Starting phenix.real_space_refine on Fri Feb 23 09:18:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p63_13216/02_2024/7p63_13216_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p63_13216/02_2024/7p63_13216.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p63_13216/02_2024/7p63_13216.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p63_13216/02_2024/7p63_13216.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p63_13216/02_2024/7p63_13216_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p63_13216/02_2024/7p63_13216_updated.pdb" } resolution = 3.4 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= 0.002 sd= 0.009 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 11 5.49 5 S 267 5.16 5 C 24556 2.51 5 N 6265 2.21 5 O 6638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 298": "OD1" <-> "OD2" Residue "G ASP 19": "OD1" <-> "OD2" Residue "G GLU 84": "OE1" <-> "OE2" Residue "G ASP 266": "OD1" <-> "OD2" Residue "G PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 437": "OD1" <-> "OD2" Residue "G ASP 468": "OD1" <-> "OD2" Residue "G GLU 480": "OE1" <-> "OE2" Residue "G ASP 486": "OD1" <-> "OD2" Residue "G ASP 528": "OD1" <-> "OD2" Residue "G GLU 684": "OE1" <-> "OE2" Residue "G TYR 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 862": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 19": "OD1" <-> "OD2" Residue "C GLU 28": "OE1" <-> "OE2" Residue "C ASP 110": "OD1" <-> "OD2" Residue "C ASP 121": "OD1" <-> "OD2" Residue "C TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 348": "OD1" <-> "OD2" Residue "C TYR 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 119": "OE1" <-> "OE2" Residue "B TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 29": "OE1" <-> "OE2" Residue "I ASP 53": "OD1" <-> "OD2" Residue "I PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 136": "OD1" <-> "OD2" Residue "I ASP 162": "OD1" <-> "OD2" Residue "H TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 216": "OE1" <-> "OE2" Residue "H GLU 228": "OE1" <-> "OE2" Residue "A GLU 51": "OE1" <-> "OE2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 79": "OD1" <-> "OD2" Residue "L TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 144": "OE1" <-> "OE2" Residue "L ASP 160": "OD1" <-> "OD2" Residue "L TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 202": "OE1" <-> "OE2" Residue "L ASP 400": "OD1" <-> "OD2" Residue "L ASP 546": "OD1" <-> "OD2" Residue "M PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 144": "OE1" <-> "OE2" Residue "M PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 258": "OD1" <-> "OD2" Residue "M TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 487": "OD1" <-> "OD2" Residue "N PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 154": "OE1" <-> "OE2" Residue "N ASP 183": "OD1" <-> "OD2" Residue "N PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 267": "OE1" <-> "OE2" Residue "N TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 82": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 37770 Number of models: 1 Model: "" Number of chains: 25 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: 7012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7012 Classifications: {'peptide': 905} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 41, 'TRANS': 863} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 4762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4762 Classifications: {'peptide': 589} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 551} Chain: "B" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1672 Classifications: {'peptide': 210} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 195} 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: 2534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2534 Classifications: {'peptide': 322} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 306} Chain: "A" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1021 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain: "L" Number of atoms: 4560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4560 Classifications: {'peptide': 598} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 579} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 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: 3614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3614 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 457} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 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: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1226 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 29 Unusual residues: {' CA': 1, 'FES': 1, 'SF4': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'DCQ': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'LFA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 158 Unusual residues: {'3PE': 3, 'LFA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "M" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 94 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "N" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {'LFA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "J" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 24 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2721 SG CYS F 354 77.428 60.861 190.533 1.00 38.66 S ATOM 2741 SG CYS F 357 81.028 60.754 195.126 1.00 32.68 S ATOM 3062 SG CYS F 398 75.234 57.498 195.785 1.00 49.01 S ATOM 2697 SG CYS F 351 79.655 54.746 192.305 1.00 14.69 S ATOM 4054 SG CYS E 92 88.332 53.081 211.981 1.00 40.80 S ATOM 4088 SG CYS E 97 88.392 54.133 215.354 1.00 51.52 S ATOM 4366 SG CYS E 133 83.036 52.387 211.654 1.00 48.16 S ATOM 4392 SG CYS E 137 82.235 53.337 214.766 1.00 36.95 S ATOM 5472 SG CYS G 114 88.001 66.538 173.122 1.00 26.39 S ATOM 5412 SG CYS G 105 93.248 70.238 174.726 1.00 16.65 S ATOM 5432 SG CYS G 108 93.993 64.332 172.243 1.00 16.90 S ATOM 5826 SG CYS G 156 82.131 58.743 178.191 1.00 30.27 S ATOM 5807 SG CYS G 153 88.021 57.966 181.170 1.00 34.08 S ATOM 5855 SG CYS G 159 85.334 53.065 177.907 1.00 27.41 S ATOM 6199 SG CYS G 203 87.292 58.178 174.581 1.00 0.00 S ATOM 6424 SG CYS G 230 84.031 49.265 153.699 1.00 18.83 S ATOM 6709 SG CYS G 265 84.039 45.690 159.249 1.00 10.53 S ATOM 6472 SG CYS G 237 78.676 48.838 156.794 1.00 6.87 S ATOM 6448 SG CYS G 233 81.077 43.449 154.001 1.00 7.38 S ATOM 4877 SG CYS G 36 75.768 59.907 180.661 1.00 22.33 S ATOM 4953 SG CYS G 47 77.301 63.368 181.025 1.00 40.49 S ATOM 4979 SG CYS G 50 71.515 64.856 181.191 1.00 41.74 S ATOM 5124 SG CYS G 69 71.035 61.296 180.735 1.00 24.92 S ATOM 17351 SG CYS B 129 98.011 93.016 148.307 1.00 35.33 S ATOM 16848 SG CYS B 64 103.168 96.969 149.639 1.00 22.01 S ATOM 16842 SG CYS B 63 97.648 98.958 151.686 1.00 43.29 S ATOM 17568 SG CYS B 158 100.083 93.363 154.107 1.00 43.27 S ATOM 18899 SG CYS I 102 98.668 87.668 160.368 1.00 24.52 S ATOM 18874 SG CYS I 99 104.041 86.285 156.584 1.00 25.84 S ATOM 18917 SG CYS I 105 102.933 83.127 162.048 1.00 32.02 S ATOM 18632 SG CYS I 70 98.825 82.315 156.980 1.00 6.84 S ATOM 18946 SG CYS I 109 103.855 77.746 168.490 1.00 34.59 S ATOM 18609 SG CYS I 66 101.786 76.837 162.391 1.00 17.88 S ATOM 18569 SG CYS I 60 105.825 72.572 164.905 1.00 42.18 S ATOM 18587 SG CYS I 63 99.593 73.196 167.326 1.00 11.44 S Time building chain proxies: 19.99, per 1000 atoms: 0.53 Number of scatterers: 37770 At special positions: 0 Unit cell: (161.12, 217.3, 242.74, 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 267 16.00 P 11 15.00 O 6638 8.00 N 6265 7.00 C 24556 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: 15.16 Conformation dependent library (CDL) restraints added in 7.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 137 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 97 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 133 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 92 " pdb=" FES G1004 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 50 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 47 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 36 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 69 " 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="FE4 SF4 G1002 " - pdb=" SG CYS G 203 " pdb="FE2 SF4 G1002 " - pdb=" SG CYS G 153 " pdb="FE1 SF4 G1002 " - pdb=" SG CYS G 156 " pdb=" SF4 G1003 " pdb="FE4 SF4 G1003 " - pdb=" SG CYS G 233 " pdb="FE3 SF4 G1003 " - pdb=" SG CYS G 237 " pdb="FE1 SF4 G1003 " - pdb=" SG CYS G 230 " pdb="FE2 SF4 G1003 " - pdb=" SG CYS G 265 " pdb=" SF4 I 201 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 105 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 70 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 99 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 102 " pdb=" SF4 I 202 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 66 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 60 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 63 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 109 " Number of angles added : 93 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8718 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 189 helices and 26 sheets defined 53.5% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.66 Creating SS restraints... Processing helix chain 'F' and resid 26 through 31 Processing helix chain 'F' and resid 36 through 44 Processing helix chain 'F' and resid 47 through 57 Processing helix chain 'F' and resid 69 through 75 Processing helix chain 'F' and resid 100 through 106 Processing helix chain 'F' and resid 109 through 122 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 231 Proline residue: F 226 - end of helix Processing helix chain 'F' and resid 233 through 238 Processing helix chain 'F' and resid 270 through 275 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 311 through 316 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 380 through 390 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: 4.054A pdb=" N GLY F 422 " --> pdb=" O GLU F 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 28 removed outlier: 3.655A pdb=" N HIS E 28 " --> pdb=" O HIS E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 47 removed outlier: 3.531A pdb=" N ALA E 35 " --> pdb=" O PRO E 32 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE E 37 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU E 38 " --> pdb=" O ALA E 35 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG E 47 " --> pdb=" O GLN E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 62 removed outlier: 4.021A 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 137 through 139 No H-bonds generated for 'chain 'E' and resid 137 through 139' Processing helix chain 'E' and resid 155 through 164 Proline residue: E 159 - end of helix removed outlier: 3.552A pdb=" N LEU E 162 " --> pdb=" O PRO E 159 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU E 163 " --> pdb=" O GLU E 160 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG E 164 " --> pdb=" O LEU E 161 " (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 115 through 122 Processing helix chain 'G' and resid 150 through 152 No H-bonds generated for 'chain 'G' and resid 150 through 152' Processing helix chain 'G' and resid 158 through 165 Processing helix chain 'G' and resid 196 through 202 removed outlier: 3.737A pdb=" N ILE G 202 " --> pdb=" O LEU G 199 " (cutoff:3.500A) 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 368 through 373 removed outlier: 4.157A pdb=" N GLU G 372 " --> pdb=" O LEU G 368 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N SER G 373 " --> pdb=" O ARG G 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 368 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: 4.422A pdb=" N LYS G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ALA G 403 " --> pdb=" O VAL G 399 " (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 493 Processing helix chain 'G' and resid 504 through 506 No H-bonds generated for 'chain 'G' and resid 504 through 506' Processing helix chain 'G' and resid 510 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 604 removed outlier: 4.112A pdb=" N GLU G 604 " --> pdb=" O ALA G 601 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 601 through 604' Processing helix chain 'G' and resid 650 through 663 Processing helix chain 'G' and resid 671 through 681 Processing helix chain 'G' and resid 683 through 689 removed outlier: 5.322A pdb=" N GLY G 687 " --> pdb=" O GLU G 684 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE G 688 " --> pdb=" O LEU G 685 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS G 689 " --> pdb=" O ALA G 686 " (cutoff:3.500A) Processing helix chain 'G' and resid 764 through 770 Processing helix chain 'G' and resid 827 through 829 No H-bonds generated for 'chain 'G' and resid 827 through 829' 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: 4.725A pdb=" N LEU C 58 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 145 removed outlier: 3.742A pdb=" N ASN C 135 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N TRP C 136 " --> pdb=" O ASN C 133 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU C 144 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE C 145 " --> pdb=" O TRP C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'C' and resid 201 through 204 removed outlier: 3.505A pdb=" N TRP C 204 " --> pdb=" O PRO C 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 201 through 204' 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 431 Processing helix chain 'C' and resid 438 through 441 No H-bonds generated for 'chain 'C' and resid 438 through 441' Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 463 through 486 Processing helix chain 'C' and resid 505 through 510 Processing helix chain 'C' and resid 512 through 523 Processing helix chain 'C' and resid 564 through 576 Proline residue: C 573 - end of helix Processing helix chain 'C' and resid 581 through 589 Processing helix chain 'C' and resid 595 through 599 Processing helix chain 'B' and resid 39 through 51 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: 3.552A pdb=" N LYS B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 208 removed outlier: 4.541A pdb=" N GLY B 206 " --> pdb=" O GLU B 202 " (cutoff:3.500A) removed outlier: 4.960A 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 107 No H-bonds generated for 'chain 'I' and resid 104 through 107' Processing helix chain 'I' and resid 134 through 137 No H-bonds generated for 'chain 'I' and resid 134 through 137' 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 69 Processing helix chain 'H' and resid 80 through 100 Proline residue: H 87 - end of helix removed outlier: 4.721A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU H 95 " --> pdb=" O PHE H 91 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 136 removed outlier: 4.491A pdb=" N TYR H 128 " --> pdb=" O GLY H 124 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA H 129 " --> pdb=" O LEU H 125 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL H 130 " --> pdb=" O ALA H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 157 Processing helix chain 'H' and resid 160 through 171 removed outlier: 4.229A pdb=" N GLY H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 4.798A 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 194 through 206 Processing helix chain 'H' and resid 224 through 227 removed outlier: 3.851A pdb=" N ILE H 227 " --> pdb=" O GLY H 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 224 through 227' 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 7 through 36 Processing helix chain 'A' and resid 69 through 119 removed outlier: 3.727A pdb=" N THR A 90 " --> pdb=" O PHE A 86 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N SER A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ARG A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLU A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY A 96 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TRP A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N VAL A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 21 removed outlier: 4.979A pdb=" N LEU L 10 " --> pdb=" O THR L 7 " (cutoff:3.500A) Proline residue: L 11 - end of helix removed outlier: 3.551A pdb=" N PHE L 20 " --> pdb=" O LEU L 17 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER L 21 " --> pdb=" O LEU L 18 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 53 Processing helix chain 'L' and resid 83 through 106 Processing helix chain 'L' and resid 113 through 131 Processing helix chain 'L' and resid 136 through 154 Processing helix chain 'L' and resid 161 through 192 Processing helix chain 'L' and resid 197 through 207 Proline residue: L 205 - end of helix Processing helix chain 'L' and resid 214 through 229 Processing helix chain 'L' and resid 239 through 242 No H-bonds generated for 'chain 'L' and resid 239 through 242' Processing helix chain 'L' and resid 247 through 255 Processing helix chain 'L' and resid 261 through 268 Processing helix chain 'L' and resid 270 through 274 Processing helix chain 'L' and resid 277 through 299 Processing helix chain 'L' and resid 304 through 324 Processing helix chain 'L' and resid 328 through 356 Processing helix chain 'L' and resid 362 through 364 No H-bonds generated for 'chain 'L' and resid 362 through 364' Processing helix chain 'L' and resid 373 through 386 Processing helix chain 'L' and resid 395 through 408 Processing helix chain 'L' and resid 412 through 437 Processing helix chain 'L' and resid 455 through 463 Processing helix chain 'L' and resid 466 through 470 Processing helix chain 'L' and resid 487 through 512 Processing helix chain 'L' and resid 517 through 523 removed outlier: 3.834A pdb=" N ILE L 522 " --> pdb=" O LEU L 518 " (cutoff:3.500A) Processing helix chain 'L' and resid 526 through 536 Processing helix chain 'L' and resid 541 through 548 Processing helix chain 'L' and resid 550 through 562 removed outlier: 4.872A pdb=" N ARG L 562 " --> pdb=" O TRP L 558 " (cutoff:3.500A) Processing helix chain 'L' and resid 564 through 586 Proline residue: L 572 - end of helix removed outlier: 3.648A pdb=" N LEU L 585 " --> pdb=" O LYS L 581 " (cutoff:3.500A) removed outlier: 4.345A 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 22 Proline residue: M 10 - end of helix removed outlier: 3.707A pdb=" N GLU M 21 " --> pdb=" O CYS M 17 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ARG M 22 " --> pdb=" O TRP M 18 " (cutoff:3.500A) 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: 4.539A pdb=" N LEU M 147 " --> pdb=" O TRP M 143 " (cutoff:3.500A) removed outlier: 4.226A 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 removed outlier: 4.049A pdb=" N ASP M 246 " --> pdb=" O GLY M 242 " (cutoff:3.500A) 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 307 Proline residue: M 288 - end of helix removed outlier: 3.527A pdb=" N ALA M 307 " --> pdb=" O TRP M 303 " (cutoff:3.500A) Processing helix chain 'M' and resid 311 through 332 removed outlier: 3.807A pdb=" N TYR M 331 " --> pdb=" O LEU M 327 " (cutoff:3.500A) removed outlier: 4.113A 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 371 through 373 No H-bonds generated for 'chain 'M' and resid 371 through 373' Processing helix chain 'M' and resid 384 through 396 Processing helix chain 'M' and resid 402 through 417 Processing helix chain 'M' and resid 419 through 443 Processing helix chain 'M' and resid 462 through 480 Processing helix chain 'M' and resid 483 through 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: 4.423A pdb=" N TRP N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N PHE N 54 " --> pdb=" O VAL N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 71 through 96 Proline residue: N 93 - end of helix 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 226 through 233 Processing helix chain 'N' and resid 236 through 260 removed outlier: 4.242A pdb=" N SER N 246 " --> pdb=" O LEU N 242 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LYS N 247 " --> pdb=" O ALA N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 262 through 265 removed outlier: 3.547A pdb=" N ASP N 265 " --> pdb=" O PRO N 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 262 through 265' Processing helix chain 'N' and resid 267 through 287 Processing helix chain 'N' and resid 294 through 316 removed outlier: 4.029A pdb=" N ALA N 315 " --> pdb=" O VAL N 311 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU N 316 " --> pdb=" O ALA N 312 " (cutoff:3.500A) Processing helix chain 'N' and resid 322 through 348 Processing helix chain 'N' and resid 370 through 383 Processing helix chain 'N' and resid 390 through 404 Processing helix chain 'N' and resid 408 through 433 removed outlier: 3.987A pdb=" N TYR N 433 " --> pdb=" O ALA N 429 " (cutoff:3.500A) Processing helix chain 'N' and resid 448 through 469 Processing helix chain 'N' and resid 472 through 480 Processing helix chain 'K' and resid 4 through 23 Processing helix chain 'K' and resid 28 through 53 removed outlier: 3.564A pdb=" N TRP K 53 " --> pdb=" O ALA K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 57 through 87 Processing helix chain 'J' and resid 2 through 20 Processing helix chain 'J' and resid 25 through 45 Processing helix chain 'J' and resid 49 through 73 removed outlier: 3.867A pdb=" N TYR J 59 " --> pdb=" O GLU J 55 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA J 60 " --> pdb=" O ILE J 56 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY J 61 " --> pdb=" O ILE J 57 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 87 Processing helix chain 'J' and resid 90 through 112 Proline residue: J 96 - end of helix removed outlier: 4.314A pdb=" N LEU J 99 " --> pdb=" O GLY J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 133 Processing helix chain 'J' and resid 138 through 159 Processing sheet with id= A, first strand: chain 'F' and resid 213 through 218 removed outlier: 6.661A pdb=" N ARG F 127 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N CYS F 89 " --> pdb=" O ARG F 127 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N TYR F 129 " --> pdb=" O CYS F 89 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ALA F 91 " --> pdb=" O TYR F 129 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N PHE F 131 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLU F 168 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ILE F 130 " --> pdb=" O GLU F 168 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N PHE F 170 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N LEU F 132 " --> pdb=" O PHE F 170 " (cutoff:3.500A) removed outlier: 6.030A 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 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: 6.445A pdb=" N THR G 77 " --> pdb=" O HIS G 7 " (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: 6.377A pdb=" N ARG G 244 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N LEU G 248 " --> pdb=" O ARG G 244 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 284 through 288 Processing sheet with id= K, first strand: chain 'G' and resid 314 through 317 removed outlier: 6.500A pdb=" N ALA G 565 " --> pdb=" O ILE G 315 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ILE G 317 " --> pdb=" O ALA G 565 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL G 567 " --> pdb=" O ILE G 317 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU G 608 " --> pdb=" O VAL G 594 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ASP G 596 " --> pdb=" O LEU G 608 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N LEU G 610 " --> pdb=" O ASP G 596 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 530 through 534 removed outlier: 6.202A pdb=" N TRP G 447 " --> pdb=" O VAL G 433 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ASN G 435 " --> pdb=" O TRP G 447 " (cutoff:3.500A) removed outlier: 5.776A 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 813 through 816 Processing sheet with id= O, first strand: chain 'G' and resid 841 through 844 removed outlier: 7.818A pdb=" N ILE G 842 " --> pdb=" O THR G 870 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N LEU G 844 " --> pdb=" O PRO G 872 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLU G 874 " --> pdb=" O LEU G 844 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 38 through 41 removed outlier: 4.234A pdb=" N VAL C 49 " --> pdb=" O GLN C 41 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA C 116 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE C 103 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LEU C 74 " --> pdb=" O ILE C 103 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 123 through 125 removed outlier: 6.604A pdb=" N THR C 148 " --> pdb=" O VAL C 124 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'C' and resid 216 through 219 Processing sheet with id= S, first strand: chain 'C' and resid 532 through 538 Processing sheet with id= T, first strand: chain 'B' and resid 20 through 25 Processing sheet with id= U, first strand: chain 'B' and resid 96 through 99 removed outlier: 6.425A pdb=" N VAL B 153 " --> pdb=" O SER B 125 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'I' and resid 48 through 50 Processing sheet with id= W, first strand: chain 'I' and resid 75 through 81 removed outlier: 3.590A pdb=" N GLN I 78 " --> pdb=" O PHE I 91 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N PHE I 91 " --> pdb=" O GLN I 78 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ALA I 80 " --> pdb=" O PRO I 89 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'L' and resid 68 through 70 Processing sheet with id= Y, first strand: chain 'L' and resid 60 through 66 removed outlier: 6.993A pdb=" N PHE L 77 " --> pdb=" O LEU L 64 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'M' and resid 65 through 72 removed outlier: 6.877A pdb=" N ILE M 77 " --> pdb=" O TRP M 71 " (cutoff:3.500A) 1858 hydrogen bonds defined for protein. 5379 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: 14.45 Time building geometry restraints manager: 16.21 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: 16102 1.42 - 1.64: 22113 1.64 - 1.86: 409 1.86 - 2.08: 0 2.08 - 2.31: 92 Bond restraints: 38716 Sorted by residual: bond pdb=" O13 3PE L 803 " pdb=" P 3PE L 803 " ideal model delta sigma weight residual 1.654 1.594 0.060 2.00e-02 2.50e+03 8.97e+00 bond pdb=" O13 3PE L 801 " pdb=" P 3PE L 801 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.82e+00 bond pdb=" O13 3PE A 201 " pdb=" P 3PE A 201 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.68e+00 bond pdb=" O13 3PE M1002 " pdb=" P 3PE M1002 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.62e+00 bond pdb=" O13 3PE L 804 " pdb=" P 3PE L 804 " ideal model delta sigma weight residual 1.654 1.596 0.058 2.00e-02 2.50e+03 8.51e+00 ... (remaining 38711 not shown) Histogram of bond angle deviations from ideal: 69.70 - 83.23: 88 83.23 - 96.76: 1 96.76 - 110.29: 8652 110.29 - 123.82: 42656 123.82 - 137.35: 1140 Bond angle restraints: 52537 Sorted by residual: angle pdb=" CA MET F 161 " pdb=" CB MET F 161 " pdb=" CG MET F 161 " ideal model delta sigma weight residual 114.10 124.49 -10.39 2.00e+00 2.50e-01 2.70e+01 angle pdb=" N THR N 64 " pdb=" CA THR N 64 " pdb=" C THR N 64 " ideal model delta sigma weight residual 109.81 98.48 11.33 2.21e+00 2.05e-01 2.63e+01 angle pdb=" CA GLN N 180 " pdb=" CB GLN N 180 " pdb=" CG GLN N 180 " ideal model delta sigma weight residual 114.10 122.87 -8.77 2.00e+00 2.50e-01 1.92e+01 angle pdb=" CB GLN N 180 " pdb=" CG GLN N 180 " pdb=" CD GLN N 180 " ideal model delta sigma weight residual 112.60 120.05 -7.45 1.70e+00 3.46e-01 1.92e+01 angle pdb=" CA ILE K 33 " pdb=" CB ILE K 33 " pdb=" CG1 ILE K 33 " ideal model delta sigma weight residual 110.40 117.79 -7.39 1.70e+00 3.46e-01 1.89e+01 ... (remaining 52532 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.87: 22101 33.87 - 67.73: 676 67.73 - 101.60: 39 101.60 - 135.47: 4 135.47 - 169.33: 1 Dihedral angle restraints: 22821 sinusoidal: 9188 harmonic: 13633 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 180.00 133.40 46.60 0 5.00e+00 4.00e-02 8.69e+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 180.00 144.54 35.46 0 5.00e+00 4.00e-02 5.03e+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 88.26 169.33 1 2.00e+01 2.50e-03 4.76e+01 ... (remaining 22818 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.243: 5831 4.243 - 8.486: 0 8.486 - 12.729: 0 12.729 - 16.972: 0 16.972 - 21.215: 28 Chirality restraints: 5859 Sorted by residual: 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 -10.66 21.22 2.00e-01 2.50e+01 1.13e+04 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="FE1 SF4 I 201 " pdb=" S2 SF4 I 201 " pdb=" S3 SF4 I 201 " pdb=" S4 SF4 I 201 " 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 5856 not shown) Planarity restraints: 6577 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 DCQ C 701 " 0.029 2.00e-02 2.50e+03 4.91e-02 7.22e+01 pdb=" C1M DCQ C 701 " 0.055 2.00e-02 2.50e+03 pdb=" C2 DCQ C 701 " 0.010 2.00e-02 2.50e+03 pdb=" C3 DCQ C 701 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DCQ C 701 " 0.027 2.00e-02 2.50e+03 pdb=" C5 DCQ C 701 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DCQ C 701 " -0.010 2.00e-02 2.50e+03 pdb=" C7 DCQ C 701 " -0.065 2.00e-02 2.50e+03 pdb=" O2 DCQ C 701 " -0.004 2.00e-02 2.50e+03 pdb=" O3 DCQ C 701 " -0.105 2.00e-02 2.50e+03 pdb=" O4 DCQ C 701 " 0.089 2.00e-02 2.50e+03 pdb=" O5 DCQ C 701 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE G 682 " 0.081 5.00e-02 4.00e+02 1.21e-01 2.35e+01 pdb=" N PRO G 683 " -0.210 5.00e-02 4.00e+02 pdb=" CA PRO G 683 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO G 683 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR N 4 " -0.066 5.00e-02 4.00e+02 9.97e-02 1.59e+01 pdb=" N PRO N 5 " 0.172 5.00e-02 4.00e+02 pdb=" CA PRO N 5 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO N 5 " -0.054 5.00e-02 4.00e+02 ... (remaining 6574 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1467 2.72 - 3.27: 37239 3.27 - 3.81: 66462 3.81 - 4.36: 83672 4.36 - 4.90: 141129 Nonbonded interactions: 329969 Sorted by model distance: nonbonded pdb=" O LEU M 16 " pdb=" OG1 THR M 20 " model vdw 2.178 2.440 nonbonded pdb=" O ILE N 386 " pdb=" OG1 THR N 389 " model vdw 2.195 2.440 nonbonded pdb=" OG1 THR C 334 " pdb=" O ALA H 287 " model vdw 2.230 2.440 nonbonded pdb=" O ILE M 315 " pdb=" OG1 THR M 318 " model vdw 2.242 2.440 nonbonded pdb=" O ARG F 39 " pdb=" OG1 THR F 43 " model vdw 2.250 2.440 ... (remaining 329964 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: 0.330 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: 0.030 Extract box with map and model: 4.060 Check model and map are aligned: 0.560 Set scattering table: 0.340 Process input model: 108.470 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 38716 Z= 0.285 Angle : 0.766 12.117 52537 Z= 0.393 Chirality : 1.461 21.215 5859 Planarity : 0.006 0.121 6577 Dihedral : 15.727 169.335 14103 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.17 % Favored : 96.81 % Rotamer: Outliers : 0.49 % Allowed : 16.15 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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: -0.69 (0.11), residues: 4738 helix: 0.24 (0.09), residues: 2678 sheet: -0.74 (0.28), residues: 321 loop : -1.40 (0.14), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 143 HIS 0.010 0.001 HIS M 248 PHE 0.044 0.002 PHE M 175 TYR 0.037 0.002 TYR L 428 ARG 0.013 0.001 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 3902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 545 time to evaluate : 4.005 Fit side-chains REVERT: F 48 ASP cc_start: 0.7424 (m-30) cc_final: 0.7201 (p0) REVERT: F 106 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7572 (tm-30) REVERT: G 583 ASN cc_start: 0.8510 (m-40) cc_final: 0.7667 (t0) REVERT: C 206 MET cc_start: 0.7285 (mmm) cc_final: 0.6937 (mmm) REVERT: C 555 MET cc_start: 0.8691 (mtt) cc_final: 0.8237 (mtt) REVERT: C 581 VAL cc_start: 0.7822 (OUTLIER) cc_final: 0.7601 (t) REVERT: B 170 MET cc_start: 0.8136 (mtp) cc_final: 0.7718 (mtm) REVERT: H 282 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.8119 (m-80) REVERT: A 88 TRP cc_start: 0.8527 (t60) cc_final: 0.8327 (t60) REVERT: L 119 TYR cc_start: 0.8849 (m-10) cc_final: 0.8557 (m-80) REVERT: L 236 GLN cc_start: 0.8700 (pt0) cc_final: 0.8261 (pm20) REVERT: L 265 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8762 (mt) REVERT: L 400 ASP cc_start: 0.9118 (m-30) cc_final: 0.8398 (t0) REVERT: N 30 TRP cc_start: 0.7917 (t-100) cc_final: 0.7235 (t60) REVERT: N 482 MET cc_start: 0.6904 (tmm) cc_final: 0.6379 (ppp) REVERT: K 97 GLU cc_start: 0.7282 (tt0) cc_final: 0.6975 (tt0) REVERT: J 85 ARG cc_start: 0.5564 (tpt90) cc_final: 0.5183 (tpt-90) REVERT: J 91 GLN cc_start: 0.5977 (mp10) cc_final: 0.5089 (pm20) outliers start: 19 outliers final: 4 residues processed: 557 average time/residue: 0.5011 time to fit residues: 463.0198 Evaluate side-chains 508 residues out of total 3902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 501 time to evaluate : 4.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain H residue 282 PHE Chi-restraints excluded: chain L residue 265 LEU Chi-restraints excluded: chain K residue 89 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 397 optimal weight: 9.9990 chunk 356 optimal weight: 10.0000 chunk 198 optimal weight: 0.9990 chunk 121 optimal weight: 8.9990 chunk 240 optimal weight: 8.9990 chunk 190 optimal weight: 20.0000 chunk 369 optimal weight: 4.9990 chunk 142 optimal weight: 0.5980 chunk 224 optimal weight: 20.0000 chunk 274 optimal weight: 5.9990 chunk 427 optimal weight: 10.0000 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 291 GLN F 304 HIS F 341 ASN G 261 HIS ** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 HIS C 223 ASN C 359 HIS H 45 ASN ** N 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 404 GLN K 91 ASN J 83 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.267 38716 Z= 0.780 Angle : 2.183 51.146 52537 Z= 1.432 Chirality : 0.437 6.508 5859 Planarity : 0.005 0.082 6577 Dihedral : 8.843 170.040 5656 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.14 % Favored : 96.83 % Rotamer: Outliers : 2.77 % Allowed : 15.20 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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: 0.09 (0.12), residues: 4738 helix: 0.95 (0.10), residues: 2683 sheet: -0.74 (0.28), residues: 336 loop : -1.13 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 353 HIS 0.006 0.001 HIS G 709 PHE 0.028 0.002 PHE L 341 TYR 0.024 0.002 TYR M 435 ARG 0.005 0.000 ARG F 416 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 3902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 509 time to evaluate : 4.242 Fit side-chains REVERT: F 106 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7750 (tm-30) REVERT: F 114 GLU cc_start: 0.8694 (tt0) cc_final: 0.8476 (tt0) REVERT: F 161 MET cc_start: 0.6887 (tpt) cc_final: 0.6556 (tpt) REVERT: G 583 ASN cc_start: 0.8638 (m-40) cc_final: 0.7790 (t0) REVERT: G 631 ARG cc_start: 0.9123 (OUTLIER) cc_final: 0.7523 (ttp80) REVERT: C 127 PHE cc_start: 0.8515 (OUTLIER) cc_final: 0.8274 (t80) REVERT: C 453 GLU cc_start: 0.7459 (mp0) cc_final: 0.7209 (mp0) REVERT: H 31 PHE cc_start: 0.6813 (m-10) cc_final: 0.6555 (m-10) REVERT: H 229 TYR cc_start: 0.8830 (m-80) cc_final: 0.8479 (m-80) REVERT: H 282 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.8204 (m-80) REVERT: A 62 LEU cc_start: 0.5228 (mp) cc_final: 0.5006 (mp) REVERT: L 178 ASP cc_start: 0.8279 (m-30) cc_final: 0.7996 (m-30) REVERT: L 236 GLN cc_start: 0.8720 (pt0) cc_final: 0.8382 (pm20) REVERT: L 253 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8714 (mp) REVERT: L 313 MET cc_start: 0.9014 (tpp) cc_final: 0.8782 (ttt) REVERT: L 379 PHE cc_start: 0.8797 (OUTLIER) cc_final: 0.8505 (t80) REVERT: L 389 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.6940 (mp) REVERT: L 400 ASP cc_start: 0.9093 (m-30) cc_final: 0.8425 (t0) REVERT: L 415 MET cc_start: 0.7703 (mtp) cc_final: 0.7473 (mtp) REVERT: L 430 PHE cc_start: 0.8967 (m-80) cc_final: 0.8652 (m-80) REVERT: M 325 PHE cc_start: 0.8545 (OUTLIER) cc_final: 0.7534 (t80) REVERT: M 481 TYR cc_start: 0.7915 (t80) cc_final: 0.7652 (t80) REVERT: N 30 TRP cc_start: 0.7933 (t-100) cc_final: 0.7262 (t60) REVERT: N 63 VAL cc_start: 0.7370 (OUTLIER) cc_final: 0.7158 (p) REVERT: N 379 MET cc_start: 0.8714 (mmt) cc_final: 0.8282 (mmt) REVERT: K 97 GLU cc_start: 0.7446 (tt0) cc_final: 0.7134 (tt0) REVERT: J 85 ARG cc_start: 0.5693 (tpt90) cc_final: 0.5353 (tpt-90) REVERT: J 91 GLN cc_start: 0.5806 (mp10) cc_final: 0.4981 (pm20) REVERT: J 152 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8097 (tt) outliers start: 108 outliers final: 64 residues processed: 582 average time/residue: 0.4845 time to fit residues: 469.7147 Evaluate side-chains 552 residues out of total 3902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 479 time to evaluate : 4.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 57 ASN Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 343 ILE Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 556 THR Chi-restraints excluded: chain G residue 600 THR Chi-restraints excluded: chain G residue 617 GLU Chi-restraints excluded: chain G residue 631 ARG Chi-restraints excluded: chain G residue 707 GLU Chi-restraints excluded: chain G residue 725 GLU Chi-restraints excluded: chain G residue 735 MET Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain G residue 870 THR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 282 PHE Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 160 ASP Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 145 MET Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 325 PHE Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 395 THR Chi-restraints excluded: chain M residue 440 LEU Chi-restraints excluded: chain N residue 25 MET Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 174 MET Chi-restraints excluded: chain N residue 211 ILE Chi-restraints excluded: chain N residue 313 LEU Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain K residue 24 ILE Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 152 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 237 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 chunk 355 optimal weight: 6.9990 chunk 291 optimal weight: 0.0470 chunk 117 optimal weight: 3.9990 chunk 428 optimal weight: 10.0000 chunk 462 optimal weight: 20.0000 chunk 381 optimal weight: 10.0000 chunk 424 optimal weight: 0.0980 chunk 146 optimal weight: 1.9990 chunk 343 optimal weight: 1.9990 overall best weight: 1.6284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 409 GLN ** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 ASN H 152 GLN H 208 HIS N 404 GLN K 91 ASN J 83 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.253 38716 Z= 0.742 Angle : 2.156 50.870 52537 Z= 1.421 Chirality : 0.439 6.430 5859 Planarity : 0.004 0.073 6577 Dihedral : 8.363 169.026 5648 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.62 % Allowed : 16.53 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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: 0.55 (0.12), residues: 4738 helix: 1.37 (0.10), residues: 2661 sheet: -0.82 (0.28), residues: 331 loop : -0.93 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 143 HIS 0.005 0.001 HIS G 178 PHE 0.031 0.001 PHE L 341 TYR 0.028 0.001 TYR M 435 ARG 0.004 0.000 ARG K 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 3902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 514 time to evaluate : 4.274 Fit side-chains revert: symmetry clash REVERT: F 48 ASP cc_start: 0.7476 (m-30) cc_final: 0.7215 (p0) REVERT: F 106 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7755 (tm-30) REVERT: F 161 MET cc_start: 0.6926 (tpt) cc_final: 0.6724 (tpt) REVERT: G 583 ASN cc_start: 0.8619 (m-40) cc_final: 0.7772 (t0) REVERT: C 127 PHE cc_start: 0.8461 (OUTLIER) cc_final: 0.8244 (t80) REVERT: C 453 GLU cc_start: 0.7588 (mp0) cc_final: 0.7243 (mp0) REVERT: H 31 PHE cc_start: 0.6684 (m-10) cc_final: 0.6450 (m-10) REVERT: H 43 PHE cc_start: 0.8617 (m-80) cc_final: 0.8206 (m-80) REVERT: H 229 TYR cc_start: 0.8804 (m-80) cc_final: 0.8341 (m-80) REVERT: L 51 ASP cc_start: 0.8360 (t0) cc_final: 0.7781 (t0) REVERT: L 236 GLN cc_start: 0.8588 (pt0) cc_final: 0.8381 (pm20) REVERT: L 253 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8679 (mp) REVERT: L 379 PHE cc_start: 0.8741 (OUTLIER) cc_final: 0.8454 (t80) REVERT: L 389 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.6984 (mp) REVERT: L 400 ASP cc_start: 0.9085 (m-30) cc_final: 0.8415 (t0) REVERT: L 415 MET cc_start: 0.7787 (OUTLIER) cc_final: 0.7358 (mtp) REVERT: M 325 PHE cc_start: 0.8391 (OUTLIER) cc_final: 0.7395 (t80) REVERT: M 481 TYR cc_start: 0.7907 (t80) cc_final: 0.7622 (t80) REVERT: N 30 TRP cc_start: 0.7787 (t-100) cc_final: 0.7174 (t60) REVERT: N 379 MET cc_start: 0.8754 (mmt) cc_final: 0.8375 (mmt) REVERT: K 97 GLU cc_start: 0.7479 (tt0) cc_final: 0.7168 (tt0) REVERT: J 85 ARG cc_start: 0.5792 (tpt90) cc_final: 0.5465 (tpt-90) REVERT: J 91 GLN cc_start: 0.5779 (mp10) cc_final: 0.5063 (pm20) REVERT: J 152 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.7994 (tt) outliers start: 102 outliers final: 56 residues processed: 589 average time/residue: 0.4879 time to fit residues: 479.7283 Evaluate side-chains 552 residues out of total 3902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 489 time to evaluate : 4.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 6 ARG Chi-restraints excluded: chain F residue 327 MET Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 343 ILE Chi-restraints excluded: chain G residue 439 THR Chi-restraints excluded: chain G residue 504 THR Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 617 GLU Chi-restraints excluded: chain G residue 735 MET Chi-restraints excluded: chain G residue 870 THR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 160 ASP Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 253 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 472 VAL Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 588 ASN Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain M residue 145 MET Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 325 PHE Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 440 LEU Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 25 MET Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 174 MET Chi-restraints excluded: chain N residue 313 LEU Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain J residue 152 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 423 optimal weight: 9.9990 chunk 322 optimal weight: 10.0000 chunk 222 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 204 optimal weight: 30.0000 chunk 287 optimal weight: 9.9990 chunk 430 optimal weight: 10.0000 chunk 455 optimal weight: 20.0000 chunk 224 optimal weight: 7.9990 chunk 407 optimal weight: 7.9990 chunk 122 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 52 ASN F 409 GLN ** E 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 ASN C 236 GLN B 111 GLN B 116 GLN H 45 ASN H 152 GLN A 13 HIS L 315 GLN L 358 HIS N 199 ASN ** N 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 404 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.243 38716 Z= 0.845 Angle : 2.204 50.895 52537 Z= 1.440 Chirality : 0.440 6.454 5859 Planarity : 0.005 0.072 6577 Dihedral : 9.099 170.524 5646 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.05 % Favored : 95.93 % Rotamer: Outliers : 3.95 % Allowed : 16.48 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: 0.20 (0.12), residues: 4738 helix: 1.03 (0.10), residues: 2662 sheet: -0.63 (0.29), residues: 309 loop : -1.05 (0.14), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 386 HIS 0.007 0.002 HIS M 117 PHE 0.038 0.002 PHE J 156 TYR 0.030 0.002 TYR L 189 ARG 0.005 0.001 ARG G 369 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 3902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 487 time to evaluate : 4.329 Fit side-chains REVERT: F 114 GLU cc_start: 0.8795 (tt0) cc_final: 0.8551 (tt0) REVERT: F 161 MET cc_start: 0.7315 (tpt) cc_final: 0.7112 (tpt) REVERT: G 178 HIS cc_start: 0.8645 (OUTLIER) cc_final: 0.8410 (p-80) REVERT: G 583 ASN cc_start: 0.8605 (m-40) cc_final: 0.7810 (t0) REVERT: G 631 ARG cc_start: 0.9139 (OUTLIER) cc_final: 0.7429 (ttp80) REVERT: C 127 PHE cc_start: 0.8596 (OUTLIER) cc_final: 0.8312 (t80) REVERT: B 119 GLU cc_start: 0.8748 (mp0) cc_final: 0.8452 (mp0) REVERT: B 170 MET cc_start: 0.8283 (mtp) cc_final: 0.7817 (mtm) REVERT: I 122 MET cc_start: 0.8880 (mtp) cc_final: 0.8659 (mtm) REVERT: H 216 GLU cc_start: 0.6882 (pm20) cc_final: 0.6569 (pm20) REVERT: L 253 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8694 (mp) REVERT: L 379 PHE cc_start: 0.8796 (OUTLIER) cc_final: 0.8447 (t80) REVERT: L 389 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.6898 (mp) REVERT: L 400 ASP cc_start: 0.9131 (m-30) cc_final: 0.8434 (t0) REVERT: L 415 MET cc_start: 0.7917 (OUTLIER) cc_final: 0.7501 (mtp) REVERT: M 325 PHE cc_start: 0.8709 (OUTLIER) cc_final: 0.7572 (t80) REVERT: N 30 TRP cc_start: 0.7962 (t-100) cc_final: 0.7309 (t60) REVERT: N 379 MET cc_start: 0.8746 (mmt) cc_final: 0.8361 (mmt) REVERT: K 26 ARG cc_start: 0.8214 (mtm-85) cc_final: 0.7827 (mtm-85) REVERT: J 91 GLN cc_start: 0.5901 (mp10) cc_final: 0.5150 (pm20) REVERT: J 152 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8111 (tt) outliers start: 154 outliers final: 101 residues processed: 597 average time/residue: 0.4710 time to fit residues: 469.1592 Evaluate side-chains 567 residues out of total 3902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 457 time to evaluate : 4.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 6 ARG Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 57 ASN Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 178 HIS Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 343 ILE Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 439 THR Chi-restraints excluded: chain G residue 504 THR Chi-restraints excluded: chain G residue 556 THR Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 600 THR Chi-restraints excluded: chain G residue 617 GLU Chi-restraints excluded: chain G residue 618 SER Chi-restraints excluded: chain G residue 631 ARG Chi-restraints excluded: chain G residue 725 GLU Chi-restraints excluded: chain G residue 735 MET Chi-restraints excluded: chain G residue 842 ILE Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain G residue 870 THR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 536 MET Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain H residue 5 SER Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 120 THR Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 160 ASP Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 265 LEU Chi-restraints excluded: chain L residue 352 VAL 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 472 VAL Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 588 ASN Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 145 MET Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 181 SER Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 325 PHE Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 395 THR Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 440 LEU Chi-restraints excluded: chain M residue 501 VAL Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 25 MET Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 102 LYS Chi-restraints excluded: chain N residue 110 LEU Chi-restraints excluded: chain N residue 121 ASN Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 174 MET Chi-restraints excluded: chain N residue 211 ILE Chi-restraints excluded: chain N residue 255 MET Chi-restraints excluded: chain N residue 313 LEU Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 89 ASN Chi-restraints excluded: chain K residue 92 ILE Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 152 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 379 optimal weight: 9.9990 chunk 258 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 338 optimal weight: 10.0000 chunk 187 optimal weight: 10.0000 chunk 388 optimal weight: 4.9990 chunk 314 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 232 optimal weight: 3.9990 chunk 408 optimal weight: 7.9990 chunk 114 optimal weight: 3.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 GLN ** H 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 208 HIS H 214 GLN A 13 HIS M 502 ASN ** N 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 404 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.242 38716 Z= 0.806 Angle : 2.189 50.920 52537 Z= 1.434 Chirality : 0.439 6.459 5859 Planarity : 0.005 0.074 6577 Dihedral : 8.979 170.548 5646 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.50 % Favored : 96.48 % Rotamer: Outliers : 3.88 % Allowed : 17.46 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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: 0.22 (0.12), residues: 4738 helix: 1.07 (0.10), residues: 2663 sheet: -0.82 (0.28), residues: 317 loop : -1.05 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 143 HIS 0.005 0.001 HIS C 518 PHE 0.036 0.002 PHE J 156 TYR 0.023 0.002 TYR N 76 ARG 0.004 0.000 ARG K 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 3902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 485 time to evaluate : 4.549 Fit side-chains REVERT: F 114 GLU cc_start: 0.8743 (tt0) cc_final: 0.8497 (tt0) REVERT: E 160 GLU cc_start: 0.7415 (tm-30) cc_final: 0.6705 (tm-30) REVERT: G 583 ASN cc_start: 0.8588 (m-40) cc_final: 0.7797 (t0) REVERT: G 631 ARG cc_start: 0.9138 (OUTLIER) cc_final: 0.8255 (tpp80) REVERT: C 127 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.8323 (t80) REVERT: B 119 GLU cc_start: 0.8791 (mp0) cc_final: 0.8488 (mp0) REVERT: B 170 MET cc_start: 0.8286 (mtp) cc_final: 0.7832 (mtm) REVERT: H 216 GLU cc_start: 0.6865 (pm20) cc_final: 0.6603 (pm20) REVERT: L 51 ASP cc_start: 0.8527 (t0) cc_final: 0.7875 (t0) REVERT: L 189 TYR cc_start: 0.9122 (t80) cc_final: 0.8792 (t80) REVERT: L 214 MET cc_start: 0.8176 (mmt) cc_final: 0.7905 (mmt) REVERT: L 253 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8705 (mp) REVERT: L 379 PHE cc_start: 0.8799 (OUTLIER) cc_final: 0.8486 (t80) REVERT: L 389 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.6886 (mp) REVERT: L 400 ASP cc_start: 0.9140 (m-30) cc_final: 0.8459 (t0) REVERT: M 325 PHE cc_start: 0.8679 (OUTLIER) cc_final: 0.7508 (t80) REVERT: N 30 TRP cc_start: 0.7896 (t-100) cc_final: 0.7283 (t60) REVERT: N 379 MET cc_start: 0.8752 (mmt) cc_final: 0.8359 (mmt) REVERT: J 91 GLN cc_start: 0.5771 (mp10) cc_final: 0.5149 (pm20) REVERT: J 152 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.7746 (tp) outliers start: 151 outliers final: 115 residues processed: 603 average time/residue: 0.4900 time to fit residues: 495.4023 Evaluate side-chains 592 residues out of total 3902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 470 time to evaluate : 4.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 6 ARG Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 189 SER Chi-restraints excluded: chain F residue 327 MET Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 57 ASN Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 234 SER Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 343 ILE Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 439 THR Chi-restraints excluded: chain G residue 455 ASP Chi-restraints excluded: chain G residue 504 THR Chi-restraints excluded: chain G residue 556 THR Chi-restraints excluded: chain G residue 617 GLU Chi-restraints excluded: chain G residue 618 SER Chi-restraints excluded: chain G residue 631 ARG Chi-restraints excluded: chain G residue 707 GLU Chi-restraints excluded: chain G residue 725 GLU Chi-restraints excluded: chain G residue 735 MET Chi-restraints excluded: chain G residue 745 GLN Chi-restraints excluded: chain G residue 842 ILE Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain G residue 870 THR Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 536 MET Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 230 SER Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 120 THR Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 160 ASP Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 352 VAL 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 419 LEU Chi-restraints excluded: chain L residue 431 ARG Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 588 ASN Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 39 THR Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 145 MET Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 181 SER Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 325 PHE Chi-restraints excluded: chain M residue 328 ILE Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 423 VAL Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 440 LEU Chi-restraints excluded: chain M residue 501 VAL Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 25 MET Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 102 LYS Chi-restraints excluded: chain N residue 110 LEU Chi-restraints excluded: chain N residue 121 ASN Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 174 MET Chi-restraints excluded: chain N residue 211 ILE Chi-restraints excluded: chain N residue 313 LEU Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain N residue 382 SER Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 89 ASN Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 152 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 153 optimal weight: 9.9990 chunk 409 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 267 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 chunk 455 optimal weight: 10.0000 chunk 378 optimal weight: 9.9990 chunk 210 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 150 optimal weight: 5.9990 chunk 239 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 78 GLN ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 GLN H 208 HIS L 357 HIS ** N 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 404 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.242 38716 Z= 0.799 Angle : 2.188 50.907 52537 Z= 1.434 Chirality : 0.439 6.453 5859 Planarity : 0.005 0.074 6577 Dihedral : 8.829 170.650 5646 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.07 % Favored : 95.91 % Rotamer: Outliers : 4.24 % Allowed : 17.56 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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: 0.26 (0.12), residues: 4738 helix: 1.11 (0.10), residues: 2661 sheet: -0.85 (0.28), residues: 320 loop : -1.02 (0.15), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 143 HIS 0.005 0.001 HIS C 518 PHE 0.036 0.002 PHE J 156 TYR 0.024 0.002 TYR N 76 ARG 0.009 0.000 ARG K 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 3902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 482 time to evaluate : 4.124 Fit side-chains REVERT: F 114 GLU cc_start: 0.8741 (tt0) cc_final: 0.8485 (tt0) REVERT: F 141 VAL cc_start: 0.8401 (t) cc_final: 0.8122 (m) REVERT: F 161 MET cc_start: 0.7684 (tpt) cc_final: 0.7430 (tpp) REVERT: E 160 GLU cc_start: 0.7387 (tm-30) cc_final: 0.6634 (tm-30) REVERT: G 158 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.8272 (mtp180) REVERT: G 583 ASN cc_start: 0.8587 (m-40) cc_final: 0.7795 (t0) REVERT: G 631 ARG cc_start: 0.9125 (OUTLIER) cc_final: 0.8251 (tpp80) REVERT: C 127 PHE cc_start: 0.8651 (OUTLIER) cc_final: 0.8312 (t80) REVERT: C 206 MET cc_start: 0.7148 (mmm) cc_final: 0.6742 (mmm) REVERT: B 119 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8390 (mp0) REVERT: B 170 MET cc_start: 0.8246 (mtp) cc_final: 0.7863 (mtm) REVERT: L 51 ASP cc_start: 0.8528 (t0) cc_final: 0.7840 (t0) REVERT: L 189 TYR cc_start: 0.9129 (t80) cc_final: 0.8764 (t80) REVERT: L 214 MET cc_start: 0.8231 (mmt) cc_final: 0.7956 (mmt) REVERT: L 253 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8738 (mp) REVERT: L 379 PHE cc_start: 0.8807 (OUTLIER) cc_final: 0.8497 (t80) REVERT: L 389 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.6995 (mp) REVERT: L 400 ASP cc_start: 0.9135 (m-30) cc_final: 0.8462 (t0) REVERT: M 325 PHE cc_start: 0.8676 (OUTLIER) cc_final: 0.7507 (t80) REVERT: N 30 TRP cc_start: 0.7904 (t-100) cc_final: 0.7286 (t60) REVERT: N 379 MET cc_start: 0.8748 (mmt) cc_final: 0.8347 (mmt) REVERT: J 91 GLN cc_start: 0.5789 (mp10) cc_final: 0.5186 (pm20) REVERT: J 152 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8057 (tt) outliers start: 165 outliers final: 129 residues processed: 608 average time/residue: 0.4832 time to fit residues: 494.9016 Evaluate side-chains 604 residues out of total 3902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 466 time to evaluate : 4.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 6 ARG Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 189 SER Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 327 MET Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 57 ASN Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 158 ARG Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 234 SER Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 343 ILE Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 439 THR Chi-restraints excluded: chain G residue 504 THR Chi-restraints excluded: chain G residue 556 THR Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 600 THR Chi-restraints excluded: chain G residue 617 GLU Chi-restraints excluded: chain G residue 618 SER Chi-restraints excluded: chain G residue 631 ARG Chi-restraints excluded: chain G residue 707 GLU Chi-restraints excluded: chain G residue 725 GLU Chi-restraints excluded: chain G residue 735 MET Chi-restraints excluded: chain G residue 745 GLN Chi-restraints excluded: chain G residue 799 THR Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain G residue 870 THR Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 484 CYS Chi-restraints excluded: chain C residue 536 MET Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 230 SER Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain L residue 68 MET Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 120 THR Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 160 ASP Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain L residue 419 LEU Chi-restraints excluded: chain L residue 431 ARG Chi-restraints excluded: chain L residue 457 LEU Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 588 ASN Chi-restraints excluded: chain L residue 608 LEU Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 39 THR Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 69 MET Chi-restraints excluded: chain M residue 145 MET Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 181 SER Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 325 PHE Chi-restraints excluded: chain M residue 328 ILE Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 395 THR Chi-restraints excluded: chain M residue 423 VAL Chi-restraints excluded: chain M residue 425 SER Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 437 LEU Chi-restraints excluded: chain M residue 440 LEU Chi-restraints excluded: chain M residue 501 VAL Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 25 MET Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 110 LEU Chi-restraints excluded: chain N residue 121 ASN Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 174 MET Chi-restraints excluded: chain N residue 211 ILE Chi-restraints excluded: chain N residue 255 MET Chi-restraints excluded: chain N residue 313 LEU Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain N residue 382 SER Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 89 ASN Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain J residue 152 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 439 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 259 optimal weight: 5.9990 chunk 332 optimal weight: 10.0000 chunk 257 optimal weight: 5.9990 chunk 383 optimal weight: 8.9990 chunk 254 optimal weight: 7.9990 chunk 453 optimal weight: 9.9990 chunk 284 optimal weight: 0.9990 chunk 276 optimal weight: 6.9990 chunk 209 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 78 GLN ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 855 ASN B 116 GLN H 208 HIS ** M 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 404 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.243 38716 Z= 0.774 Angle : 2.178 50.911 52537 Z= 1.430 Chirality : 0.439 6.449 5859 Planarity : 0.004 0.073 6577 Dihedral : 8.622 170.369 5646 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.57 % Favored : 96.41 % Rotamer: Outliers : 4.21 % Allowed : 17.89 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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: 0.39 (0.12), residues: 4738 helix: 1.23 (0.10), residues: 2654 sheet: -0.89 (0.28), residues: 329 loop : -0.97 (0.15), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 143 HIS 0.006 0.001 HIS C 518 PHE 0.037 0.002 PHE J 156 TYR 0.024 0.002 TYR H 156 ARG 0.007 0.000 ARG K 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 3902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 494 time to evaluate : 4.330 Fit side-chains REVERT: F 106 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7743 (tm-30) REVERT: F 114 GLU cc_start: 0.8709 (tt0) cc_final: 0.8455 (tt0) REVERT: F 141 VAL cc_start: 0.8409 (t) cc_final: 0.8176 (m) REVERT: F 161 MET cc_start: 0.7716 (tpt) cc_final: 0.7494 (tpp) REVERT: E 160 GLU cc_start: 0.7632 (tm-30) cc_final: 0.6872 (tm-30) REVERT: G 583 ASN cc_start: 0.8577 (m-40) cc_final: 0.7769 (t0) REVERT: G 631 ARG cc_start: 0.9113 (OUTLIER) cc_final: 0.7415 (ttp80) REVERT: C 127 PHE cc_start: 0.8639 (OUTLIER) cc_final: 0.8371 (t80) REVERT: C 206 MET cc_start: 0.7145 (mmm) cc_final: 0.6762 (mmm) REVERT: C 374 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7965 (mmt90) REVERT: B 119 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8392 (mp0) REVERT: B 170 MET cc_start: 0.8246 (mtp) cc_final: 0.7833 (mtm) REVERT: I 122 MET cc_start: 0.8841 (mtp) cc_final: 0.8587 (mtm) REVERT: A 86 PHE cc_start: 0.8149 (m-10) cc_final: 0.7937 (m-10) REVERT: L 51 ASP cc_start: 0.8514 (t0) cc_final: 0.7817 (t0) REVERT: L 127 MET cc_start: 0.8965 (tpt) cc_final: 0.8641 (tpt) REVERT: L 189 TYR cc_start: 0.9148 (t80) cc_final: 0.8846 (t80) REVERT: L 214 MET cc_start: 0.8207 (mmt) cc_final: 0.7935 (mmt) REVERT: L 253 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8709 (mp) REVERT: L 379 PHE cc_start: 0.8788 (OUTLIER) cc_final: 0.8479 (t80) REVERT: L 389 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7068 (mp) REVERT: L 400 ASP cc_start: 0.9134 (m-30) cc_final: 0.8475 (t0) REVERT: L 424 MET cc_start: 0.8628 (mmm) cc_final: 0.8353 (mmm) REVERT: M 304 MET cc_start: 0.8823 (mmm) cc_final: 0.8489 (mmm) REVERT: M 325 PHE cc_start: 0.8629 (OUTLIER) cc_final: 0.7492 (t80) REVERT: M 481 TYR cc_start: 0.8106 (t80) cc_final: 0.7873 (t80) REVERT: N 30 TRP cc_start: 0.7869 (t-100) cc_final: 0.7264 (t60) REVERT: N 379 MET cc_start: 0.8749 (mmt) cc_final: 0.8369 (mmt) REVERT: J 91 GLN cc_start: 0.5803 (mp10) cc_final: 0.5198 (pm20) REVERT: J 152 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8148 (tt) outliers start: 164 outliers final: 128 residues processed: 617 average time/residue: 0.4715 time to fit residues: 484.8319 Evaluate side-chains 614 residues out of total 3902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 477 time to evaluate : 3.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 6 ARG Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 189 SER Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 327 MET Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 57 ASN Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 234 SER Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 343 ILE Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 439 THR Chi-restraints excluded: chain G residue 455 ASP Chi-restraints excluded: chain G residue 504 THR Chi-restraints excluded: chain G residue 556 THR Chi-restraints excluded: chain G residue 600 THR Chi-restraints excluded: chain G residue 617 GLU Chi-restraints excluded: chain G residue 618 SER Chi-restraints excluded: chain G residue 631 ARG Chi-restraints excluded: chain G residue 707 GLU Chi-restraints excluded: chain G residue 725 GLU Chi-restraints excluded: chain G residue 735 MET Chi-restraints excluded: chain G residue 745 GLN Chi-restraints excluded: chain G residue 799 THR Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain G residue 870 THR Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 374 ARG Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 484 CYS Chi-restraints excluded: chain C residue 536 MET Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 230 SER Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain L residue 68 MET Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 120 THR Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 160 ASP Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 269 THR Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain L residue 419 LEU Chi-restraints excluded: chain L residue 431 ARG Chi-restraints excluded: chain L residue 457 LEU Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 588 ASN Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 39 THR Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 145 MET Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 181 SER Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 325 PHE Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 395 THR Chi-restraints excluded: chain M residue 423 VAL Chi-restraints excluded: chain M residue 425 SER Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 437 LEU Chi-restraints excluded: chain M residue 440 LEU Chi-restraints excluded: chain M residue 501 VAL Chi-restraints excluded: chain M residue 502 ASN Chi-restraints excluded: chain N residue 25 MET Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 110 LEU Chi-restraints excluded: chain N residue 121 ASN Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 211 ILE Chi-restraints excluded: chain N residue 255 MET Chi-restraints excluded: chain N residue 313 LEU Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain N residue 382 SER Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 89 ASN Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 152 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 280 optimal weight: 6.9990 chunk 181 optimal weight: 6.9990 chunk 271 optimal weight: 7.9990 chunk 136 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 288 optimal weight: 9.9990 chunk 309 optimal weight: 0.4980 chunk 224 optimal weight: 20.0000 chunk 42 optimal weight: 2.9990 chunk 356 optimal weight: 8.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 409 GLN E 78 GLN ** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 855 ASN H 208 HIS M 502 ASN N 404 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.246 38716 Z= 0.745 Angle : 2.164 50.886 52537 Z= 1.425 Chirality : 0.437 6.426 5859 Planarity : 0.004 0.072 6577 Dihedral : 8.121 169.188 5646 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.00 % Allowed : 19.28 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: 0.69 (0.12), residues: 4738 helix: 1.49 (0.10), residues: 2645 sheet: -0.85 (0.28), residues: 315 loop : -0.85 (0.15), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 143 HIS 0.006 0.001 HIS G 178 PHE 0.031 0.001 PHE L 341 TYR 0.027 0.001 TYR M 435 ARG 0.007 0.000 ARG G 750 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 3902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 505 time to evaluate : 4.447 Fit side-chains REVERT: F 30 ARG cc_start: 0.6153 (mmm160) cc_final: 0.5749 (mtm110) REVERT: F 106 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7702 (tm-30) REVERT: F 141 VAL cc_start: 0.8360 (t) cc_final: 0.8147 (m) REVERT: E 160 GLU cc_start: 0.7657 (tm-30) cc_final: 0.6880 (tm-30) REVERT: G 631 ARG cc_start: 0.9100 (OUTLIER) cc_final: 0.8860 (ttm110) REVERT: C 127 PHE cc_start: 0.8662 (OUTLIER) cc_final: 0.8391 (t80) REVERT: C 206 MET cc_start: 0.7468 (mmm) cc_final: 0.7106 (mmm) REVERT: C 374 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7926 (mmt90) REVERT: B 119 GLU cc_start: 0.8670 (mp0) cc_final: 0.8365 (mp0) REVERT: B 170 MET cc_start: 0.8184 (mtp) cc_final: 0.7754 (mtm) REVERT: I 122 MET cc_start: 0.8852 (mtp) cc_final: 0.8621 (mtm) REVERT: H 229 TYR cc_start: 0.8701 (m-80) cc_final: 0.8097 (m-80) REVERT: H 252 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7906 (mtt) REVERT: H 282 PHE cc_start: 0.8543 (OUTLIER) cc_final: 0.8328 (m-80) REVERT: H 314 LEU cc_start: 0.8643 (mt) cc_final: 0.8404 (tp) REVERT: L 51 ASP cc_start: 0.8525 (t0) cc_final: 0.7862 (t0) REVERT: L 189 TYR cc_start: 0.9109 (t80) cc_final: 0.8885 (t80) REVERT: L 214 MET cc_start: 0.8276 (mmt) cc_final: 0.8018 (mmt) REVERT: L 253 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8685 (mp) REVERT: L 313 MET cc_start: 0.8988 (tpp) cc_final: 0.8642 (ttt) REVERT: L 379 PHE cc_start: 0.8755 (OUTLIER) cc_final: 0.8471 (t80) REVERT: L 400 ASP cc_start: 0.9130 (m-30) cc_final: 0.8466 (t0) REVERT: M 304 MET cc_start: 0.8879 (mmm) cc_final: 0.8458 (mmm) REVERT: M 325 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.7391 (t80) REVERT: M 481 TYR cc_start: 0.8081 (t80) cc_final: 0.7793 (t80) REVERT: N 30 TRP cc_start: 0.7774 (t-100) cc_final: 0.7195 (t60) REVERT: N 379 MET cc_start: 0.8721 (mmt) cc_final: 0.8362 (mmt) REVERT: K 31 MET cc_start: 0.8617 (mtp) cc_final: 0.8389 (mtp) REVERT: J 91 GLN cc_start: 0.5701 (mp10) cc_final: 0.5115 (pm20) REVERT: J 152 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8106 (tt) outliers start: 117 outliers final: 91 residues processed: 589 average time/residue: 0.5015 time to fit residues: 493.6420 Evaluate side-chains 587 residues out of total 3902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 487 time to evaluate : 4.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 6 ARG Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 327 MET Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 234 SER Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 343 ILE Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 439 THR Chi-restraints excluded: chain G residue 504 THR Chi-restraints excluded: chain G residue 600 THR Chi-restraints excluded: chain G residue 617 GLU Chi-restraints excluded: chain G residue 631 ARG Chi-restraints excluded: chain G residue 707 GLU Chi-restraints excluded: chain G residue 725 GLU Chi-restraints excluded: chain G residue 735 MET Chi-restraints excluded: chain G residue 799 THR Chi-restraints excluded: chain G residue 870 THR Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 374 ARG Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 484 CYS Chi-restraints excluded: chain C residue 536 MET Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 230 SER Chi-restraints excluded: chain H residue 252 MET Chi-restraints excluded: chain H residue 282 PHE Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain L residue 68 MET Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 120 THR Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 160 ASP Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 588 ASN Chi-restraints excluded: chain L residue 608 LEU Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 145 MET Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 325 PHE Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 395 THR Chi-restraints excluded: chain M residue 425 SER Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 437 LEU Chi-restraints excluded: chain M residue 440 LEU Chi-restraints excluded: chain M residue 502 ASN Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 25 MET Chi-restraints excluded: chain N residue 110 LEU Chi-restraints excluded: chain N residue 121 ASN Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 255 MET Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 89 ASN Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 152 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 412 optimal weight: 10.0000 chunk 434 optimal weight: 9.9990 chunk 396 optimal weight: 8.9990 chunk 423 optimal weight: 0.8980 chunk 254 optimal weight: 2.9990 chunk 184 optimal weight: 5.9990 chunk 332 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 chunk 382 optimal weight: 5.9990 chunk 400 optimal weight: 0.9990 chunk 421 optimal weight: 10.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 78 GLN ** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 855 ASN C 518 HIS B 116 GLN M 502 ASN ** N 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 404 GLN J 83 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.244 38716 Z= 0.761 Angle : 2.173 50.900 52537 Z= 1.428 Chirality : 0.438 6.437 5859 Planarity : 0.004 0.072 6577 Dihedral : 8.126 169.229 5646 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.11 % Allowed : 19.41 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: 0.68 (0.12), residues: 4738 helix: 1.47 (0.10), residues: 2649 sheet: -0.86 (0.28), residues: 315 loop : -0.84 (0.15), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 143 HIS 0.006 0.001 HIS C 518 PHE 0.029 0.002 PHE L 341 TYR 0.025 0.002 TYR L 428 ARG 0.011 0.000 ARG K 86 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 3902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 488 time to evaluate : 4.699 Fit side-chains REVERT: F 30 ARG cc_start: 0.6252 (mmm160) cc_final: 0.5801 (mtm110) REVERT: F 141 VAL cc_start: 0.8424 (t) cc_final: 0.8186 (m) REVERT: E 160 GLU cc_start: 0.7644 (tm-30) cc_final: 0.6887 (tm-30) REVERT: G 631 ARG cc_start: 0.9108 (OUTLIER) cc_final: 0.7440 (ttp80) REVERT: C 127 PHE cc_start: 0.8687 (OUTLIER) cc_final: 0.8378 (t80) REVERT: C 206 MET cc_start: 0.7478 (mmm) cc_final: 0.7069 (mmm) REVERT: C 374 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7952 (mmt90) REVERT: B 119 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8386 (mp0) REVERT: B 170 MET cc_start: 0.8214 (mtp) cc_final: 0.7805 (mtm) REVERT: I 122 MET cc_start: 0.8849 (mtp) cc_final: 0.8625 (mtm) REVERT: H 252 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.7884 (mtt) REVERT: H 282 PHE cc_start: 0.8553 (OUTLIER) cc_final: 0.8346 (m-80) REVERT: L 51 ASP cc_start: 0.8514 (t0) cc_final: 0.7823 (t0) REVERT: L 214 MET cc_start: 0.8279 (mmt) cc_final: 0.7986 (mmt) REVERT: L 236 GLN cc_start: 0.8498 (pm20) cc_final: 0.8241 (pm20) REVERT: L 253 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8675 (mp) REVERT: L 313 MET cc_start: 0.8918 (tpp) cc_final: 0.8619 (ttt) REVERT: L 379 PHE cc_start: 0.8765 (OUTLIER) cc_final: 0.8512 (t80) REVERT: L 400 ASP cc_start: 0.9131 (m-30) cc_final: 0.8469 (t0) REVERT: M 304 MET cc_start: 0.8855 (mmm) cc_final: 0.8420 (mmm) REVERT: M 325 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.7421 (t80) REVERT: M 481 TYR cc_start: 0.8099 (t80) cc_final: 0.7834 (t80) REVERT: N 30 TRP cc_start: 0.7827 (t-100) cc_final: 0.7223 (t60) REVERT: N 368 HIS cc_start: 0.7368 (OUTLIER) cc_final: 0.7143 (p-80) REVERT: N 379 MET cc_start: 0.8734 (mmt) cc_final: 0.8349 (mmt) REVERT: J 91 GLN cc_start: 0.5720 (mp10) cc_final: 0.5119 (pm20) REVERT: J 152 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8119 (tt) outliers start: 121 outliers final: 98 residues processed: 577 average time/residue: 0.4995 time to fit residues: 481.6088 Evaluate side-chains 594 residues out of total 3902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 485 time to evaluate : 4.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 6 ARG Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 327 MET Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 234 SER Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 343 ILE Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 439 THR Chi-restraints excluded: chain G residue 504 THR Chi-restraints excluded: chain G residue 600 THR Chi-restraints excluded: chain G residue 617 GLU Chi-restraints excluded: chain G residue 631 ARG Chi-restraints excluded: chain G residue 707 GLU Chi-restraints excluded: chain G residue 725 GLU Chi-restraints excluded: chain G residue 735 MET Chi-restraints excluded: chain G residue 799 THR Chi-restraints excluded: chain G residue 870 THR Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 374 ARG Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 484 CYS Chi-restraints excluded: chain C residue 536 MET Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 230 SER Chi-restraints excluded: chain H residue 252 MET Chi-restraints excluded: chain H residue 282 PHE Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain L residue 68 MET Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 120 THR Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 160 ASP Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 431 ARG Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 588 ASN Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 145 MET Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 325 PHE Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 395 THR Chi-restraints excluded: chain M residue 423 VAL Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 437 LEU Chi-restraints excluded: chain M residue 440 LEU Chi-restraints excluded: chain M residue 502 ASN Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 25 MET Chi-restraints excluded: chain N residue 102 LYS Chi-restraints excluded: chain N residue 110 LEU Chi-restraints excluded: chain N residue 121 ASN Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 174 MET Chi-restraints excluded: chain N residue 255 MET Chi-restraints excluded: chain N residue 313 LEU Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain N residue 368 HIS Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 89 ASN Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 152 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 277 optimal weight: 9.9990 chunk 447 optimal weight: 6.9990 chunk 273 optimal weight: 0.5980 chunk 212 optimal weight: 4.9990 chunk 310 optimal weight: 0.8980 chunk 469 optimal weight: 20.0000 chunk 431 optimal weight: 3.9990 chunk 373 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 288 optimal weight: 8.9990 chunk 229 optimal weight: 10.0000 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 78 GLN ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 855 ASN B 116 GLN H 208 HIS M 502 ASN N 404 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.244 38716 Z= 0.763 Angle : 2.175 50.899 52537 Z= 1.429 Chirality : 0.438 6.438 5859 Planarity : 0.004 0.072 6577 Dihedral : 8.114 169.332 5646 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.08 % Allowed : 19.46 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: 0.66 (0.12), residues: 4738 helix: 1.46 (0.10), residues: 2648 sheet: -0.85 (0.28), residues: 321 loop : -0.85 (0.15), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 143 HIS 0.005 0.001 HIS C 518 PHE 0.037 0.002 PHE J 156 TYR 0.024 0.002 TYR L 189 ARG 0.012 0.000 ARG K 86 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 3902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 486 time to evaluate : 4.344 Fit side-chains REVERT: F 30 ARG cc_start: 0.6226 (mmm160) cc_final: 0.5788 (mtm110) REVERT: F 141 VAL cc_start: 0.8423 (t) cc_final: 0.8181 (m) REVERT: E 160 GLU cc_start: 0.7640 (tm-30) cc_final: 0.6883 (tm-30) REVERT: G 631 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.7422 (ttp80) REVERT: C 127 PHE cc_start: 0.8688 (OUTLIER) cc_final: 0.8388 (t80) REVERT: C 206 MET cc_start: 0.7474 (mmm) cc_final: 0.7068 (mmm) REVERT: C 374 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7945 (mmt90) REVERT: B 119 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8335 (mp0) REVERT: B 170 MET cc_start: 0.8216 (mtp) cc_final: 0.7796 (mtm) REVERT: I 122 MET cc_start: 0.8845 (mtp) cc_final: 0.8616 (mtm) REVERT: H 229 TYR cc_start: 0.8735 (m-80) cc_final: 0.8129 (m-80) REVERT: H 252 MET cc_start: 0.8097 (OUTLIER) cc_final: 0.7882 (mtt) REVERT: L 51 ASP cc_start: 0.8516 (t0) cc_final: 0.7816 (t0) REVERT: L 214 MET cc_start: 0.8285 (mmt) cc_final: 0.8018 (mmt) REVERT: L 236 GLN cc_start: 0.8514 (pm20) cc_final: 0.8240 (pm20) REVERT: L 253 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8627 (mp) REVERT: L 313 MET cc_start: 0.8924 (tpp) cc_final: 0.8623 (ttt) REVERT: L 336 MET cc_start: 0.8740 (ttp) cc_final: 0.8397 (ttm) REVERT: L 379 PHE cc_start: 0.8769 (OUTLIER) cc_final: 0.8519 (t80) REVERT: L 400 ASP cc_start: 0.9133 (m-30) cc_final: 0.8470 (t0) REVERT: M 325 PHE cc_start: 0.8581 (OUTLIER) cc_final: 0.7445 (t80) REVERT: M 481 TYR cc_start: 0.8093 (t80) cc_final: 0.7796 (t80) REVERT: N 30 TRP cc_start: 0.7823 (t-100) cc_final: 0.7201 (t60) REVERT: N 369 ARG cc_start: 0.7670 (tpp-160) cc_final: 0.7434 (mmt90) REVERT: N 379 MET cc_start: 0.8743 (mmt) cc_final: 0.8350 (mmt) REVERT: K 86 ARG cc_start: 0.8460 (mtp-110) cc_final: 0.8254 (mtp85) REVERT: J 91 GLN cc_start: 0.5719 (mp10) cc_final: 0.5117 (pm20) REVERT: J 152 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8119 (tt) outliers start: 120 outliers final: 102 residues processed: 573 average time/residue: 0.5028 time to fit residues: 480.5999 Evaluate side-chains 593 residues out of total 3902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 482 time to evaluate : 4.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 6 ARG Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 327 MET Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 142 ASN Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 234 SER Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 343 ILE Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 439 THR Chi-restraints excluded: chain G residue 504 THR Chi-restraints excluded: chain G residue 600 THR Chi-restraints excluded: chain G residue 617 GLU Chi-restraints excluded: chain G residue 631 ARG Chi-restraints excluded: chain G residue 707 GLU Chi-restraints excluded: chain G residue 725 GLU Chi-restraints excluded: chain G residue 735 MET Chi-restraints excluded: chain G residue 799 THR Chi-restraints excluded: chain G residue 870 THR Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 374 ARG Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 484 CYS Chi-restraints excluded: chain C residue 536 MET Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 230 SER Chi-restraints excluded: chain H residue 252 MET Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain L residue 68 MET Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 120 THR Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 160 ASP Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 431 ARG Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 588 ASN Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 145 MET Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 325 PHE Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 395 THR Chi-restraints excluded: chain M residue 423 VAL Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 437 LEU Chi-restraints excluded: chain M residue 440 LEU Chi-restraints excluded: chain M residue 501 VAL Chi-restraints excluded: chain M residue 502 ASN Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 25 MET Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 110 LEU Chi-restraints excluded: chain N residue 121 ASN Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 174 MET Chi-restraints excluded: chain N residue 255 MET Chi-restraints excluded: chain N residue 313 LEU Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 89 ASN Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 152 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 296 optimal weight: 0.9980 chunk 398 optimal weight: 20.0000 chunk 114 optimal weight: 5.9990 chunk 344 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 374 optimal weight: 9.9990 chunk 156 optimal weight: 3.9990 chunk 384 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 78 GLN ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 855 ASN H 208 HIS M 502 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.084453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.074802 restraints weight = 72475.618| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 0.99 r_work: 0.2962 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.244 38716 Z= 0.768 Angle : 2.177 50.910 52537 Z= 1.429 Chirality : 0.438 6.440 5859 Planarity : 0.004 0.072 6577 Dihedral : 8.143 169.474 5646 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.34 % Allowed : 19.33 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: 0.63 (0.12), residues: 4738 helix: 1.43 (0.10), residues: 2654 sheet: -0.82 (0.28), residues: 318 loop : -0.86 (0.15), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 143 HIS 0.006 0.001 HIS C 518 PHE 0.034 0.002 PHE J 156 TYR 0.028 0.002 TYR L 189 ARG 0.011 0.000 ARG K 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9733.30 seconds wall clock time: 176 minutes 15.45 seconds (10575.45 seconds total)