYR 0.019 0.002 TYR L 428 ARG 0.011 0.000 ARG C 374 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 437 time to evaluate : 4.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 46 GLN cc_start: 0.8343 (mm110) cc_final: 0.8109 (mm-40) REVERT: E 143 MET cc_start: 0.7959 (ttp) cc_final: 0.7722 (ttp) REVERT: G 56 GLN cc_start: 0.8454 (mp10) cc_final: 0.8129 (mp10) REVERT: G 85 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8337 (tp30) REVERT: G 215 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.8725 (tm-30) REVERT: G 877 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8289 (tp30) REVERT: G 904 ASP cc_start: 0.8413 (t0) cc_final: 0.7968 (t0) REVERT: C 488 MET cc_start: 0.6683 (OUTLIER) cc_final: 0.6094 (mmp) REVERT: I 27 LYS cc_start: 0.9098 (ttpt) cc_final: 0.8365 (tptp) REVERT: I 153 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.6967 (mtt) REVERT: H 71 GLU cc_start: 0.8431 (tt0) cc_final: 0.8151 (tt0) REVERT: H 122 MET cc_start: 0.8856 (mmm) cc_final: 0.8652 (mmp) REVERT: L 72 ASP cc_start: 0.8115 (t0) cc_final: 0.7854 (t0) REVERT: L 139 MET cc_start: 0.9165 (OUTLIER) cc_final: 0.8714 (ttp) REVERT: L 198 ARG cc_start: 0.8755 (mtm110) cc_final: 0.8501 (ttp-110) REVERT: L 318 TYR cc_start: 0.8435 (OUTLIER) cc_final: 0.7295 (t80) REVERT: L 490 MET cc_start: 0.8516 (ttm) cc_final: 0.8081 (ttp) REVERT: L 491 LEU cc_start: 0.9035 (mm) cc_final: 0.8577 (mm) REVERT: M 303 TRP cc_start: 0.9008 (OUTLIER) cc_final: 0.8427 (m-10) REVERT: M 310 ASP cc_start: 0.9011 (t0) cc_final: 0.8770 (t0) REVERT: N 30 TRP cc_start: 0.8798 (t-100) cc_final: 0.7840 (t60) REVERT: N 485 MET cc_start: 0.2959 (mmt) cc_final: 0.2457 (mmp) REVERT: K 46 PHE cc_start: 0.8813 (OUTLIER) cc_final: 0.8245 (t80) outliers start: 131 outliers final: 72 residues processed: 515 average time/residue: 1.5524 time to fit residues: 969.7708 Evaluate side-chains 508 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 428 time to evaluate : 4.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 89 CYS Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 129 ARG Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 215 GLU Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 593 MET Chi-restraints excluded: chain G residue 617 GLU Chi-restraints excluded: chain G residue 643 SER Chi-restraints excluded: chain G residue 694 ASP Chi-restraints excluded: chain G residue 796 ASP Chi-restraints excluded: chain G residue 799 THR Chi-restraints excluded: chain G residue 828 GLN Chi-restraints excluded: chain G residue 905 LEU Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 273 LEU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 200 MET Chi-restraints excluded: chain L residue 230 SER Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 313 MET Chi-restraints excluded: chain L residue 318 TYR Chi-restraints excluded: chain L residue 351 SER Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 457 LEU Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 499 VAL Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 109 ILE Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 414 SER Chi-restraints excluded: chain M residue 425 SER Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 183 ASP Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 431 SER Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 98 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 151 optimal weight: 8.9990 chunk 405 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 264 optimal weight: 20.0000 chunk 111 optimal weight: 5.9990 chunk 450 optimal weight: 0.7980 chunk 374 optimal weight: 3.9990 chunk 208 optimal weight: 10.0000 chunk 37 optimal weight: 20.0000 chunk 149 optimal weight: 7.9990 chunk 236 optimal weight: 5.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 90 ASN F 425 GLN E 27 HIS ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 GLN ** H 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 323 GLN ** L 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 GLN ** L 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 361 GLN N 57 GLN N 317 GLN J 115 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.242 38506 Z= 0.781 Angle : 2.181 50.627 52152 Z= 1.432 Chirality : 0.443 6.419 5790 Planarity : 0.004 0.061 6490 Dihedral : 10.311 179.357 5878 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.63 % Favored : 97.34 % Rotamer: Outliers : 3.39 % Allowed : 15.29 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.78 (0.12), residues: 4668 helix: 1.39 (0.10), residues: 2659 sheet: -0.62 (0.28), residues: 320 loop : -0.58 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP L 143 HIS 0.005 0.001 HIS N 124 PHE 0.029 0.002 PHE L 341 TYR 0.019 0.002 TYR L 428 ARG 0.011 0.000 ARG C 374 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 444 time to evaluate : 4.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 291 GLN cc_start: 0.7643 (tt0) cc_final: 0.7403 (tt0) REVERT: E 46 GLN cc_start: 0.8354 (mm110) cc_final: 0.8143 (mm-40) REVERT: E 143 MET cc_start: 0.7964 (ttp) cc_final: 0.7729 (ttp) REVERT: G 56 GLN cc_start: 0.8400 (mp10) cc_final: 0.8050 (mp10) REVERT: G 85 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8317 (tp30) REVERT: G 215 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.8729 (tm-30) REVERT: G 714 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.7705 (ptt-90) REVERT: G 904 ASP cc_start: 0.8452 (t0) cc_final: 0.7986 (t0) REVERT: C 190 GLN cc_start: 0.7697 (mt0) cc_final: 0.7275 (mm-40) REVERT: I 27 LYS cc_start: 0.9079 (ttpt) cc_final: 0.8383 (tptp) REVERT: I 153 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.7016 (mtt) REVERT: H 71 GLU cc_start: 0.8422 (tt0) cc_final: 0.8153 (tt0) REVERT: A 64 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8155 (mm) REVERT: L 72 ASP cc_start: 0.8122 (t0) cc_final: 0.7860 (t0) REVERT: L 139 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.8735 (ttp) REVERT: L 318 TYR cc_start: 0.8422 (OUTLIER) cc_final: 0.7286 (t80) REVERT: L 490 MET cc_start: 0.8530 (ttm) cc_final: 0.8090 (ttp) REVERT: L 491 LEU cc_start: 0.9066 (mm) cc_final: 0.8545 (mm) REVERT: M 303 TRP cc_start: 0.8979 (OUTLIER) cc_final: 0.8422 (m-10) REVERT: M 310 ASP cc_start: 0.8997 (t0) cc_final: 0.8762 (t0) REVERT: M 466 PHE cc_start: 0.8403 (OUTLIER) cc_final: 0.7326 (p90) REVERT: N 30 TRP cc_start: 0.8788 (t-100) cc_final: 0.7828 (t60) REVERT: N 485 MET cc_start: 0.2985 (mmt) cc_final: 0.2481 (mmp) REVERT: K 46 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.8239 (t80) REVERT: J 89 LYS cc_start: 0.8569 (mttm) cc_final: 0.8315 (mttm) outliers start: 130 outliers final: 77 residues processed: 523 average time/residue: 1.5329 time to fit residues: 973.3199 Evaluate side-chains 510 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 423 time to evaluate : 4.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 89 CYS Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 129 ARG Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 215 GLU Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 593 MET Chi-restraints excluded: chain G residue 617 GLU Chi-restraints excluded: chain G residue 643 SER Chi-restraints excluded: chain G residue 694 ASP Chi-restraints excluded: chain G residue 714 ARG Chi-restraints excluded: chain G residue 721 ILE Chi-restraints excluded: chain G residue 796 ASP Chi-restraints excluded: chain G residue 799 THR Chi-restraints excluded: chain G residue 828 GLN Chi-restraints excluded: chain G residue 905 LEU Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 273 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 230 SER Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 313 MET Chi-restraints excluded: chain L residue 318 TYR Chi-restraints excluded: chain L residue 351 SER Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 415 MET Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain L residue 499 VAL Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 109 ILE Chi-restraints excluded: chain M residue 159 HIS Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 414 SER Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 466 PHE Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 14 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 431 SER Chi-restraints excluded: chain N residue 462 LEU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 65 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 434 optimal weight: 3.9990 chunk 50 optimal weight: 40.0000 chunk 256 optimal weight: 20.0000 chunk 329 optimal weight: 1.9990 chunk 255 optimal weight: 4.9990 chunk 379 optimal weight: 9.9990 chunk 251 optimal weight: 0.9980 chunk 449 optimal weight: 10.0000 chunk 281 optimal weight: 0.9990 chunk 273 optimal weight: 2.9990 chunk 207 optimal weight: 20.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 425 GLN E 27 HIS G 283 GLN ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 GLN H 323 GLN ** L 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 GLN ** L 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 57 GLN N 317 GLN J 115 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.244 38506 Z= 0.745 Angle : 2.171 50.639 52152 Z= 1.428 Chirality : 0.441 6.373 5790 Planarity : 0.004 0.058 6490 Dihedral : 10.023 179.759 5878 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.42 % Favored : 97.56 % Rotamer: Outliers : 2.74 % Allowed : 16.28 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.02 (0.12), residues: 4668 helix: 1.61 (0.10), residues: 2657 sheet: -0.53 (0.28), residues: 320 loop : -0.53 (0.15), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP L 143 HIS 0.004 0.001 HIS N 124 PHE 0.029 0.001 PHE L 341 TYR 0.024 0.001 TYR M 435 ARG 0.013 0.000 ARG C 374 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 434 time to evaluate : 4.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 291 GLN cc_start: 0.7724 (tt0) cc_final: 0.7239 (tt0) REVERT: E 46 GLN cc_start: 0.8333 (mm110) cc_final: 0.8126 (mm-40) REVERT: E 143 MET cc_start: 0.7974 (ttp) cc_final: 0.7733 (ttp) REVERT: G 56 GLN cc_start: 0.8411 (mp10) cc_final: 0.8051 (mp10) REVERT: G 85 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8279 (tp30) REVERT: G 129 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8496 (ptm-80) REVERT: G 215 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8600 (tm-30) REVERT: G 478 GLU cc_start: 0.7106 (tm-30) cc_final: 0.6888 (tm-30) REVERT: G 714 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.8091 (ptp-110) REVERT: G 904 ASP cc_start: 0.8473 (t0) cc_final: 0.7980 (t0) REVERT: C 190 GLN cc_start: 0.7704 (mt0) cc_final: 0.7285 (mm-40) REVERT: C 488 MET cc_start: 0.6601 (OUTLIER) cc_final: 0.6018 (mmp) REVERT: I 27 LYS cc_start: 0.9084 (ttpt) cc_final: 0.8371 (tptp) REVERT: I 153 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.6980 (mtt) REVERT: H 71 GLU cc_start: 0.8413 (tt0) cc_final: 0.8148 (tt0) REVERT: H 281 MET cc_start: 0.9028 (mmm) cc_final: 0.8812 (mmm) REVERT: A 64 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8107 (mm) REVERT: L 72 ASP cc_start: 0.8153 (t0) cc_final: 0.7910 (t0) REVERT: L 139 MET cc_start: 0.9107 (OUTLIER) cc_final: 0.8720 (ttp) REVERT: L 198 ARG cc_start: 0.8666 (mtm110) cc_final: 0.8406 (ttp-110) REVERT: L 318 TYR cc_start: 0.8387 (OUTLIER) cc_final: 0.7259 (t80) REVERT: L 491 LEU cc_start: 0.9095 (mm) cc_final: 0.8666 (mm) REVERT: M 303 TRP cc_start: 0.8986 (OUTLIER) cc_final: 0.8395 (m-10) REVERT: M 310 ASP cc_start: 0.8867 (t0) cc_final: 0.8652 (t0) REVERT: M 466 PHE cc_start: 0.8363 (OUTLIER) cc_final: 0.7291 (p90) REVERT: N 30 TRP cc_start: 0.8758 (t-100) cc_final: 0.7753 (t60) REVERT: N 31 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8391 (ttp-110) REVERT: N 485 MET cc_start: 0.2833 (mmt) cc_final: 0.2333 (mmp) REVERT: K 46 PHE cc_start: 0.8816 (OUTLIER) cc_final: 0.8245 (t80) outliers start: 105 outliers final: 60 residues processed: 498 average time/residue: 1.5562 time to fit residues: 940.9615 Evaluate side-chains 494 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 421 time to evaluate : 4.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain E residue 29 TYR Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 129 ARG Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 215 GLU Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 531 ILE Chi-restraints excluded: chain G residue 617 GLU Chi-restraints excluded: chain G residue 643 SER Chi-restraints excluded: chain G residue 694 ASP Chi-restraints excluded: chain G residue 714 ARG Chi-restraints excluded: chain G residue 796 ASP Chi-restraints excluded: chain G residue 799 THR Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 905 LEU Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 273 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 230 SER Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 318 TYR Chi-restraints excluded: chain L residue 351 SER Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 109 ILE Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 414 SER Chi-restraints excluded: chain M residue 425 SER Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 466 PHE Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 14 LEU Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 431 SER Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 65 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 277 optimal weight: 10.0000 chunk 179 optimal weight: 5.9990 chunk 268 optimal weight: 6.9990 chunk 135 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 285 optimal weight: 1.9990 chunk 306 optimal weight: 10.0000 chunk 222 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 353 optimal weight: 6.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 425 GLN E 27 HIS E 106 GLN ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 HIS ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 175 ASN H 323 GLN ** L 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 GLN ** L 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 57 GLN N 317 GLN J 115 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.243 38506 Z= 0.770 Angle : 2.180 50.663 52152 Z= 1.432 Chirality : 0.443 6.419 5790 Planarity : 0.004 0.060 6490 Dihedral : 10.129 179.925 5878 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.66 % Favored : 97.32 % Rotamer: Outliers : 3.00 % Allowed : 15.92 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.93 (0.12), residues: 4668 helix: 1.52 (0.10), residues: 2661 sheet: -0.55 (0.28), residues: 320 loop : -0.52 (0.15), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 143 HIS 0.005 0.001 HIS C 78 PHE 0.029 0.002 PHE L 341 TYR 0.020 0.002 TYR L 428 ARG 0.013 0.000 ARG C 374 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 428 time to evaluate : 4.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 143 MET cc_start: 0.7976 (ttp) cc_final: 0.7739 (ttp) REVERT: G 56 GLN cc_start: 0.8434 (mp10) cc_final: 0.8060 (mp10) REVERT: G 85 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8308 (tp30) REVERT: G 215 GLU cc_start: 0.8963 (OUTLIER) cc_final: 0.8698 (tm-30) REVERT: G 714 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7741 (ptt-90) REVERT: G 806 GLN cc_start: 0.9140 (OUTLIER) cc_final: 0.8892 (mp10) REVERT: G 904 ASP cc_start: 0.8505 (t0) cc_final: 0.8015 (t0) REVERT: C 190 GLN cc_start: 0.7700 (mt0) cc_final: 0.7353 (mm-40) REVERT: C 488 MET cc_start: 0.6697 (OUTLIER) cc_final: 0.5946 (tpt) REVERT: I 27 LYS cc_start: 0.9090 (ttpt) cc_final: 0.8374 (tptp) REVERT: I 153 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.7007 (mtt) REVERT: H 71 GLU cc_start: 0.8429 (tt0) cc_final: 0.8176 (tt0) REVERT: A 64 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8117 (mm) REVERT: L 72 ASP cc_start: 0.8161 (t0) cc_final: 0.7910 (t0) REVERT: L 139 MET cc_start: 0.9140 (OUTLIER) cc_final: 0.8716 (ttp) REVERT: L 198 ARG cc_start: 0.8684 (mtm110) cc_final: 0.8444 (ttp-110) REVERT: L 318 TYR cc_start: 0.8415 (OUTLIER) cc_final: 0.7266 (t80) REVERT: L 491 LEU cc_start: 0.9116 (mm) cc_final: 0.8669 (mm) REVERT: M 303 TRP cc_start: 0.8989 (OUTLIER) cc_final: 0.8398 (m-10) REVERT: M 310 ASP cc_start: 0.8934 (t0) cc_final: 0.8708 (t0) REVERT: M 466 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.7331 (p90) REVERT: N 30 TRP cc_start: 0.8777 (t-100) cc_final: 0.7773 (t60) REVERT: N 31 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.8408 (ttp-110) REVERT: N 485 MET cc_start: 0.2865 (mmt) cc_final: 0.2367 (mmp) REVERT: K 1 MET cc_start: 0.7175 (OUTLIER) cc_final: 0.6854 (pmm) REVERT: K 46 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.8258 (t80) outliers start: 115 outliers final: 77 residues processed: 501 average time/residue: 1.5424 time to fit residues: 932.2309 Evaluate side-chains 516 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 425 time to evaluate : 4.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain E residue 29 TYR Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 129 ARG Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 215 GLU Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 593 MET Chi-restraints excluded: chain G residue 617 GLU Chi-restraints excluded: chain G residue 643 SER Chi-restraints excluded: chain G residue 694 ASP Chi-restraints excluded: chain G residue 714 ARG Chi-restraints excluded: chain G residue 796 ASP Chi-restraints excluded: chain G residue 799 THR Chi-restraints excluded: chain G residue 806 GLN Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 905 LEU Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 273 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 230 SER Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 313 MET Chi-restraints excluded: chain L residue 318 TYR Chi-restraints excluded: chain L residue 351 SER Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain L residue 415 MET Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain L residue 457 LEU Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 499 VAL Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 109 ILE Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 414 SER Chi-restraints excluded: chain M residue 425 SER Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 466 PHE Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 14 LEU Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 183 ASP Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 431 SER Chi-restraints excluded: chain N residue 462 LEU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 65 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 408 optimal weight: 4.9990 chunk 430 optimal weight: 2.9990 chunk 392 optimal weight: 9.9990 chunk 418 optimal weight: 9.9990 chunk 251 optimal weight: 3.9990 chunk 182 optimal weight: 0.8980 chunk 328 optimal weight: 10.0000 chunk 128 optimal weight: 7.9990 chunk 378 optimal weight: 5.9990 chunk 395 optimal weight: 7.9990 chunk 417 optimal weight: 0.8980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 425 GLN E 27 HIS E 46 GLN ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 808 GLN ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 323 GLN ** L 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 57 GLN N 317 GLN J 115 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.244 38506 Z= 0.751 Angle : 2.176 50.645 52152 Z= 1.430 Chirality : 0.442 6.389 5790 Planarity : 0.004 0.059 6490 Dihedral : 10.024 179.844 5878 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.53 % Favored : 97.45 % Rotamer: Outliers : 2.74 % Allowed : 16.33 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.03 (0.12), residues: 4668 helix: 1.60 (0.10), residues: 2656 sheet: -0.47 (0.28), residues: 320 loop : -0.50 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP L 143 HIS 0.004 0.001 HIS N 124 PHE 0.029 0.001 PHE L 341 TYR 0.022 0.001 TYR M 435 ARG 0.014 0.000 ARG C 374 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 431 time to evaluate : 4.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 291 GLN cc_start: 0.7685 (tt0) cc_final: 0.7384 (tt0) REVERT: E 24 HIS cc_start: 0.8567 (t70) cc_final: 0.8184 (t-90) REVERT: E 46 GLN cc_start: 0.8091 (mm110) cc_final: 0.7756 (mm110) REVERT: E 143 MET cc_start: 0.7974 (ttp) cc_final: 0.7772 (ttp) REVERT: G 56 GLN cc_start: 0.8334 (mp10) cc_final: 0.7882 (mp10) REVERT: G 85 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8285 (tp30) REVERT: G 215 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8627 (tm-30) REVERT: G 714 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.8011 (ptp-110) REVERT: G 904 ASP cc_start: 0.8518 (t0) cc_final: 0.8005 (t0) REVERT: C 190 GLN cc_start: 0.7706 (mt0) cc_final: 0.7376 (mm-40) REVERT: C 488 MET cc_start: 0.6645 (OUTLIER) cc_final: 0.6219 (tpt) REVERT: I 27 LYS cc_start: 0.9088 (ttpt) cc_final: 0.8380 (tptp) REVERT: I 153 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.6986 (mtt) REVERT: H 71 GLU cc_start: 0.8414 (tt0) cc_final: 0.8150 (tt0) REVERT: A 64 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8094 (mm) REVERT: L 72 ASP cc_start: 0.8252 (t0) cc_final: 0.8005 (t0) REVERT: L 139 MET cc_start: 0.9110 (OUTLIER) cc_final: 0.8708 (ttp) REVERT: L 198 ARG cc_start: 0.8654 (mtm110) cc_final: 0.8409 (ttp-110) REVERT: L 318 TYR cc_start: 0.8399 (OUTLIER) cc_final: 0.7261 (t80) REVERT: L 344 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8640 (tt) REVERT: L 491 LEU cc_start: 0.9128 (mm) cc_final: 0.8652 (mm) REVERT: M 303 TRP cc_start: 0.8986 (OUTLIER) cc_final: 0.8407 (m-10) REVERT: M 310 ASP cc_start: 0.8886 (t0) cc_final: 0.8680 (t0) REVERT: M 466 PHE cc_start: 0.8348 (OUTLIER) cc_final: 0.7294 (p90) REVERT: N 30 TRP cc_start: 0.8759 (t-100) cc_final: 0.7766 (t60) REVERT: N 31 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.8399 (ttp-110) REVERT: N 485 MET cc_start: 0.2790 (mmt) cc_final: 0.2329 (mmp) REVERT: K 1 MET cc_start: 0.7134 (OUTLIER) cc_final: 0.6876 (pmm) REVERT: K 46 PHE cc_start: 0.8831 (OUTLIER) cc_final: 0.8272 (t80) outliers start: 105 outliers final: 72 residues processed: 498 average time/residue: 1.5712 time to fit residues: 945.9906 Evaluate side-chains 511 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 425 time to evaluate : 4.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain E residue 29 TYR Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 129 ARG Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 215 GLU Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 617 GLU Chi-restraints excluded: chain G residue 643 SER Chi-restraints excluded: chain G residue 714 ARG Chi-restraints excluded: chain G residue 796 ASP Chi-restraints excluded: chain G residue 799 THR Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 905 LEU Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 84 ASP Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 273 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 230 SER Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 318 TYR Chi-restraints excluded: chain L residue 344 LEU Chi-restraints excluded: chain L residue 351 SER Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain L residue 481 GLN Chi-restraints excluded: chain L residue 499 VAL Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 109 ILE Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 414 SER Chi-restraints excluded: chain M residue 425 SER Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 466 PHE Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 14 LEU Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 431 SER Chi-restraints excluded: chain N residue 462 LEU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 65 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 274 optimal weight: 0.0170 chunk 442 optimal weight: 10.0000 chunk 270 optimal weight: 0.9980 chunk 209 optimal weight: 9.9990 chunk 307 optimal weight: 0.0020 chunk 464 optimal weight: 0.9990 chunk 427 optimal weight: 6.9990 chunk 369 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 chunk 285 optimal weight: 1.9990 chunk 226 optimal weight: 0.9980 overall best weight: 0.6028 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 425 GLN E 27 HIS ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 323 GLN ** L 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 206 ASN N 57 GLN N 317 GLN J 115 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.247 38506 Z= 0.738 Angle : 2.168 50.655 52152 Z= 1.427 Chirality : 0.440 6.356 5790 Planarity : 0.004 0.060 6490 Dihedral : 9.550 178.465 5878 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.93 % Allowed : 17.27 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.28 (0.13), residues: 4668 helix: 1.83 (0.10), residues: 2645 sheet: -0.32 (0.29), residues: 324 loop : -0.44 (0.15), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP H 260 HIS 0.003 0.000 HIS L 338 PHE 0.029 0.001 PHE L 341 TYR 0.031 0.001 TYR M 435 ARG 0.016 0.000 ARG G 727 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 450 time to evaluate : 4.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 291 GLN cc_start: 0.7755 (tt0) cc_final: 0.7505 (tt0) REVERT: E 26 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8688 (ttp) REVERT: E 143 MET cc_start: 0.7952 (ttp) cc_final: 0.7716 (ttp) REVERT: G 56 GLN cc_start: 0.8443 (mp10) cc_final: 0.8004 (mp10) REVERT: G 85 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8274 (tp30) REVERT: G 129 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.8333 (ptm-80) REVERT: G 215 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8502 (tm-30) REVERT: G 904 ASP cc_start: 0.8504 (t0) cc_final: 0.8000 (t0) REVERT: C 190 GLN cc_start: 0.7709 (mt0) cc_final: 0.7344 (mm-40) REVERT: C 317 ASN cc_start: 0.9035 (t0) cc_final: 0.8745 (t0) REVERT: I 27 LYS cc_start: 0.9063 (ttpt) cc_final: 0.8362 (tptp) REVERT: I 153 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.6930 (mtt) REVERT: H 71 GLU cc_start: 0.8393 (tt0) cc_final: 0.8124 (tt0) REVERT: A 64 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8039 (mm) REVERT: L 72 ASP cc_start: 0.8280 (t0) cc_final: 0.8039 (t0) REVERT: L 198 ARG cc_start: 0.8587 (mtm110) cc_final: 0.8350 (ttp-110) REVERT: L 318 TYR cc_start: 0.8395 (OUTLIER) cc_final: 0.7239 (t80) REVERT: L 490 MET cc_start: 0.8548 (ttm) cc_final: 0.8154 (ttp) REVERT: L 491 LEU cc_start: 0.9120 (mm) cc_final: 0.8487 (mm) REVERT: L 529 ARG cc_start: 0.8400 (ttm170) cc_final: 0.8195 (ttm170) REVERT: M 303 TRP cc_start: 0.8954 (OUTLIER) cc_final: 0.8247 (m-10) REVERT: M 466 PHE cc_start: 0.8242 (OUTLIER) cc_final: 0.7187 (p90) REVERT: N 30 TRP cc_start: 0.8706 (t-100) cc_final: 0.7749 (t60) REVERT: N 485 MET cc_start: 0.2704 (mmt) cc_final: 0.2199 (mmp) REVERT: K 46 PHE cc_start: 0.8776 (OUTLIER) cc_final: 0.8184 (t80) REVERT: K 87 ARG cc_start: 0.8787 (ptp-110) cc_final: 0.8322 (mtp-110) REVERT: J 162 GLU cc_start: 0.6987 (tm-30) cc_final: 0.6680 (tm-30) outliers start: 74 outliers final: 36 residues processed: 497 average time/residue: 1.5628 time to fit residues: 941.4388 Evaluate side-chains 476 residues out of total 3851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 430 time to evaluate : 3.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain E residue 26 MET Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 129 ARG Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 215 GLU Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 796 ASP Chi-restraints excluded: chain G residue 799 THR Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 905 LEU Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain L residue 230 SER Chi-restraints excluded: chain L residue 258 MET Chi-restraints excluded: chain L residue 318 TYR Chi-restraints excluded: chain L residue 351 SER Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain L residue 499 VAL Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 466 PHE Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 14 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 431 SER Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 65 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 293 optimal weight: 4.9990 chunk 393 optimal weight: 0.9990 chunk 113 optimal weight: 9.9990 chunk 340 optimal weight: 9.9990 chunk 54 optimal weight: 40.0000 chunk 102 optimal weight: 7.9990 chunk 370 optimal weight: 0.9980 chunk 154 optimal weight: 10.0000 chunk 380 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 chunk 68 optimal weight: 9.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 425 GLN E 27 HIS E 46 GLN G 218 ASN G 283 GLN ** G 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 323 GLN ** L 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 GLN ** L 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 206 ASN N 57 GLN J 115 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.092405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.068077 restraints weight = 55857.335| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 1.58 r_work: 0.2823 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.242 38506 Z= 0.783 Angle : 2.190 50.664 52152 Z= 1.434 Chirality : 0.444 6.582 5790 Planarity : 0.004 0.086 6490 Dihedral : 9.887 179.526 5875 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.70 % Favored : 97.28 % Rotamer: Outliers : 1.88 % Allowed : 17.69 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.04 (0.12), residues: 4668 helix: 1.58 (0.10), residues: 2656 sheet: -0.39 (0.28), residues: 323 loop : -0.46 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 54 HIS 0.005 0.001 HIS N 124 PHE 0.029 0.002 PHE L 341 TYR 0.020 0.002 TYR L 428 ARG 0.021 0.001 ARG G 727 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14430.66 seconds wall clock time: 257 minutes 15.24 seconds (15435.24 seconds total)