Starting phenix.real_space_refine on Fri Feb 23 08:29:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z83_14541/02_2024/7z83_14541_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z83_14541/02_2024/7z83_14541.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z83_14541/02_2024/7z83_14541.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z83_14541/02_2024/7z83_14541.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z83_14541/02_2024/7z83_14541_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z83_14541/02_2024/7z83_14541_updated.pdb" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.015 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 12 5.49 5 S 267 5.16 5 C 24448 2.51 5 N 6201 2.21 5 O 6585 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F GLU 80": "OE1" <-> "OE2" Residue "F GLU 183": "OE1" <-> "OE2" Residue "E GLU 20": "OE1" <-> "OE2" Residue "E ASP 52": "OD1" <-> "OD2" Residue "E ASP 93": "OD1" <-> "OD2" Residue "E ASP 148": "OD1" <-> "OD2" Residue "G GLU 84": "OE1" <-> "OE2" Residue "G GLU 298": "OE1" <-> "OE2" Residue "G TYR 841": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 862": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 36": "OD1" <-> "OD2" Residue "C ASP 62": "OD1" <-> "OD2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 435": "OD1" <-> "OD2" Residue "B ASP 44": "OD1" <-> "OD2" Residue "B TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 94": "OD1" <-> "OD2" Residue "B ASP 115": "OD1" <-> "OD2" Residue "B ASP 137": "OD1" <-> "OD2" Residue "B GLU 163": "OE1" <-> "OE2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "I ASP 53": "OD1" <-> "OD2" Residue "I ASP 162": "OD1" <-> "OD2" Residue "H TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 71": "OE1" <-> "OE2" Residue "H PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 228": "OE1" <-> "OE2" Residue "H TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 124": "OD1" <-> "OD2" Residue "L PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 484": "OE1" <-> "OE2" Residue "M PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 68": "OD1" <-> "OD2" Residue "M TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 364": "OE1" <-> "OE2" Residue "M ASP 487": "OD1" <-> "OD2" Residue "N PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 103": "OD1" <-> "OD2" Residue "N PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 183": "OD1" <-> "OD2" Residue "N GLU 200": "OE1" <-> "OE2" Residue "N GLU 267": "OE1" <-> "OE2" Residue "N PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 72": "OE1" <-> "OE2" Residue "J GLU 2": "OE1" <-> "OE2" Residue "J TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 120": "OD1" <-> "OD2" 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: 37546 Number of models: 1 Model: "" Number of chains: 23 Chain: "F" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3407 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 413} Chain: "E" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1220 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 146} Chain: "G" Number of atoms: 7022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7022 Classifications: {'peptide': 905} Link IDs: {'PTRANS': 41, 'TRANS': 863} Chain: "C" Number of atoms: 4741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4741 Classifications: {'peptide': 588} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 550} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1568 Classifications: {'peptide': 198} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 185} Chain breaks: 2 Chain: "I" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1436 Classifications: {'peptide': 180} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 166} Chain: "H" Number of atoms: 2475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2475 Classifications: {'peptide': 314} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 299} Chain breaks: 1 Chain: "A" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 808 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain breaks: 1 Chain: "L" Number of atoms: 4637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4637 Classifications: {'peptide': 606} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 587} Chain breaks: 1 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: 3620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3620 Classifications: {'peptide': 478} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 457} Chain breaks: 1 Chain: "K" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 760 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Chain: "J" Number of atoms: 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: "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: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 71 Unusual residues: {'3PE': 1, 'LFA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 204 Unusual residues: {'3PE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "M" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 122 Unusual residues: {'3PE': 2, 'LFA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'LFA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "J" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2721 SG CYS F 354 68.366 59.841 192.806 1.00 4.46 S ATOM 2741 SG CYS F 357 71.773 59.423 197.325 1.00 13.98 S ATOM 3062 SG CYS F 398 66.038 56.002 197.662 1.00 14.83 S ATOM 2697 SG CYS F 351 70.624 53.556 194.145 1.00 6.41 S ATOM 4054 SG CYS E 92 78.774 51.884 213.913 1.00 41.59 S ATOM 4088 SG CYS E 97 78.972 52.551 217.454 1.00 30.20 S ATOM 4366 SG CYS E 133 73.608 51.092 213.694 1.00 38.82 S ATOM 4392 SG CYS E 137 72.860 51.860 216.950 1.00 32.41 S ATOM 5476 SG CYS G 114 78.911 66.167 175.714 1.00 5.59 S ATOM 5416 SG CYS G 105 83.999 70.096 177.071 1.00 8.84 S ATOM 5436 SG CYS G 108 84.909 64.064 174.830 1.00 5.92 S ATOM 5830 SG CYS G 156 73.198 58.342 180.322 1.00 16.09 S ATOM 5811 SG CYS G 153 79.002 57.349 183.465 1.00 19.68 S ATOM 5859 SG CYS G 159 76.372 52.710 179.965 1.00 8.57 S ATOM 6203 SG CYS G 203 78.440 57.927 176.810 1.00 3.31 S ATOM 6428 SG CYS G 230 75.560 49.588 155.665 1.00 7.51 S ATOM 6713 SG CYS G 265 75.493 45.713 160.970 1.00 11.29 S ATOM 6476 SG CYS G 237 70.213 49.098 158.682 1.00 7.08 S ATOM 6452 SG CYS G 233 72.590 43.713 155.712 1.00 23.19 S ATOM 4877 SG CYS G 36 66.779 59.213 183.065 1.00 2.92 S ATOM 4953 SG CYS G 47 68.253 62.514 183.397 1.00 7.83 S ATOM 4979 SG CYS G 50 62.468 64.137 183.260 1.00 4.89 S ATOM 5128 SG CYS G 69 61.971 60.453 182.933 1.00 8.51 S ATOM 17236 SG CYS B 129 89.070 93.729 151.930 1.00 31.62 S ATOM 16733 SG CYS B 64 94.195 97.563 153.563 1.00 30.44 S ATOM 16727 SG CYS B 63 88.618 99.611 155.364 1.00 46.19 S ATOM 17453 SG CYS B 158 90.809 93.763 157.723 1.00 40.96 S ATOM 18784 SG CYS I 102 89.476 87.911 163.774 1.00 19.96 S ATOM 18759 SG CYS I 99 95.047 86.654 160.263 1.00 10.27 S ATOM 18802 SG CYS I 105 93.574 83.248 165.558 1.00 20.35 S ATOM 18517 SG CYS I 70 89.777 82.647 160.318 1.00 12.39 S ATOM 18831 SG CYS I 109 94.635 77.775 171.830 1.00 14.15 S ATOM 18494 SG CYS I 66 92.752 77.028 165.690 1.00 14.32 S ATOM 18454 SG CYS I 60 96.886 72.777 168.034 1.00 0.00 S ATOM 18472 SG CYS I 63 90.590 73.201 170.461 1.00 11.15 S Time building chain proxies: 20.12, per 1000 atoms: 0.54 Number of scatterers: 37546 At special positions: 0 Unit cell: (154.76, 217.3, 244.86, 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 12 15.00 O 6585 8.00 N 6201 7.00 C 24448 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.59 Conformation dependent library (CDL) restraints added in 6.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 137 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 92 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 133 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 97 " pdb=" FES G1004 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 50 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 36 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 47 " 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="FE2 SF4 B 301 " - pdb=" SG CYS B 64 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 63 " pdb=" SF4 F 501 " pdb="FE2 SF4 F 501 " - pdb=" SG CYS F 357 " pdb="FE1 SF4 F 501 " - pdb=" SG CYS F 354 " pdb="FE4 SF4 F 501 " - pdb=" SG CYS F 351 " pdb="FE3 SF4 F 501 " - pdb=" SG CYS F 398 " pdb=" SF4 G1001 " pdb="FE3 SF4 G1001 " - pdb=" NE2 HIS G 101 " pdb="FE4 SF4 G1001 " - pdb=" SG CYS G 108 " pdb="FE1 SF4 G1001 " - pdb=" SG CYS G 114 " pdb="FE2 SF4 G1001 " - pdb=" SG CYS G 105 " pdb=" SF4 G1002 " pdb="FE3 SF4 G1002 " - pdb=" SG CYS G 159 " pdb="FE2 SF4 G1002 " - pdb=" SG CYS G 153 " pdb="FE4 SF4 G1002 " - pdb=" SG CYS G 203 " pdb="FE1 SF4 G1002 " - pdb=" SG CYS G 156 " pdb=" SF4 G1003 " pdb="FE4 SF4 G1003 " - pdb=" SG CYS G 233 " pdb="FE1 SF4 G1003 " - pdb=" SG CYS G 230 " pdb="FE2 SF4 G1003 " - pdb=" SG CYS G 265 " pdb="FE3 SF4 G1003 " - pdb=" SG CYS G 237 " pdb=" SF4 I 201 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 105 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 70 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 99 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 102 " pdb=" SF4 I 202 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 66 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 60 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 109 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 63 " Number of angles added : 93 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8642 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 191 helices and 24 sheets defined 54.4% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.44 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 56 Processing helix chain 'F' and resid 69 through 74 Processing helix chain 'F' and resid 100 through 107 removed outlier: 3.713A pdb=" N GLN F 107 " --> pdb=" O LEU F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 122 Processing helix chain 'F' and resid 137 through 152 Processing helix chain 'F' and resid 160 through 162 No H-bonds generated for 'chain 'F' and resid 160 through 162' Processing helix chain 'F' and resid 178 through 181 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: 3.910A pdb=" N GLY F 422 " --> pdb=" O GLU F 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 28 removed outlier: 3.871A pdb=" N HIS E 28 " --> pdb=" O HIS E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 47 removed outlier: 4.828A pdb=" N ILE E 37 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU E 38 " --> pdb=" O ALA E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 62 removed outlier: 4.009A 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 158 through 164 removed outlier: 3.533A pdb=" N GLU E 163 " --> pdb=" O PRO E 159 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG E 164 " --> pdb=" O GLU E 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 27 Processing helix chain 'G' and resid 84 through 99 Processing helix chain 'G' and resid 105 through 107 No H-bonds generated for 'chain 'G' and resid 105 through 107' Processing helix chain 'G' and resid 115 through 123 Processing helix chain 'G' and resid 150 through 152 No H-bonds generated for 'chain 'G' and resid 150 through 152' Processing helix chain 'G' and resid 158 through 165 Processing helix chain 'G' and resid 196 through 202 Processing helix chain 'G' and resid 211 through 215 Processing helix chain 'G' and resid 220 through 222 No H-bonds generated for 'chain 'G' and resid 220 through 222' Processing helix chain 'G' and resid 266 through 270 Processing helix chain 'G' and resid 297 through 310 Processing helix chain 'G' and resid 324 through 334 Processing helix chain 'G' and resid 345 through 360 Processing helix chain 'G' and resid 370 through 373 Processing helix chain 'G' and resid 384 through 387 No H-bonds generated for 'chain 'G' and resid 384 through 387' Processing helix chain 'G' and resid 389 through 410 removed outlier: 4.459A pdb=" N LYS G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ALA G 403 " --> pdb=" O VAL G 399 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN G 410 " --> pdb=" O MET G 406 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 423 Processing helix chain 'G' and resid 453 through 467 Processing helix chain 'G' and resid 479 through 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 509 through 524 Processing helix chain 'G' and resid 540 through 546 Processing helix chain 'G' and resid 551 through 560 Processing helix chain 'G' and resid 579 through 588 Processing helix chain 'G' and resid 601 through 603 No H-bonds generated for 'chain 'G' and resid 601 through 603' Processing helix chain 'G' and resid 615 through 617 No H-bonds generated for 'chain 'G' and resid 615 through 617' Processing helix chain 'G' and resid 650 through 662 Processing helix chain 'G' and resid 671 through 681 Processing helix chain 'G' and resid 686 through 690 removed outlier: 3.907A pdb=" N LYS G 689 " --> pdb=" O ALA G 686 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP G 690 " --> pdb=" O GLY G 687 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 686 through 690' Processing helix chain 'G' and resid 764 through 768 Processing helix chain 'G' and resid 825 through 828 No H-bonds generated for 'chain 'G' and resid 825 through 828' Processing helix chain 'G' and resid 846 through 852 Processing helix chain 'G' and resid 895 through 897 No H-bonds generated for 'chain 'G' and resid 895 through 897' Processing helix chain 'C' and resid 24 through 33 Processing helix chain 'C' and resid 54 through 65 removed outlier: 5.194A pdb=" N LEU C 58 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 145 removed outlier: 3.530A pdb=" N TYR C 137 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU C 144 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE C 145 " --> pdb=" O TRP C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 194 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 38 through 52 Processing helix chain 'B' and resid 63 through 71 Processing helix chain 'B' and resid 78 through 81 Processing helix chain 'B' and resid 104 through 116 Proline residue: B 108 - end of helix Processing helix chain 'B' and resid 128 through 132 Processing helix chain 'B' and resid 145 through 147 No H-bonds generated for 'chain 'B' and resid 145 through 147' Processing helix chain 'B' and resid 162 through 178 removed outlier: 4.013A pdb=" N LYS B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 208 removed outlier: 4.557A pdb=" N GLY B 206 " --> pdb=" O GLU B 202 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N GLU B 207 " --> pdb=" O ARG B 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 24 Processing helix chain 'I' and resid 65 through 69 Processing helix chain 'I' and resid 104 through 108 Processing helix chain 'I' and resid 127 through 130 Processing helix chain 'I' and resid 134 through 136 No H-bonds generated for 'chain 'I' and resid 134 through 136' Processing helix chain 'I' and resid 150 through 152 No H-bonds generated for 'chain 'I' and resid 150 through 152' Processing helix chain 'H' and resid 6 through 43 Processing helix chain 'H' and resid 54 through 56 No H-bonds generated for 'chain 'H' and resid 54 through 56' Processing helix chain 'H' and resid 59 through 69 Processing helix chain 'H' and resid 80 through 100 Proline residue: H 87 - end of helix removed outlier: 4.778A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ILE H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 136 removed outlier: 4.484A pdb=" N TYR H 128 " --> pdb=" O GLY H 124 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA H 129 " --> pdb=" O LEU H 125 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N VAL H 130 " --> pdb=" O ALA H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 171 removed outlier: 5.013A pdb=" N PHE H 159 " --> pdb=" O SER H 155 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLY H 161 " --> pdb=" O GLU H 157 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N LEU H 162 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLY H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N VAL H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 181 Processing helix chain 'H' and resid 188 through 191 No H-bonds generated for 'chain 'H' and resid 188 through 191' Processing helix chain 'H' and resid 193 through 206 Processing helix chain 'H' and resid 232 through 256 Processing helix chain 'H' and resid 267 through 288 Processing helix chain 'H' and resid 294 through 303 Processing helix chain 'H' and resid 305 through 323 Processing helix chain 'A' and resid 7 through 36 Processing helix chain 'A' and resid 67 through 119 removed outlier: 3.793A pdb=" N THR A 90 " --> pdb=" O PHE A 86 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N SER A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A 92 " --> pdb=" O TRP A 88 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ARG A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLU A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N TRP A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N VAL A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 21 removed outlier: 4.600A pdb=" N ALA L 5 " --> pdb=" O ASN L 2 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR L 7 " --> pdb=" O LEU L 4 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N LEU L 10 " --> pdb=" O THR L 7 " (cutoff:3.500A) Proline residue: L 11 - end of helix removed outlier: 3.683A pdb=" N SER L 21 " --> pdb=" O LEU L 18 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 55 Processing helix chain 'L' and resid 83 through 106 Processing helix chain 'L' and resid 113 through 132 Processing helix chain 'L' and resid 136 through 154 Processing helix chain 'L' and resid 161 through 192 Processing helix chain 'L' and resid 197 through 209 Proline residue: L 205 - end of helix Processing helix chain 'L' and resid 213 through 229 Processing helix chain 'L' and resid 238 through 244 removed outlier: 5.596A pdb=" N ALA L 244 " --> pdb=" O ALA L 240 " (cutoff:3.500A) Processing helix chain 'L' and resid 247 through 254 Processing helix chain 'L' and resid 260 through 268 Processing helix chain 'L' and resid 270 through 274 Processing helix chain 'L' and resid 277 through 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 373 through 386 Processing helix chain 'L' and resid 394 through 409 removed outlier: 3.597A pdb=" N ASN L 409 " --> pdb=" O GLY L 405 " (cutoff:3.500A) Processing helix chain 'L' and resid 413 through 437 Processing helix chain 'L' and resid 454 through 463 Processing helix chain 'L' and resid 466 through 470 Processing helix chain 'L' and resid 487 through 511 Processing helix chain 'L' and resid 518 through 523 Processing helix chain 'L' and resid 526 through 536 Processing helix chain 'L' and resid 538 through 548 removed outlier: 6.122A pdb=" N ASP L 542 " --> pdb=" O TRP L 539 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TRP L 543 " --> pdb=" O GLY L 540 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL L 548 " --> pdb=" O TYR L 545 " (cutoff:3.500A) Processing helix chain 'L' and resid 551 through 560 Processing helix chain 'L' and resid 564 through 586 Proline residue: L 572 - end of helix removed outlier: 3.796A pdb=" N LEU L 585 " --> pdb=" O LYS L 581 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N SER L 586 " --> pdb=" O GLY L 582 " (cutoff:3.500A) Processing helix chain 'L' and resid 591 through 612 Processing helix chain 'M' and resid 2 through 21 Proline residue: M 10 - end of helix removed outlier: 3.843A pdb=" N GLU M 21 " --> pdb=" O CYS M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 27 through 50 Processing helix chain 'M' and resid 85 through 105 Processing helix chain 'M' and resid 113 through 132 Processing helix chain 'M' and resid 136 through 156 removed outlier: 4.578A pdb=" N LEU M 147 " --> pdb=" O TRP M 143 " (cutoff:3.500A) removed outlier: 4.297A 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 200 Processing helix chain 'M' and resid 207 through 210 No H-bonds generated for 'chain 'M' and resid 207 through 210' Processing helix chain 'M' and resid 219 through 233 Processing helix chain 'M' and resid 242 through 249 Processing helix chain 'M' and resid 256 through 260 Processing helix chain 'M' and resid 266 through 273 Processing helix chain 'M' and resid 275 through 278 No H-bonds generated for 'chain 'M' and resid 275 through 278' Processing helix chain 'M' and resid 280 through 306 Proline residue: M 288 - end of helix Processing helix chain 'M' and resid 311 through 332 removed outlier: 3.627A pdb=" N TYR M 331 " --> pdb=" O LEU M 327 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR M 332 " --> pdb=" O ILE M 328 " (cutoff:3.500A) Processing helix chain 'M' and resid 335 through 366 Processing helix chain 'M' and resid 377 through 379 No H-bonds generated for 'chain 'M' and resid 377 through 379' Processing helix chain 'M' and resid 384 through 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 452 through 454 No H-bonds generated for 'chain 'M' and resid 452 through 454' Processing helix chain 'M' and resid 462 through 480 Processing helix chain 'M' and resid 483 through 488 Processing helix chain 'M' and resid 490 through 501 Processing helix chain 'N' and resid 5 through 30 removed outlier: 3.646A pdb=" N LEU N 12 " --> pdb=" O LEU N 8 " (cutoff:3.500A) Proline residue: N 13 - end of helix Processing helix chain 'N' and resid 34 through 58 removed outlier: 4.330A pdb=" N TRP N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE N 54 " --> pdb=" O VAL N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 71 through 97 Proline residue: N 93 - end of helix removed outlier: 4.154A pdb=" N GLY N 97 " --> pdb=" O PRO N 93 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 120 Processing helix chain 'N' and resid 125 through 143 Proline residue: N 138 - end of helix Processing helix chain 'N' and resid 150 through 181 Processing helix chain 'N' and resid 201 through 217 Processing helix chain 'N' and resid 226 through 233 Processing helix chain 'N' and resid 236 through 260 removed outlier: 4.484A pdb=" N SER N 246 " --> pdb=" O LEU N 242 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LYS N 247 " --> pdb=" O ALA N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 262 through 265 Processing helix chain 'N' and resid 267 through 288 removed outlier: 4.094A pdb=" N ALA N 288 " --> pdb=" O GLY N 284 " (cutoff:3.500A) Processing helix chain 'N' and resid 294 through 316 removed outlier: 4.024A pdb=" N ALA N 315 " --> pdb=" O VAL N 311 " (cutoff:3.500A) removed outlier: 4.262A 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 365 through 367 No H-bonds generated for 'chain 'N' and resid 365 through 367' Processing helix chain 'N' and resid 370 through 383 Processing helix chain 'N' and resid 390 through 404 Processing helix chain 'N' and resid 408 through 433 removed outlier: 4.315A 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 24 Processing helix chain 'K' and resid 28 through 53 Processing helix chain 'K' and resid 57 through 87 Processing helix chain 'J' and resid 2 through 20 Processing helix chain 'J' and resid 25 through 45 Processing helix chain 'J' and resid 49 through 57 Processing helix chain 'J' and resid 63 through 74 Processing helix chain 'J' and resid 90 through 113 removed outlier: 5.600A pdb=" N GLY J 95 " --> pdb=" O GLN J 91 " (cutoff:3.500A) Proline residue: J 96 - end of helix removed outlier: 3.719A pdb=" N GLY J 113 " --> pdb=" O TYR J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 133 Processing helix chain 'J' and resid 138 through 158 Processing sheet with id= A, first strand: chain 'F' and resid 213 through 218 removed outlier: 6.621A pdb=" N ARG F 127 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N CYS F 89 " --> pdb=" O ARG F 127 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N TYR F 129 " --> pdb=" O CYS F 89 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ALA F 91 " --> pdb=" O TYR F 129 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N PHE F 131 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLU F 168 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ILE F 130 " --> pdb=" O GLU F 168 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N PHE F 170 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU F 132 " --> pdb=" O PHE F 170 " (cutoff:3.500A) removed outlier: 5.856A 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 'G' and resid 11 through 14 removed outlier: 6.728A pdb=" N THR G 77 " --> pdb=" O HIS G 7 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N PHE G 78 " --> pdb=" O TYR G 55 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'G' and resid 146 through 148 Processing sheet with id= G, first strand: chain 'G' and resid 173 through 175 Processing sheet with id= H, first strand: chain 'G' and resid 224 through 229 removed outlier: 6.486A pdb=" N ARG G 244 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N LEU G 248 " --> pdb=" O ARG G 244 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'G' and resid 285 through 288 Processing sheet with id= J, first strand: chain 'G' and resid 314 through 317 removed outlier: 6.457A pdb=" N ALA G 565 " --> pdb=" O ILE G 315 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ILE G 317 " --> pdb=" O ALA G 565 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL G 567 " --> pdb=" O ILE G 317 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU G 608 " --> pdb=" O VAL G 594 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ASP G 596 " --> pdb=" O LEU G 608 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N LEU G 610 " --> pdb=" O ASP G 596 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 530 through 534 removed outlier: 6.287A pdb=" N ALA G 376 " --> pdb=" O LEU G 499 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ILE G 501 " --> pdb=" O ALA G 376 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU G 378 " --> pdb=" O ILE G 501 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N GLY G 503 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N LEU G 380 " --> pdb=" O GLY G 503 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N VAL G 379 " --> pdb=" O PRO G 430 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N PHE G 432 " --> pdb=" O VAL G 379 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N TRP G 447 " --> pdb=" O VAL G 433 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ASN G 435 " --> pdb=" O TRP G 447 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N TYR G 449 " --> pdb=" O ASN G 435 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 620 through 623 Processing sheet with id= M, first strand: chain 'G' and resid 901 through 903 removed outlier: 7.352A pdb=" N TYR G 841 " --> pdb=" O PRO G 887 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N ILE G 842 " --> pdb=" O THR G 870 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LEU G 844 " --> pdb=" O PRO G 872 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLU G 874 " --> pdb=" O LEU G 844 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 38 through 41 removed outlier: 4.223A pdb=" N VAL C 49 " --> pdb=" O GLN C 41 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ALA C 116 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE C 103 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N LEU C 74 " --> pdb=" O ILE C 103 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 123 through 125 removed outlier: 6.378A pdb=" N THR C 148 " --> pdb=" O VAL C 124 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'C' and resid 216 through 219 removed outlier: 3.651A pdb=" N ASP C 244 " --> pdb=" O GLN C 236 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASP C 238 " --> pdb=" O ILE C 242 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ILE C 242 " --> pdb=" O ASP C 238 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 532 through 539 removed outlier: 3.698A pdb=" N GLY C 542 " --> pdb=" O ALA C 539 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 3 through 6 Processing sheet with id= S, first strand: chain 'B' and resid 95 through 99 removed outlier: 6.534A pdb=" N TRP B 122 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N VAL B 98 " --> pdb=" O TRP B 122 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE B 124 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL B 153 " --> pdb=" O SER B 125 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'I' and resid 48 through 50 Processing sheet with id= U, first strand: chain 'I' and resid 75 through 81 removed outlier: 3.906A pdb=" N PHE I 91 " --> pdb=" O GLN I 78 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ALA I 80 " --> pdb=" O PRO I 89 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'L' and resid 68 through 70 Processing sheet with id= W, first strand: chain 'L' and resid 60 through 66 removed outlier: 6.908A pdb=" N PHE L 77 " --> pdb=" O LEU L 64 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'M' and resid 65 through 72 removed outlier: 6.800A pdb=" N ILE M 77 " --> pdb=" O TRP M 71 " (cutoff:3.500A) 1868 hydrogen bonds defined for protein. 5388 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: 13.13 Time building geometry restraints manager: 15.77 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: 15969 1.42 - 1.64: 22012 1.64 - 1.86: 410 1.86 - 2.08: 0 2.08 - 2.31: 92 Bond restraints: 38483 Sorted by residual: bond pdb=" CG PRO N 437 " pdb=" CD PRO N 437 " ideal model delta sigma weight residual 1.503 1.371 0.132 3.40e-02 8.65e+02 1.50e+01 bond pdb=" CB PRO N 437 " pdb=" CG PRO N 437 " ideal model delta sigma weight residual 1.492 1.678 -0.186 5.00e-02 4.00e+02 1.39e+01 bond pdb=" N PRO N 437 " pdb=" CD PRO N 437 " ideal model delta sigma weight residual 1.473 1.522 -0.049 1.40e-02 5.10e+03 1.21e+01 bond pdb=" CA MET L 243 " pdb=" C MET L 243 " ideal model delta sigma weight residual 1.523 1.567 -0.044 1.34e-02 5.57e+03 1.07e+01 bond pdb=" N PRO N 437 " pdb=" CA PRO N 437 " ideal model delta sigma weight residual 1.466 1.418 0.048 1.50e-02 4.44e+03 1.03e+01 ... (remaining 38478 not shown) Histogram of bond angle deviations from ideal: 69.17 - 82.85: 88 82.85 - 96.52: 4 96.52 - 110.19: 7661 110.19 - 123.86: 43296 123.86 - 137.53: 1142 Bond angle restraints: 52191 Sorted by residual: angle pdb=" CA PRO N 437 " pdb=" N PRO N 437 " pdb=" CD PRO N 437 " ideal model delta sigma weight residual 112.00 94.70 17.30 1.40e+00 5.10e-01 1.53e+02 angle pdb=" N PRO N 437 " pdb=" CD PRO N 437 " pdb=" CG PRO N 437 " ideal model delta sigma weight residual 103.20 92.03 11.17 1.50e+00 4.44e-01 5.54e+01 angle pdb=" CB LYS C 200 " pdb=" CG LYS C 200 " pdb=" CD LYS C 200 " ideal model delta sigma weight residual 111.30 125.33 -14.03 2.30e+00 1.89e-01 3.72e+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 96.68 13.13 2.21e+00 2.05e-01 3.53e+01 angle pdb=" CB LYS I 27 " pdb=" CG LYS I 27 " pdb=" CD LYS I 27 " ideal model delta sigma weight residual 111.30 124.75 -13.45 2.30e+00 1.89e-01 3.42e+01 ... (remaining 52186 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.14: 21813 34.14 - 68.27: 821 68.27 - 102.41: 65 102.41 - 136.54: 4 136.54 - 170.68: 1 Dihedral angle restraints: 22704 sinusoidal: 9191 harmonic: 13513 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 180.00 136.13 43.87 0 5.00e+00 4.00e-02 7.70e+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 86.92 170.68 1 2.00e+01 2.50e-03 4.77e+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 180.00 145.96 34.04 0 5.00e+00 4.00e-02 4.63e+01 ... (remaining 22701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.240: 5791 4.240 - 8.480: 0 8.480 - 12.720: 0 12.720 - 16.960: 0 16.960 - 21.200: 28 Chirality restraints: 5819 Sorted by residual: 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 10.64 -21.20 2.00e-01 2.50e+01 1.12e+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="FE4 SF4 G1002 " pdb=" S1 SF4 G1002 " pdb=" S2 SF4 G1002 " pdb=" S3 SF4 G1002 " both_signs ideal model delta sigma weight residual False 10.55 -10.62 21.17 2.00e-01 2.50e+01 1.12e+04 ... (remaining 5816 not shown) Planarity restraints: 6516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL N 63 " -0.018 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C VAL N 63 " 0.061 2.00e-02 2.50e+03 pdb=" O VAL N 63 " -0.023 2.00e-02 2.50e+03 pdb=" N THR N 64 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR N 64 " 0.053 5.00e-02 4.00e+02 8.06e-02 1.04e+01 pdb=" N PRO N 65 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO N 65 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO N 65 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER G 763 " -0.049 5.00e-02 4.00e+02 7.54e-02 9.08e+00 pdb=" N PRO G 764 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO G 764 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO G 764 " -0.042 5.00e-02 4.00e+02 ... (remaining 6513 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2568 2.74 - 3.28: 36908 3.28 - 3.82: 68943 3.82 - 4.36: 83268 4.36 - 4.90: 140852 Nonbonded interactions: 332539 Sorted by model distance: nonbonded pdb=" OH TYR L 318 " pdb=" O GLY L 418 " model vdw 2.199 2.440 nonbonded pdb=" O TYR M 177 " pdb=" OG SER M 181 " model vdw 2.209 2.440 nonbonded pdb=" O TRP G 668 " pdb=" OG1 THR G 669 " model vdw 2.221 2.440 nonbonded pdb=" O ARG H 148 " pdb=" OH TYR H 294 " model vdw 2.246 2.440 nonbonded pdb=" O ARG L 516 " pdb=" OG1 THR L 520 " model vdw 2.263 2.440 ... (remaining 332534 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: 0.010 Normalize map: mean=0, sd=1: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 3.880 Check model and map are aligned: 0.500 Set scattering table: 0.300 Process input model: 104.320 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.186 38483 Z= 0.309 Angle : 0.786 17.302 52191 Z= 0.396 Chirality : 1.466 21.200 5819 Planarity : 0.006 0.081 6516 Dihedral : 17.171 170.675 14062 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.39 % Favored : 97.59 % Rotamer: Outliers : 2.59 % Allowed : 20.62 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.11), residues: 4692 helix: 0.28 (0.09), residues: 2696 sheet: -0.46 (0.28), residues: 306 loop : -0.86 (0.14), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP L 143 HIS 0.006 0.001 HIS M 441 PHE 0.040 0.002 PHE L 341 TYR 0.029 0.002 TYR L 428 ARG 0.015 0.001 ARG K 86 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 3869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 440 time to evaluate : 4.138 Fit side-chains REVERT: C 160 MET cc_start: 0.9427 (mmm) cc_final: 0.9107 (mmm) REVERT: C 190 GLN cc_start: 0.8070 (mp10) cc_final: 0.7654 (mp10) REVERT: B 119 GLU cc_start: 0.8212 (mp0) cc_final: 0.7992 (mp0) REVERT: I 16 SER cc_start: 0.7640 (OUTLIER) cc_final: 0.7053 (m) REVERT: H 51 ARG cc_start: 0.7538 (mtp-110) cc_final: 0.7187 (mtp180) REVERT: H 64 MET cc_start: 0.8005 (tmm) cc_final: 0.7725 (tpt) REVERT: N 64 THR cc_start: 0.6277 (m) cc_final: 0.6064 (m) REVERT: N 135 ILE cc_start: 0.8416 (mt) cc_final: 0.8212 (tt) outliers start: 100 outliers final: 73 residues processed: 529 average time/residue: 1.4508 time to fit residues: 935.1738 Evaluate side-chains 487 residues out of total 3869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 413 time to evaluate : 4.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 255 ARG Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 434 THR Chi-restraints excluded: chain G residue 470 SER Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 737 THR Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 791 SER Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 870 THR Chi-restraints excluded: chain G residue 906 LYS Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 78 ASN Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 241 ASP Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 304 ILE Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 457 LEU Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 516 ARG Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 181 SER Chi-restraints excluded: chain M residue 256 SER Chi-restraints excluded: chain M residue 309 THR Chi-restraints excluded: chain M residue 311 ILE Chi-restraints excluded: chain M residue 393 VAL Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 368 HIS Chi-restraints excluded: chain N residue 459 ILE Chi-restraints excluded: chain N residue 464 VAL Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 394 optimal weight: 7.9990 chunk 353 optimal weight: 9.9990 chunk 196 optimal weight: 8.9990 chunk 120 optimal weight: 8.9990 chunk 238 optimal weight: 10.0000 chunk 189 optimal weight: 6.9990 chunk 366 optimal weight: 8.9990 chunk 141 optimal weight: 10.0000 chunk 222 optimal weight: 9.9990 chunk 272 optimal weight: 10.0000 chunk 424 optimal weight: 20.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN F 400 HIS G 232 GLN G 730 GLN G 806 GLN C 359 HIS H 312 ASN A 13 HIS L 58 GLN L 281 HIS L 411 HIS ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 ASN K 91 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.255 38483 Z= 0.862 Angle : 2.210 51.060 52191 Z= 1.445 Chirality : 0.445 7.078 5819 Planarity : 0.006 0.071 6516 Dihedral : 10.141 176.021 5793 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.58 % Favored : 97.38 % Rotamer: Outliers : 4.91 % Allowed : 18.18 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.12), residues: 4692 helix: 0.84 (0.10), residues: 2674 sheet: -0.22 (0.28), residues: 305 loop : -0.64 (0.15), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP L 143 HIS 0.011 0.002 HIS G 178 PHE 0.033 0.002 PHE L 341 TYR 0.023 0.003 TYR N 76 ARG 0.008 0.001 ARG G 158 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 3869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 421 time to evaluate : 4.397 Fit side-chains REVERT: F 275 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8360 (mp0) REVERT: G 643 SER cc_start: 0.8946 (m) cc_final: 0.8644 (p) REVERT: G 670 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8310 (tt0) REVERT: C 127 PHE cc_start: 0.8947 (OUTLIER) cc_final: 0.8376 (t80) REVERT: C 191 ASP cc_start: 0.7493 (t0) cc_final: 0.7200 (m-30) REVERT: C 200 LYS cc_start: 0.9179 (mtpp) cc_final: 0.8876 (mmmt) REVERT: C 228 HIS cc_start: 0.7497 (OUTLIER) cc_final: 0.7235 (p90) REVERT: C 309 MET cc_start: 0.9220 (ttp) cc_final: 0.8991 (ttm) REVERT: C 386 TRP cc_start: 0.8638 (t-100) cc_final: 0.8385 (t-100) REVERT: I 83 LYS cc_start: 0.9014 (mppt) cc_final: 0.8749 (mtmm) REVERT: H 37 ARG cc_start: 0.7350 (OUTLIER) cc_final: 0.6532 (mtp85) REVERT: H 47 TYR cc_start: 0.8647 (m-80) cc_final: 0.8439 (m-80) REVERT: H 296 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7868 (mp10) REVERT: L 551 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8309 (mmtp) REVERT: M 20 THR cc_start: 0.9277 (p) cc_final: 0.8872 (t) REVERT: M 371 MET cc_start: 0.8170 (OUTLIER) cc_final: 0.6470 (mpp) REVERT: M 398 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.7740 (tpp) REVERT: M 439 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8734 (ttp) REVERT: N 43 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8672 (mt) REVERT: N 61 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.7304 (pmm) REVERT: N 135 ILE cc_start: 0.8512 (OUTLIER) cc_final: 0.8293 (tt) REVERT: N 362 TYR cc_start: 0.6999 (OUTLIER) cc_final: 0.4461 (p90) outliers start: 190 outliers final: 89 residues processed: 550 average time/residue: 1.4852 time to fit residues: 990.5416 Evaluate side-chains 508 residues out of total 3869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 405 time to evaluate : 4.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 107 GLN Chi-restraints excluded: chain F residue 255 ARG Chi-restraints excluded: chain F residue 275 GLU Chi-restraints excluded: chain F residue 373 ARG Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 434 ASN Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 470 SER Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 647 MET Chi-restraints excluded: chain G residue 670 GLN Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 796 ASP Chi-restraints excluded: chain G residue 827 SER Chi-restraints excluded: chain G residue 828 GLN Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 906 LYS Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 32 MET Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain H residue 37 ARG Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 296 GLN Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 78 ASN Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 168 MET Chi-restraints excluded: chain L residue 203 LEU Chi-restraints excluded: chain L residue 230 SER Chi-restraints excluded: chain L residue 241 ASP Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 387 SER Chi-restraints excluded: chain L residue 392 VAL Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain L residue 524 ASN Chi-restraints excluded: chain L residue 551 LYS Chi-restraints excluded: chain L residue 571 ILE Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 168 ILE Chi-restraints excluded: chain M residue 181 SER Chi-restraints excluded: chain M residue 291 MET Chi-restraints excluded: chain M residue 309 THR Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 398 MET Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 439 MET Chi-restraints excluded: chain M residue 454 SER Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 334 LEU Chi-restraints excluded: chain N residue 362 TYR Chi-restraints excluded: chain N residue 368 HIS Chi-restraints excluded: chain N residue 464 VAL Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 235 optimal weight: 5.9990 chunk 131 optimal weight: 0.8980 chunk 352 optimal weight: 3.9990 chunk 288 optimal weight: 6.9990 chunk 116 optimal weight: 6.9990 chunk 424 optimal weight: 10.0000 chunk 458 optimal weight: 20.0000 chunk 378 optimal weight: 2.9990 chunk 421 optimal weight: 10.0000 chunk 144 optimal weight: 0.8980 chunk 340 optimal weight: 10.0000 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN G 806 GLN C 236 GLN B 58 ASN B 196 ASN H 45 ASN M 490 HIS N 404 GLN K 27 ASN K 88 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.246 38483 Z= 0.733 Angle : 2.171 50.678 52191 Z= 1.429 Chirality : 0.443 6.520 5819 Planarity : 0.004 0.069 6516 Dihedral : 9.409 173.605 5737 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.30 % Favored : 97.68 % Rotamer: Outliers : 4.29 % Allowed : 19.17 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.12), residues: 4692 helix: 1.31 (0.10), residues: 2673 sheet: -0.26 (0.28), residues: 304 loop : -0.51 (0.15), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP L 143 HIS 0.009 0.001 HIS G 901 PHE 0.028 0.001 PHE L 341 TYR 0.024 0.002 TYR M 435 ARG 0.007 0.000 ARG H 291 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 3869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 421 time to evaluate : 4.374 Fit side-chains REVERT: F 255 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8360 (mtt180) REVERT: E 38 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8185 (tp30) REVERT: G 643 SER cc_start: 0.8930 (OUTLIER) cc_final: 0.8639 (p) REVERT: G 670 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.8118 (tt0) REVERT: G 834 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8164 (mp10) REVERT: C 191 ASP cc_start: 0.7456 (t70) cc_final: 0.7134 (m-30) REVERT: C 200 LYS cc_start: 0.9119 (mtpp) cc_final: 0.8846 (mmmt) REVERT: C 386 TRP cc_start: 0.8600 (t-100) cc_final: 0.8302 (t-100) REVERT: I 3 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7891 (tm) REVERT: H 37 ARG cc_start: 0.7304 (OUTLIER) cc_final: 0.6895 (mmm-85) REVERT: H 47 TYR cc_start: 0.8666 (m-80) cc_final: 0.8416 (m-80) REVERT: H 67 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.7733 (mtp) REVERT: L 107 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8122 (mmm) REVERT: L 424 MET cc_start: 0.8176 (tpp) cc_final: 0.7757 (mmt) REVERT: M 371 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.6277 (mpp) REVERT: N 43 ILE cc_start: 0.8953 (OUTLIER) cc_final: 0.8678 (mt) REVERT: N 61 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.6712 (pmm) outliers start: 166 outliers final: 82 residues processed: 537 average time/residue: 1.4757 time to fit residues: 965.2878 Evaluate side-chains 503 residues out of total 3869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 409 time to evaluate : 4.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 107 GLN Chi-restraints excluded: chain F residue 255 ARG Chi-restraints excluded: chain F residue 373 ARG Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain F residue 434 ASN Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 343 ILE Chi-restraints excluded: chain G residue 380 LEU Chi-restraints excluded: chain G residue 411 LYS Chi-restraints excluded: chain G residue 434 THR Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 643 SER Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 670 GLN Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 796 ASP Chi-restraints excluded: chain G residue 827 SER Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 906 LYS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain H residue 37 ARG Chi-restraints excluded: chain H residue 67 MET Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 107 MET Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 275 MET Chi-restraints excluded: chain L residue 354 LEU Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 387 SER Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain L residue 524 ASN Chi-restraints excluded: chain L residue 568 MET Chi-restraints excluded: chain L residue 571 ILE Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 181 SER Chi-restraints excluded: chain M residue 291 MET Chi-restraints excluded: chain M residue 309 THR Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 244 THR Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain N residue 334 LEU Chi-restraints excluded: chain N residue 368 HIS Chi-restraints excluded: chain N residue 455 ILE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 419 optimal weight: 10.0000 chunk 319 optimal weight: 30.0000 chunk 220 optimal weight: 9.9990 chunk 47 optimal weight: 0.7980 chunk 202 optimal weight: 10.0000 chunk 285 optimal weight: 8.9990 chunk 426 optimal weight: 6.9990 chunk 451 optimal weight: 0.2980 chunk 222 optimal weight: 20.0000 chunk 404 optimal weight: 9.9990 chunk 121 optimal weight: 5.9990 overall best weight: 4.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 196 ASN F 386 GLN G 806 GLN B 196 ASN H 45 ASN N 404 GLN K 27 ASN K 40 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.244 38483 Z= 0.758 Angle : 2.178 50.685 52191 Z= 1.431 Chirality : 0.445 6.552 5819 Planarity : 0.005 0.070 6516 Dihedral : 9.251 174.021 5723 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.58 % Favored : 97.38 % Rotamer: Outliers : 4.79 % Allowed : 19.06 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.91 (0.12), residues: 4692 helix: 1.42 (0.10), residues: 2672 sheet: -0.26 (0.28), residues: 304 loop : -0.45 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP L 143 HIS 0.009 0.001 HIS G 178 PHE 0.029 0.002 PHE L 341 TYR 0.022 0.002 TYR N 424 ARG 0.010 0.000 ARG H 291 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 3869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 415 time to evaluate : 4.571 Fit side-chains REVERT: F 255 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8422 (mtt180) REVERT: E 38 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8110 (tp30) REVERT: G 337 GLU cc_start: 0.9040 (OUTLIER) cc_final: 0.8734 (pm20) REVERT: G 643 SER cc_start: 0.8929 (OUTLIER) cc_final: 0.8634 (p) REVERT: G 670 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8164 (tt0) REVERT: G 834 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.8134 (mp10) REVERT: C 127 PHE cc_start: 0.8939 (OUTLIER) cc_final: 0.8345 (t80) REVERT: C 191 ASP cc_start: 0.7417 (t70) cc_final: 0.7105 (m-30) REVERT: C 200 LYS cc_start: 0.9108 (mtpp) cc_final: 0.8835 (mmmt) REVERT: C 386 TRP cc_start: 0.8618 (t-100) cc_final: 0.8264 (t-100) REVERT: B 116 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8694 (mt0) REVERT: I 3 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7890 (tm) REVERT: H 47 TYR cc_start: 0.8690 (m-80) cc_final: 0.8380 (m-80) REVERT: L 424 MET cc_start: 0.8186 (tpp) cc_final: 0.7767 (mmt) REVERT: M 371 MET cc_start: 0.8146 (OUTLIER) cc_final: 0.6387 (mpp) REVERT: M 398 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.7676 (tpp) REVERT: N 43 ILE cc_start: 0.8963 (OUTLIER) cc_final: 0.8695 (mt) REVERT: N 61 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.6784 (pmm) REVERT: K 97 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8382 (tt0) REVERT: J 86 GLN cc_start: 0.8175 (tp40) cc_final: 0.7776 (mm-40) outliers start: 185 outliers final: 103 residues processed: 547 average time/residue: 1.5165 time to fit residues: 1003.9003 Evaluate side-chains 534 residues out of total 3869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 417 time to evaluate : 4.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 107 GLN Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 255 ARG Chi-restraints excluded: chain F residue 373 ARG Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain F residue 434 ASN Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 312 LYS Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 337 GLU Chi-restraints excluded: chain G residue 380 LEU Chi-restraints excluded: chain G residue 411 LYS Chi-restraints excluded: chain G residue 434 THR Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 643 SER Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 670 GLN Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 796 ASP Chi-restraints excluded: chain G residue 827 SER Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 906 LYS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 116 GLN Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 86 ARG Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 78 ASN Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 230 SER Chi-restraints excluded: chain L residue 241 ASP Chi-restraints excluded: chain L residue 275 MET Chi-restraints excluded: chain L residue 354 LEU Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 387 SER Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain L residue 524 ASN Chi-restraints excluded: chain L residue 568 MET Chi-restraints excluded: chain L residue 571 ILE Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 168 ILE Chi-restraints excluded: chain M residue 181 SER Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 291 MET Chi-restraints excluded: chain M residue 309 THR Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 398 MET Chi-restraints excluded: chain M residue 403 ASN Chi-restraints excluded: chain M residue 425 SER Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 244 THR Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain N residue 334 LEU Chi-restraints excluded: chain N residue 368 HIS Chi-restraints excluded: chain N residue 455 ILE Chi-restraints excluded: chain N residue 464 VAL Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 375 optimal weight: 5.9990 chunk 256 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 336 optimal weight: 9.9990 chunk 186 optimal weight: 4.9990 chunk 385 optimal weight: 0.4980 chunk 312 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 230 optimal weight: 4.9990 chunk 405 optimal weight: 10.0000 chunk 113 optimal weight: 7.9990 overall best weight: 4.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN G 806 GLN B 196 ASN H 45 ASN ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 404 GLN K 27 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.244 38483 Z= 0.763 Angle : 2.179 50.691 52191 Z= 1.431 Chirality : 0.445 6.562 5819 Planarity : 0.004 0.069 6516 Dihedral : 9.216 174.279 5722 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.60 % Favored : 97.38 % Rotamer: Outliers : 4.91 % Allowed : 19.17 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.95 (0.12), residues: 4692 helix: 1.46 (0.10), residues: 2666 sheet: -0.24 (0.28), residues: 304 loop : -0.45 (0.15), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP L 143 HIS 0.009 0.001 HIS G 178 PHE 0.029 0.002 PHE L 341 TYR 0.022 0.002 TYR N 424 ARG 0.008 0.000 ARG L 529 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 3869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 427 time to evaluate : 4.338 Fit side-chains revert: symmetry clash REVERT: F 255 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8265 (mtt180) REVERT: F 275 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8334 (mp0) REVERT: E 38 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8117 (tp30) REVERT: G 337 GLU cc_start: 0.9043 (OUTLIER) cc_final: 0.8755 (pm20) REVERT: G 643 SER cc_start: 0.8936 (OUTLIER) cc_final: 0.8657 (p) REVERT: G 670 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8171 (tt0) REVERT: G 834 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8035 (mp10) REVERT: C 127 PHE cc_start: 0.8939 (OUTLIER) cc_final: 0.8344 (t80) REVERT: C 200 LYS cc_start: 0.9087 (mtpp) cc_final: 0.8787 (mmmt) REVERT: C 307 ARG cc_start: 0.9192 (OUTLIER) cc_final: 0.8442 (mtt180) REVERT: C 386 TRP cc_start: 0.8628 (t-100) cc_final: 0.8317 (t-100) REVERT: I 3 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7860 (tm) REVERT: H 296 GLN cc_start: 0.8081 (mp10) cc_final: 0.7704 (mp10) REVERT: L 424 MET cc_start: 0.8178 (tpp) cc_final: 0.7774 (mmt) REVERT: M 211 LEU cc_start: 0.9151 (mt) cc_final: 0.8944 (mt) REVERT: M 371 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.6398 (mpp) REVERT: M 398 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.7643 (tpp) REVERT: N 43 ILE cc_start: 0.8964 (OUTLIER) cc_final: 0.8699 (mt) REVERT: N 61 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.6921 (pmm) REVERT: K 97 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8374 (tt0) REVERT: J 86 GLN cc_start: 0.8246 (tp40) cc_final: 0.8042 (mm-40) outliers start: 190 outliers final: 108 residues processed: 563 average time/residue: 1.5093 time to fit residues: 1033.0359 Evaluate side-chains 534 residues out of total 3869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 411 time to evaluate : 4.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 107 GLN Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 255 ARG Chi-restraints excluded: chain F residue 275 GLU Chi-restraints excluded: chain F residue 373 ARG Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain F residue 434 ASN Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 312 LYS Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 337 GLU Chi-restraints excluded: chain G residue 380 LEU Chi-restraints excluded: chain G residue 411 LYS Chi-restraints excluded: chain G residue 434 THR Chi-restraints excluded: chain G residue 531 ILE Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 643 SER Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 670 GLN Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 796 ASP Chi-restraints excluded: chain G residue 827 SER Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 855 ASN Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 906 LYS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 307 ARG Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 536 MET Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 86 ARG Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 78 ASN Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 230 SER Chi-restraints excluded: chain L residue 241 ASP Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 354 LEU Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 387 SER Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain L residue 568 MET Chi-restraints excluded: chain L residue 571 ILE Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 168 ILE Chi-restraints excluded: chain M residue 181 SER Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 275 SER Chi-restraints excluded: chain M residue 309 THR Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 398 MET Chi-restraints excluded: chain M residue 403 ASN Chi-restraints excluded: chain M residue 425 SER Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 244 THR Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain N residue 334 LEU Chi-restraints excluded: chain N residue 368 HIS Chi-restraints excluded: chain N residue 395 LYS Chi-restraints excluded: chain N residue 455 ILE Chi-restraints excluded: chain N residue 464 VAL Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 151 optimal weight: 2.9990 chunk 406 optimal weight: 20.0000 chunk 89 optimal weight: 0.5980 chunk 265 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 451 optimal weight: 7.9990 chunk 375 optimal weight: 8.9990 chunk 209 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 chunk 149 optimal weight: 4.9990 chunk 237 optimal weight: 5.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN G 806 GLN B 196 ASN H 45 ASN ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 404 GLN K 27 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.244 38483 Z= 0.756 Angle : 2.179 50.693 52191 Z= 1.431 Chirality : 0.444 6.555 5819 Planarity : 0.004 0.068 6516 Dihedral : 9.177 174.101 5722 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.71 % Favored : 97.27 % Rotamer: Outliers : 4.50 % Allowed : 19.94 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.12), residues: 4692 helix: 1.50 (0.10), residues: 2663 sheet: -0.20 (0.28), residues: 302 loop : -0.42 (0.15), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP L 143 HIS 0.009 0.001 HIS G 178 PHE 0.029 0.002 PHE L 341 TYR 0.021 0.002 TYR N 424 ARG 0.008 0.000 ARG L 529 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 3869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 423 time to evaluate : 4.245 Fit side-chains REVERT: F 40 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7800 (mtpt) REVERT: F 255 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8233 (mtt180) REVERT: F 275 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8324 (mp0) REVERT: G 337 GLU cc_start: 0.9042 (OUTLIER) cc_final: 0.8751 (pm20) REVERT: G 643 SER cc_start: 0.8931 (OUTLIER) cc_final: 0.8655 (p) REVERT: G 670 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8140 (tt0) REVERT: G 834 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.8011 (mp10) REVERT: C 127 PHE cc_start: 0.8938 (OUTLIER) cc_final: 0.8349 (t80) REVERT: C 307 ARG cc_start: 0.9179 (OUTLIER) cc_final: 0.8433 (mtt180) REVERT: C 386 TRP cc_start: 0.8590 (t-100) cc_final: 0.8299 (t-100) REVERT: I 3 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7863 (tm) REVERT: H 291 ARG cc_start: 0.8027 (tpp-160) cc_final: 0.7610 (mmt90) REVERT: L 77 PHE cc_start: 0.8725 (OUTLIER) cc_final: 0.8441 (t80) REVERT: L 107 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.8172 (mmm) REVERT: L 424 MET cc_start: 0.8178 (tpp) cc_final: 0.7771 (mmt) REVERT: M 211 LEU cc_start: 0.9149 (mt) cc_final: 0.8940 (mt) REVERT: M 371 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.6384 (mpp) REVERT: M 398 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.7610 (tpp) REVERT: N 61 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.6728 (pmm) REVERT: N 207 PHE cc_start: 0.8348 (OUTLIER) cc_final: 0.8056 (m-80) REVERT: K 97 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8397 (tt0) outliers start: 174 outliers final: 115 residues processed: 549 average time/residue: 1.5174 time to fit residues: 1010.6529 Evaluate side-chains 543 residues out of total 3869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 411 time to evaluate : 4.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 40 LYS Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 107 GLN Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 255 ARG Chi-restraints excluded: chain F residue 275 GLU Chi-restraints excluded: chain F residue 373 ARG Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain F residue 434 ASN Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 203 CYS Chi-restraints excluded: chain G residue 312 LYS Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 337 GLU Chi-restraints excluded: chain G residue 380 LEU Chi-restraints excluded: chain G residue 411 LYS Chi-restraints excluded: chain G residue 434 THR Chi-restraints excluded: chain G residue 531 ILE Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 643 SER Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 670 GLN Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 796 ASP Chi-restraints excluded: chain G residue 827 SER Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 855 ASN Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 906 LYS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 307 ARG Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 536 MET Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 86 ARG Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 77 PHE Chi-restraints excluded: chain L residue 78 ASN Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 107 MET Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 230 SER Chi-restraints excluded: chain L residue 241 ASP Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 354 LEU Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 374 LEU Chi-restraints excluded: chain L residue 387 SER Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain L residue 524 ASN Chi-restraints excluded: chain L residue 568 MET Chi-restraints excluded: chain L residue 571 ILE Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 145 MET Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 168 ILE Chi-restraints excluded: chain M residue 181 SER Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 275 SER Chi-restraints excluded: chain M residue 309 THR Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 398 MET Chi-restraints excluded: chain M residue 403 ASN Chi-restraints excluded: chain M residue 425 SER Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 244 THR Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain N residue 334 LEU Chi-restraints excluded: chain N residue 368 HIS Chi-restraints excluded: chain N residue 395 LYS Chi-restraints excluded: chain N residue 455 ILE Chi-restraints excluded: chain N residue 464 VAL Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 435 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 257 optimal weight: 7.9990 chunk 329 optimal weight: 4.9990 chunk 255 optimal weight: 6.9990 chunk 380 optimal weight: 10.0000 chunk 252 optimal weight: 5.9990 chunk 450 optimal weight: 0.7980 chunk 281 optimal weight: 6.9990 chunk 274 optimal weight: 6.9990 chunk 207 optimal weight: 4.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN G 806 GLN B 196 ASN H 45 ASN ** M 361 GLN ** 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: 0.8502 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.244 38483 Z= 0.758 Angle : 2.182 50.698 52191 Z= 1.432 Chirality : 0.445 6.557 5819 Planarity : 0.004 0.069 6516 Dihedral : 9.151 174.081 5722 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.58 % Favored : 97.40 % Rotamer: Outliers : 4.63 % Allowed : 19.97 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.12), residues: 4692 helix: 1.51 (0.10), residues: 2665 sheet: -0.21 (0.28), residues: 302 loop : -0.42 (0.15), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP L 143 HIS 0.009 0.001 HIS G 178 PHE 0.029 0.002 PHE L 341 TYR 0.022 0.002 TYR N 424 ARG 0.010 0.000 ARG L 529 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 3869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 418 time to evaluate : 4.257 Fit side-chains REVERT: F 40 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7762 (mtpt) REVERT: F 255 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8098 (mtt180) REVERT: F 275 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8333 (mp0) REVERT: G 337 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.8751 (pm20) REVERT: G 643 SER cc_start: 0.8880 (OUTLIER) cc_final: 0.8631 (p) REVERT: G 670 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8115 (tt0) REVERT: G 834 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.7956 (mp10) REVERT: G 852 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8676 (tt) REVERT: C 16 GLN cc_start: 0.9051 (tp-100) cc_final: 0.8612 (tt0) REVERT: C 127 PHE cc_start: 0.8941 (OUTLIER) cc_final: 0.8350 (t80) REVERT: C 307 ARG cc_start: 0.9181 (OUTLIER) cc_final: 0.8438 (mtt180) REVERT: C 386 TRP cc_start: 0.8642 (t-100) cc_final: 0.8349 (t-100) REVERT: I 3 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7848 (tm) REVERT: I 83 LYS cc_start: 0.9006 (mppt) cc_final: 0.8733 (mttp) REVERT: H 291 ARG cc_start: 0.8002 (tpp-160) cc_final: 0.7713 (mmt90) REVERT: H 296 GLN cc_start: 0.7978 (mp10) cc_final: 0.7728 (mp10) REVERT: L 77 PHE cc_start: 0.8734 (OUTLIER) cc_final: 0.8473 (t80) REVERT: L 424 MET cc_start: 0.8195 (tpp) cc_final: 0.7789 (mmt) REVERT: M 211 LEU cc_start: 0.9154 (mt) cc_final: 0.8938 (mt) REVERT: M 371 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.6276 (mpp) REVERT: M 398 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.7984 (mmm) REVERT: M 487 ASP cc_start: 0.8183 (m-30) cc_final: 0.7961 (m-30) REVERT: N 61 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.6698 (pmm) REVERT: N 207 PHE cc_start: 0.8349 (OUTLIER) cc_final: 0.8059 (m-80) REVERT: K 97 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8444 (tt0) outliers start: 179 outliers final: 121 residues processed: 547 average time/residue: 1.5371 time to fit residues: 1027.6749 Evaluate side-chains 550 residues out of total 3869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 412 time to evaluate : 4.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 40 LYS Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 107 GLN Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 255 ARG Chi-restraints excluded: chain F residue 275 GLU Chi-restraints excluded: chain F residue 373 ARG Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain F residue 434 ASN Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 203 CYS Chi-restraints excluded: chain G residue 312 LYS Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 337 GLU Chi-restraints excluded: chain G residue 380 LEU Chi-restraints excluded: chain G residue 411 LYS Chi-restraints excluded: chain G residue 434 THR Chi-restraints excluded: chain G residue 531 ILE Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 643 SER Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 670 GLN Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 796 ASP Chi-restraints excluded: chain G residue 827 SER Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 855 ASN Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 906 LYS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 307 ARG Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 536 MET Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 86 ARG Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 77 PHE Chi-restraints excluded: chain L residue 78 ASN Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 168 MET Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 241 ASP Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 354 LEU Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 387 SER Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain L residue 524 ASN Chi-restraints excluded: chain L residue 568 MET Chi-restraints excluded: chain L residue 571 ILE Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 145 MET Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 168 ILE Chi-restraints excluded: chain M residue 181 SER Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 249 SER Chi-restraints excluded: chain M residue 275 SER Chi-restraints excluded: chain M residue 309 THR Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 398 MET Chi-restraints excluded: chain M residue 403 ASN Chi-restraints excluded: chain M residue 425 SER Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 244 THR Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain N residue 334 LEU Chi-restraints excluded: chain N residue 368 HIS Chi-restraints excluded: chain N residue 395 LYS Chi-restraints excluded: chain N residue 455 ILE Chi-restraints excluded: chain N residue 464 VAL Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 278 optimal weight: 5.9990 chunk 179 optimal weight: 7.9990 chunk 268 optimal weight: 0.6980 chunk 135 optimal weight: 0.5980 chunk 88 optimal weight: 5.9990 chunk 87 optimal weight: 8.9990 chunk 286 optimal weight: 20.0000 chunk 306 optimal weight: 5.9990 chunk 222 optimal weight: 20.0000 chunk 41 optimal weight: 7.9990 chunk 353 optimal weight: 9.9990 overall best weight: 3.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN G 806 GLN B 196 ASN H 45 ASN ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 404 GLN J 86 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.244 38483 Z= 0.747 Angle : 2.179 50.695 52191 Z= 1.431 Chirality : 0.444 6.529 5819 Planarity : 0.004 0.070 6516 Dihedral : 9.078 173.705 5721 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.62 % Favored : 97.36 % Rotamer: Outliers : 4.37 % Allowed : 20.38 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.12), residues: 4692 helix: 1.55 (0.10), residues: 2668 sheet: -0.21 (0.28), residues: 302 loop : -0.40 (0.15), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP L 143 HIS 0.010 0.001 HIS G 901 PHE 0.028 0.001 PHE L 341 TYR 0.022 0.002 TYR M 435 ARG 0.011 0.000 ARG L 529 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 3869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 418 time to evaluate : 4.477 Fit side-chains REVERT: F 40 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7758 (mtpt) REVERT: F 255 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8036 (mtt180) REVERT: F 275 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8337 (mp0) REVERT: E 38 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8138 (tp30) REVERT: G 337 GLU cc_start: 0.9040 (OUTLIER) cc_final: 0.8730 (pm20) REVERT: G 643 SER cc_start: 0.8879 (OUTLIER) cc_final: 0.8633 (p) REVERT: G 670 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.8087 (tt0) REVERT: G 834 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.7951 (mp10) REVERT: C 127 PHE cc_start: 0.8934 (OUTLIER) cc_final: 0.8337 (t80) REVERT: C 307 ARG cc_start: 0.9170 (OUTLIER) cc_final: 0.8421 (mtt180) REVERT: C 386 TRP cc_start: 0.8630 (t-100) cc_final: 0.8328 (t-100) REVERT: I 3 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7859 (tm) REVERT: I 83 LYS cc_start: 0.8989 (mppt) cc_final: 0.8780 (mttp) REVERT: H 291 ARG cc_start: 0.7957 (tpp-160) cc_final: 0.7663 (mmt90) REVERT: H 296 GLN cc_start: 0.7956 (mp10) cc_final: 0.7694 (mp10) REVERT: L 77 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.8484 (t80) REVERT: L 424 MET cc_start: 0.8187 (tpp) cc_final: 0.7779 (mmt) REVERT: M 211 LEU cc_start: 0.9150 (mt) cc_final: 0.8934 (mt) REVERT: M 371 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.6252 (mpp) REVERT: M 398 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.7967 (mmm) REVERT: M 487 ASP cc_start: 0.8189 (m-30) cc_final: 0.7965 (m-30) REVERT: N 61 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.6761 (pmm) REVERT: N 207 PHE cc_start: 0.8352 (OUTLIER) cc_final: 0.8057 (m-80) REVERT: K 97 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8424 (tt0) outliers start: 169 outliers final: 114 residues processed: 547 average time/residue: 1.5306 time to fit residues: 1014.1201 Evaluate side-chains 543 residues out of total 3869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 412 time to evaluate : 4.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 40 LYS Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 107 GLN Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 255 ARG Chi-restraints excluded: chain F residue 275 GLU Chi-restraints excluded: chain F residue 373 ARG Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain F residue 434 ASN Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 203 CYS Chi-restraints excluded: chain G residue 312 LYS Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 337 GLU Chi-restraints excluded: chain G residue 380 LEU Chi-restraints excluded: chain G residue 411 LYS Chi-restraints excluded: chain G residue 434 THR Chi-restraints excluded: chain G residue 531 ILE Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 619 ASP Chi-restraints excluded: chain G residue 643 SER Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 670 GLN Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 796 ASP Chi-restraints excluded: chain G residue 827 SER Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 906 LYS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 307 ARG Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 86 ARG Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 77 PHE Chi-restraints excluded: chain L residue 78 ASN Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 168 MET Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 241 ASP Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 354 LEU Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 387 SER Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain L residue 516 ARG Chi-restraints excluded: chain L residue 568 MET Chi-restraints excluded: chain L residue 571 ILE Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 145 MET Chi-restraints excluded: chain M residue 181 SER Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 249 SER Chi-restraints excluded: chain M residue 275 SER Chi-restraints excluded: chain M residue 309 THR Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 398 MET Chi-restraints excluded: chain M residue 403 ASN Chi-restraints excluded: chain M residue 425 SER Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 244 THR Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain N residue 334 LEU Chi-restraints excluded: chain N residue 368 HIS Chi-restraints excluded: chain N residue 395 LYS Chi-restraints excluded: chain N residue 455 ILE Chi-restraints excluded: chain N residue 464 VAL Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 409 optimal weight: 10.0000 chunk 431 optimal weight: 4.9990 chunk 393 optimal weight: 20.0000 chunk 419 optimal weight: 6.9990 chunk 252 optimal weight: 6.9990 chunk 182 optimal weight: 6.9990 chunk 329 optimal weight: 7.9990 chunk 128 optimal weight: 7.9990 chunk 379 optimal weight: 5.9990 chunk 396 optimal weight: 8.9990 chunk 417 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN G 806 GLN B 196 ASN H 45 ASN ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 404 GLN K 27 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.243 38483 Z= 0.798 Angle : 2.195 50.693 52191 Z= 1.437 Chirality : 0.447 6.618 5819 Planarity : 0.005 0.066 6516 Dihedral : 9.285 175.058 5721 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.81 % Favored : 97.17 % Rotamer: Outliers : 4.06 % Allowed : 20.74 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.90 (0.12), residues: 4692 helix: 1.42 (0.10), residues: 2661 sheet: -0.36 (0.27), residues: 306 loop : -0.44 (0.15), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP L 143 HIS 0.011 0.001 HIS G 178 PHE 0.029 0.002 PHE L 341 TYR 0.023 0.002 TYR G 641 ARG 0.012 0.001 ARG L 529 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 3869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 415 time to evaluate : 4.088 Fit side-chains revert: symmetry clash REVERT: F 40 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7729 (mtpt) REVERT: F 56 ASP cc_start: 0.8801 (p0) cc_final: 0.8287 (t70) REVERT: F 255 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8330 (mtt180) REVERT: F 275 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8328 (mp0) REVERT: E 38 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8166 (tp30) REVERT: G 337 GLU cc_start: 0.9046 (OUTLIER) cc_final: 0.8753 (pm20) REVERT: G 643 SER cc_start: 0.8915 (OUTLIER) cc_final: 0.8654 (p) REVERT: G 670 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.8252 (tt0) REVERT: G 834 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.7947 (mp10) REVERT: G 852 LEU cc_start: 0.8926 (mt) cc_final: 0.8669 (tt) REVERT: G 859 ARG cc_start: 0.8919 (mtp85) cc_final: 0.8689 (mtp85) REVERT: C 16 GLN cc_start: 0.9050 (tp-100) cc_final: 0.8613 (tt0) REVERT: C 127 PHE cc_start: 0.8961 (OUTLIER) cc_final: 0.8385 (t80) REVERT: C 307 ARG cc_start: 0.9190 (OUTLIER) cc_final: 0.8435 (mtt180) REVERT: C 386 TRP cc_start: 0.8663 (t-100) cc_final: 0.8379 (t-100) REVERT: I 3 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7867 (tm) REVERT: I 83 LYS cc_start: 0.9005 (mppt) cc_final: 0.8779 (mttp) REVERT: H 291 ARG cc_start: 0.8089 (tpp-160) cc_final: 0.7882 (mmt90) REVERT: H 296 GLN cc_start: 0.8048 (mp10) cc_final: 0.7763 (mp10) REVERT: L 77 PHE cc_start: 0.8819 (OUTLIER) cc_final: 0.8525 (t80) REVERT: L 424 MET cc_start: 0.8227 (tpp) cc_final: 0.7809 (mmt) REVERT: L 529 ARG cc_start: 0.8493 (mmm160) cc_final: 0.8269 (mmm160) REVERT: L 530 LEU cc_start: 0.8096 (tm) cc_final: 0.7747 (pp) REVERT: M 211 LEU cc_start: 0.9153 (mt) cc_final: 0.8934 (mt) REVERT: M 371 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.6721 (mpp) REVERT: M 398 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.7723 (tpp) REVERT: M 487 ASP cc_start: 0.8170 (m-30) cc_final: 0.7950 (m-30) REVERT: N 61 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.6741 (pmm) REVERT: N 207 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.8039 (m-80) REVERT: K 97 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8435 (tt0) REVERT: J 86 GLN cc_start: 0.8318 (tp40) cc_final: 0.7914 (tm130) outliers start: 157 outliers final: 116 residues processed: 536 average time/residue: 1.5568 time to fit residues: 1009.3741 Evaluate side-chains 545 residues out of total 3869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 412 time to evaluate : 4.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 40 LYS Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 107 GLN Chi-restraints excluded: chain F residue 255 ARG Chi-restraints excluded: chain F residue 275 GLU Chi-restraints excluded: chain F residue 373 ARG Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain F residue 434 ASN Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 203 CYS Chi-restraints excluded: chain G residue 312 LYS Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 337 GLU Chi-restraints excluded: chain G residue 380 LEU Chi-restraints excluded: chain G residue 411 LYS Chi-restraints excluded: chain G residue 434 THR Chi-restraints excluded: chain G residue 531 ILE Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 619 ASP Chi-restraints excluded: chain G residue 643 SER Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 670 GLN Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 796 ASP Chi-restraints excluded: chain G residue 827 SER Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 906 LYS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 307 ARG Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 86 ARG Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 77 PHE Chi-restraints excluded: chain L residue 78 ASN Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 168 MET Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 241 ASP Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 354 LEU Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 387 SER Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain L residue 516 ARG Chi-restraints excluded: chain L residue 524 ASN Chi-restraints excluded: chain L residue 568 MET Chi-restraints excluded: chain L residue 571 ILE Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 145 MET Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 181 SER Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 249 SER Chi-restraints excluded: chain M residue 275 SER Chi-restraints excluded: chain M residue 309 THR Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 398 MET Chi-restraints excluded: chain M residue 425 SER Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 244 THR Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 334 LEU Chi-restraints excluded: chain N residue 368 HIS Chi-restraints excluded: chain N residue 395 LYS Chi-restraints excluded: chain N residue 411 VAL Chi-restraints excluded: chain N residue 455 ILE Chi-restraints excluded: chain N residue 464 VAL Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 275 optimal weight: 10.0000 chunk 443 optimal weight: 2.9990 chunk 270 optimal weight: 6.9990 chunk 210 optimal weight: 9.9990 chunk 308 optimal weight: 5.9990 chunk 465 optimal weight: 10.0000 chunk 428 optimal weight: 0.7980 chunk 370 optimal weight: 0.0270 chunk 38 optimal weight: 0.9980 chunk 286 optimal weight: 20.0000 chunk 227 optimal weight: 30.0000 overall best weight: 2.1642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN G 806 GLN B 196 ASN H 45 ASN H 188 ASN M 117 HIS M 344 GLN N 404 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.244 38483 Z= 0.726 Angle : 2.176 50.699 52191 Z= 1.430 Chirality : 0.442 6.468 5819 Planarity : 0.004 0.071 6516 Dihedral : 8.960 172.563 5721 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.08 % Allowed : 21.93 % Favored : 74.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.12), residues: 4692 helix: 1.65 (0.10), residues: 2668 sheet: -0.22 (0.28), residues: 304 loop : -0.36 (0.15), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP L 143 HIS 0.009 0.001 HIS G 901 PHE 0.027 0.001 PHE L 341 TYR 0.027 0.001 TYR M 435 ARG 0.011 0.000 ARG L 529 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 3869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 417 time to evaluate : 4.404 Fit side-chains REVERT: F 40 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7789 (mtpt) REVERT: F 56 ASP cc_start: 0.8821 (p0) cc_final: 0.8321 (t70) REVERT: F 255 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.7834 (mtt180) REVERT: F 275 GLU cc_start: 0.8690 (mp0) cc_final: 0.8329 (mp0) REVERT: E 38 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8117 (tp30) REVERT: G 337 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.8718 (pm20) REVERT: G 643 SER cc_start: 0.8879 (OUTLIER) cc_final: 0.8629 (p) REVERT: G 834 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8046 (mp10) REVERT: C 127 PHE cc_start: 0.8898 (OUTLIER) cc_final: 0.8281 (t80) REVERT: C 190 GLN cc_start: 0.8177 (mm110) cc_final: 0.7704 (mp10) REVERT: C 386 TRP cc_start: 0.8592 (t-100) cc_final: 0.8292 (t-100) REVERT: I 3 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7854 (tm) REVERT: I 83 LYS cc_start: 0.8982 (mppt) cc_final: 0.8765 (mttp) REVERT: H 37 ARG cc_start: 0.7250 (OUTLIER) cc_final: 0.6583 (mtp85) REVERT: H 51 ARG cc_start: 0.7780 (mtp180) cc_final: 0.7243 (mtp180) REVERT: H 291 ARG cc_start: 0.7988 (tpp-160) cc_final: 0.7718 (mmt90) REVERT: H 296 GLN cc_start: 0.7746 (mp10) cc_final: 0.7486 (mp10) REVERT: L 107 MET cc_start: 0.8429 (mmt) cc_final: 0.8195 (mmm) REVERT: L 424 MET cc_start: 0.8171 (tpp) cc_final: 0.7769 (mmt) REVERT: L 530 LEU cc_start: 0.8063 (tm) cc_final: 0.7722 (pp) REVERT: M 211 LEU cc_start: 0.9146 (mt) cc_final: 0.8928 (mt) REVERT: M 398 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.7928 (mmm) REVERT: N 207 PHE cc_start: 0.8310 (OUTLIER) cc_final: 0.7988 (m-80) REVERT: K 97 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8457 (tt0) REVERT: J 86 GLN cc_start: 0.8225 (tp40) cc_final: 0.7852 (tm130) outliers start: 119 outliers final: 86 residues processed: 510 average time/residue: 1.5773 time to fit residues: 972.6109 Evaluate side-chains 509 residues out of total 3869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 411 time to evaluate : 4.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 40 LYS Chi-restraints excluded: chain F residue 107 GLN Chi-restraints excluded: chain F residue 255 ARG Chi-restraints excluded: chain F residue 373 ARG Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain F residue 434 ASN Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 203 CYS Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 337 GLU Chi-restraints excluded: chain G residue 411 LYS Chi-restraints excluded: chain G residue 434 THR Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 619 ASP Chi-restraints excluded: chain G residue 643 SER Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 796 ASP Chi-restraints excluded: chain G residue 827 SER Chi-restraints excluded: chain G residue 828 GLN Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 906 LYS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 37 ARG Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 78 ASN Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 168 MET Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 354 LEU Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 387 SER Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain L residue 568 MET Chi-restraints excluded: chain L residue 571 ILE Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 145 MET Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 181 SER Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 249 SER Chi-restraints excluded: chain M residue 275 SER Chi-restraints excluded: chain M residue 398 MET Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain N residue 244 THR Chi-restraints excluded: chain N residue 334 LEU Chi-restraints excluded: chain N residue 368 HIS Chi-restraints excluded: chain N residue 395 LYS Chi-restraints excluded: chain N residue 464 VAL Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 294 optimal weight: 0.8980 chunk 394 optimal weight: 20.0000 chunk 113 optimal weight: 8.9990 chunk 341 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 371 optimal weight: 8.9990 chunk 155 optimal weight: 10.0000 chunk 381 optimal weight: 0.0770 chunk 46 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 overall best weight: 2.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN G 57 ASN G 806 GLN B 196 ASN H 45 ASN K 27 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.093501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.068745 restraints weight = 56300.650| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.34 r_work: 0.2866 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.245 38483 Z= 0.731 Angle : 2.176 50.687 52191 Z= 1.430 Chirality : 0.441 6.457 5819 Planarity : 0.004 0.072 6516 Dihedral : 8.841 172.057 5716 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.72 % Allowed : 22.25 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.12), residues: 4692 helix: 1.72 (0.10), residues: 2662 sheet: -0.20 (0.28), residues: 304 loop : -0.32 (0.15), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 55 HIS 0.011 0.001 HIS G 901 PHE 0.027 0.001 PHE L 341 TYR 0.026 0.001 TYR M 435 ARG 0.013 0.000 ARG L 529 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15062.42 seconds wall clock time: 268 minutes 21.60 seconds (16101.60 seconds total)