Starting phenix.real_space_refine on Sat Apr 13 11:49:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hkq_34858/04_2024/8hkq_34858_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hkq_34858/04_2024/8hkq_34858.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hkq_34858/04_2024/8hkq_34858.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hkq_34858/04_2024/8hkq_34858.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hkq_34858/04_2024/8hkq_34858_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hkq_34858/04_2024/8hkq_34858_updated.pdb" } resolution = 2.9 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= 0.035 sd= 0.118 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: 8 Type Number sf(0) Gaussians K 11 8.98 5 Zn 4 6.06 5 S 204 5.16 5 Na 1 4.78 5 C 18572 2.51 5 N 4768 2.21 5 O 5104 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 297": "OE1" <-> "OE2" Residue "D PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 384": "OD1" <-> "OD2" Residue "D TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 601": "OE1" <-> "OE2" Residue "D PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 808": "OE1" <-> "OE2" Residue "D PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 858": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1014": "OE1" <-> "OE2" Residue "D ASP 1016": "OD1" <-> "OD2" Residue "A PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 384": "OD1" <-> "OD2" Residue "A TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 792": "OD1" <-> "OD2" Residue "A PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 830": "OE1" <-> "OE2" Residue "A GLU 1014": "OE1" <-> "OE2" Residue "A ASP 1016": "OD1" <-> "OD2" Residue "C PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 297": "OE1" <-> "OE2" Residue "C PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 347": "OE1" <-> "OE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 355": "OE1" <-> "OE2" Residue "C TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 411": "OE1" <-> "OE2" Residue "C PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 576": "OE1" <-> "OE2" Residue "C PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 631": "OE1" <-> "OE2" Residue "C PHE 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 792": "OD1" <-> "OD2" Residue "C PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 830": "OE1" <-> "OE2" Residue "C GLU 1014": "OE1" <-> "OE2" Residue "C ASP 1016": "OD1" <-> "OD2" Residue "B GLU 190": "OE1" <-> "OE2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 384": "OD1" <-> "OD2" Residue "B ASP 401": "OD1" <-> "OD2" Residue "B TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 411": "OE1" <-> "OE2" Residue "B PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 631": "OE1" <-> "OE2" Residue "B PHE 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 792": "OD1" <-> "OD2" Residue "B GLU 808": "OE1" <-> "OE2" Residue "B PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 858": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1016": "OD1" <-> "OD2" Residue "B ASP 1168": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 28676 Number of models: 1 Model: "" Number of chains: 8 Chain: "D" Number of atoms: 7137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 902, 7137 Classifications: {'peptide': 902} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 42, 'TRANS': 859} Chain breaks: 6 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 138 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 94 Chain: "A" Number of atoms: 7137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 902, 7137 Classifications: {'peptide': 902} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 42, 'TRANS': 859} Chain breaks: 6 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 138 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 94 Chain: "C" Number of atoms: 7137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 902, 7137 Classifications: {'peptide': 902} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 42, 'TRANS': 859} Chain breaks: 6 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 138 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 94 Chain: "B" Number of atoms: 7137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 902, 7137 Classifications: {'peptide': 902} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 42, 'TRANS': 859} Chain breaks: 6 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 138 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 94 Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 32 Unusual residues: {' K': 3, ' ZN': 1, 'LQ9': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 32 Unusual residues: {' K': 2, ' NA': 1, ' ZN': 1, 'LQ9': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 32 Unusual residues: {' K': 3, ' ZN': 1, 'LQ9': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 32 Unusual residues: {' K': 3, ' ZN': 1, 'LQ9': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1489 SG CYS D 308 73.247 61.132 112.428 1.00 69.48 S ATOM 4396 SG CYS D 777 53.197 83.668 14.260 1.00 73.37 S ATOM 4402 SG CYS D 778 50.227 86.150 14.478 1.00 80.19 S ATOM 4456 SG CYS D 785 53.680 87.362 13.299 1.00124.06 S ATOM 8626 SG CYS A 308 61.141 78.495 112.418 1.00 69.36 S ATOM 11533 SG CYS A 777 83.681 98.631 14.270 1.00 76.35 S ATOM 11539 SG CYS A 778 86.160 101.606 14.480 1.00 80.17 S ATOM 11593 SG CYS A 785 87.375 98.143 13.318 1.00120.40 S ATOM 15763 SG CYS C 308 90.728 73.303 112.466 1.00 70.07 S ATOM 18670 SG CYS C 777 68.176 53.235 14.281 1.00 76.42 S ATOM 18676 SG CYS C 778 65.703 50.251 14.480 1.00 82.13 S ATOM 18730 SG CYS C 785 64.478 53.719 13.338 1.00123.20 S ATOM 22900 SG CYS B 308 78.613 90.716 112.532 1.00 72.64 S ATOM 25807 SG CYS B 777 98.608 68.191 14.288 1.00 74.79 S ATOM 25813 SG CYS B 778 101.596 65.724 14.484 1.00 80.48 S ATOM 25867 SG CYS B 785 98.137 64.493 13.336 1.00122.16 S Time building chain proxies: 14.23, per 1000 atoms: 0.50 Number of scatterers: 28676 At special positions: 0 Unit cell: (152.88, 152.88, 144.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 4 29.99 K 11 19.00 S 204 16.00 Na 1 11.00 F 12 9.00 O 5104 8.00 N 4768 7.00 C 18572 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: 12.11 Conformation dependent library (CDL) restraints added in 5.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1302 " pdb="ZN ZN A1302 " - pdb=" ND1 HIS A 787 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 785 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 777 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 778 " pdb=" ZN B1302 " pdb="ZN ZN B1302 " - pdb=" ND1 HIS B 787 " pdb="ZN ZN B1302 " - pdb=" SG CYS B 785 " pdb="ZN ZN B1302 " - pdb=" SG CYS B 778 " pdb="ZN ZN B1302 " - pdb=" SG CYS B 777 " pdb=" ZN C1302 " pdb="ZN ZN C1302 " - pdb=" ND1 HIS C 787 " pdb="ZN ZN C1302 " - pdb=" SG CYS C 785 " pdb="ZN ZN C1302 " - pdb=" SG CYS C 777 " pdb="ZN ZN C1302 " - pdb=" SG CYS C 778 " pdb=" ZN D1302 " pdb="ZN ZN D1302 " - pdb=" ND1 HIS D 787 " pdb="ZN ZN D1302 " - pdb=" SG CYS D 785 " pdb="ZN ZN D1302 " - pdb=" SG CYS D 777 " pdb="ZN ZN D1302 " - pdb=" SG CYS D 778 " Number of angles added : 12 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6912 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 152 helices and 24 sheets defined 45.9% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.65 Creating SS restraints... Processing helix chain 'D' and resid 111 through 135 Processing helix chain 'D' and resid 165 through 168 No H-bonds generated for 'chain 'D' and resid 165 through 168' Processing helix chain 'D' and resid 174 through 197 Processing helix chain 'D' and resid 212 through 227 Proline residue: D 221 - end of helix removed outlier: 4.329A pdb=" N ILE D 226 " --> pdb=" O PHE D 222 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE D 227 " --> pdb=" O ILE D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 231 No H-bonds generated for 'chain 'D' and resid 229 through 231' Processing helix chain 'D' and resid 238 through 255 removed outlier: 3.777A pdb=" N CYS D 242 " --> pdb=" O PHE D 239 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASN D 254 " --> pdb=" O ASN D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 292 removed outlier: 3.632A pdb=" N ILE D 273 " --> pdb=" O ASN D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 312 Processing helix chain 'D' and resid 325 through 356 Proline residue: D 343 - end of helix Processing helix chain 'D' and resid 383 through 393 Processing helix chain 'D' and resid 397 through 399 No H-bonds generated for 'chain 'D' and resid 397 through 399' Processing helix chain 'D' and resid 414 through 420 Processing helix chain 'D' and resid 423 through 426 No H-bonds generated for 'chain 'D' and resid 423 through 426' Processing helix chain 'D' and resid 439 through 444 Processing helix chain 'D' and resid 464 through 481 Processing helix chain 'D' and resid 494 through 498 removed outlier: 4.330A pdb=" N PHE D 498 " --> pdb=" O GLU D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 522 Processing helix chain 'D' and resid 526 through 533 Processing helix chain 'D' and resid 548 through 558 removed outlier: 4.031A pdb=" N GLY D 558 " --> pdb=" O GLY D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 575 No H-bonds generated for 'chain 'D' and resid 573 through 575' Processing helix chain 'D' and resid 580 through 590 Processing helix chain 'D' and resid 634 through 643 Processing helix chain 'D' and resid 793 through 796 No H-bonds generated for 'chain 'D' and resid 793 through 796' Processing helix chain 'D' and resid 812 through 822 Proline residue: D 820 - end of helix Processing helix chain 'D' and resid 844 through 850 Processing helix chain 'D' and resid 866 through 872 Processing helix chain 'D' and resid 887 through 890 removed outlier: 3.546A pdb=" N SER D 890 " --> pdb=" O SER D 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 887 through 890' Processing helix chain 'D' and resid 894 through 911 removed outlier: 4.046A pdb=" N ASP D 898 " --> pdb=" O TYR D 895 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LYS D 900 " --> pdb=" O ALA D 897 " (cutoff:3.500A) Processing helix chain 'D' and resid 924 through 929 removed outlier: 4.324A pdb=" N ARG D 928 " --> pdb=" O SER D 925 " (cutoff:3.500A) Processing helix chain 'D' and resid 937 through 951 removed outlier: 3.716A pdb=" N SER D 943 " --> pdb=" O SER D 939 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS D 944 " --> pdb=" O LEU D 940 " (cutoff:3.500A) Processing helix chain 'D' and resid 958 through 960 No H-bonds generated for 'chain 'D' and resid 958 through 960' Processing helix chain 'D' and resid 962 through 965 No H-bonds generated for 'chain 'D' and resid 962 through 965' Processing helix chain 'D' and resid 972 through 983 Processing helix chain 'D' and resid 988 through 996 Processing helix chain 'D' and resid 1014 through 1016 No H-bonds generated for 'chain 'D' and resid 1014 through 1016' Processing helix chain 'D' and resid 1022 through 1032 Processing helix chain 'D' and resid 1130 through 1142 Processing helix chain 'D' and resid 1145 through 1160 Processing helix chain 'A' and resid 111 through 135 Processing helix chain 'A' and resid 165 through 168 No H-bonds generated for 'chain 'A' and resid 165 through 168' Processing helix chain 'A' and resid 174 through 197 Processing helix chain 'A' and resid 212 through 227 Proline residue: A 221 - end of helix removed outlier: 4.307A pdb=" N ILE A 226 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 238 through 253 removed outlier: 3.555A pdb=" N CYS A 242 " --> pdb=" O PHE A 239 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 253 " --> pdb=" O GLU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 294 Processing helix chain 'A' and resid 301 through 312 Processing helix chain 'A' and resid 325 through 357 Proline residue: A 343 - end of helix Processing helix chain 'A' and resid 383 through 393 Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 423 through 426 No H-bonds generated for 'chain 'A' and resid 423 through 426' Processing helix chain 'A' and resid 439 through 444 Processing helix chain 'A' and resid 464 through 481 Processing helix chain 'A' and resid 494 through 498 removed outlier: 4.261A pdb=" N PHE A 498 " --> pdb=" O GLU A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 522 Processing helix chain 'A' and resid 526 through 533 Processing helix chain 'A' and resid 548 through 558 removed outlier: 4.008A pdb=" N GLY A 558 " --> pdb=" O GLY A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 575 No H-bonds generated for 'chain 'A' and resid 573 through 575' Processing helix chain 'A' and resid 580 through 590 Processing helix chain 'A' and resid 632 through 643 removed outlier: 4.344A pdb=" N PHE A 635 " --> pdb=" O ASN A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 796 No H-bonds generated for 'chain 'A' and resid 793 through 796' Processing helix chain 'A' and resid 812 through 822 Proline residue: A 820 - end of helix Processing helix chain 'A' and resid 844 through 850 Processing helix chain 'A' and resid 866 through 872 Processing helix chain 'A' and resid 887 through 890 removed outlier: 3.562A pdb=" N SER A 890 " --> pdb=" O SER A 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 887 through 890' Processing helix chain 'A' and resid 894 through 911 removed outlier: 4.046A pdb=" N ASP A 898 " --> pdb=" O TYR A 895 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LYS A 900 " --> pdb=" O ALA A 897 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 911 " --> pdb=" O MET A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 929 removed outlier: 4.327A pdb=" N ARG A 928 " --> pdb=" O SER A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 951 removed outlier: 3.710A pdb=" N SER A 943 " --> pdb=" O SER A 939 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS A 944 " --> pdb=" O LEU A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 960 No H-bonds generated for 'chain 'A' and resid 958 through 960' Processing helix chain 'A' and resid 962 through 965 No H-bonds generated for 'chain 'A' and resid 962 through 965' Processing helix chain 'A' and resid 972 through 983 Processing helix chain 'A' and resid 988 through 996 Processing helix chain 'A' and resid 1014 through 1016 No H-bonds generated for 'chain 'A' and resid 1014 through 1016' Processing helix chain 'A' and resid 1022 through 1032 Processing helix chain 'A' and resid 1130 through 1142 Processing helix chain 'A' and resid 1145 through 1160 Processing helix chain 'C' and resid 111 through 135 Processing helix chain 'C' and resid 165 through 168 No H-bonds generated for 'chain 'C' and resid 165 through 168' Processing helix chain 'C' and resid 174 through 197 Processing helix chain 'C' and resid 212 through 227 Proline residue: C 221 - end of helix removed outlier: 4.278A pdb=" N ILE C 226 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N PHE C 227 " --> pdb=" O ILE C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 231 No H-bonds generated for 'chain 'C' and resid 229 through 231' Processing helix chain 'C' and resid 238 through 253 removed outlier: 4.049A pdb=" N CYS C 242 " --> pdb=" O PHE C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 292 Processing helix chain 'C' and resid 301 through 312 Processing helix chain 'C' and resid 325 through 356 Proline residue: C 343 - end of helix Processing helix chain 'C' and resid 383 through 393 Processing helix chain 'C' and resid 397 through 399 No H-bonds generated for 'chain 'C' and resid 397 through 399' Processing helix chain 'C' and resid 414 through 420 Processing helix chain 'C' and resid 423 through 426 No H-bonds generated for 'chain 'C' and resid 423 through 426' Processing helix chain 'C' and resid 439 through 444 Processing helix chain 'C' and resid 464 through 481 Processing helix chain 'C' and resid 494 through 498 removed outlier: 4.331A pdb=" N PHE C 498 " --> pdb=" O GLU C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 522 Processing helix chain 'C' and resid 526 through 533 Processing helix chain 'C' and resid 548 through 558 removed outlier: 4.020A pdb=" N GLY C 558 " --> pdb=" O GLY C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 575 No H-bonds generated for 'chain 'C' and resid 573 through 575' Processing helix chain 'C' and resid 580 through 590 Processing helix chain 'C' and resid 632 through 643 removed outlier: 4.343A pdb=" N PHE C 635 " --> pdb=" O ASN C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 793 through 796 No H-bonds generated for 'chain 'C' and resid 793 through 796' Processing helix chain 'C' and resid 812 through 822 Proline residue: C 820 - end of helix Processing helix chain 'C' and resid 844 through 850 Processing helix chain 'C' and resid 866 through 872 Processing helix chain 'C' and resid 887 through 890 removed outlier: 3.556A pdb=" N SER C 890 " --> pdb=" O SER C 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 887 through 890' Processing helix chain 'C' and resid 894 through 911 removed outlier: 4.061A pdb=" N ASP C 898 " --> pdb=" O TYR C 895 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LYS C 900 " --> pdb=" O ALA C 897 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU C 911 " --> pdb=" O MET C 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 924 through 929 removed outlier: 4.321A pdb=" N ARG C 928 " --> pdb=" O SER C 925 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 951 removed outlier: 3.720A pdb=" N SER C 943 " --> pdb=" O SER C 939 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS C 944 " --> pdb=" O LEU C 940 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 960 No H-bonds generated for 'chain 'C' and resid 958 through 960' Processing helix chain 'C' and resid 962 through 965 No H-bonds generated for 'chain 'C' and resid 962 through 965' Processing helix chain 'C' and resid 972 through 983 Processing helix chain 'C' and resid 988 through 996 Processing helix chain 'C' and resid 1014 through 1016 No H-bonds generated for 'chain 'C' and resid 1014 through 1016' Processing helix chain 'C' and resid 1022 through 1032 Processing helix chain 'C' and resid 1130 through 1142 Processing helix chain 'C' and resid 1145 through 1160 Processing helix chain 'B' and resid 111 through 135 Processing helix chain 'B' and resid 165 through 168 No H-bonds generated for 'chain 'B' and resid 165 through 168' Processing helix chain 'B' and resid 174 through 197 Processing helix chain 'B' and resid 212 through 227 Proline residue: B 221 - end of helix removed outlier: 3.931A pdb=" N ILE B 226 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE B 227 " --> pdb=" O ILE B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 231 No H-bonds generated for 'chain 'B' and resid 229 through 231' Processing helix chain 'B' and resid 238 through 255 removed outlier: 3.556A pdb=" N CYS B 242 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE B 253 " --> pdb=" O GLU B 250 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN B 254 " --> pdb=" O ASN B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 292 removed outlier: 3.587A pdb=" N ILE B 273 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 312 Processing helix chain 'B' and resid 325 through 356 Proline residue: B 343 - end of helix Processing helix chain 'B' and resid 383 through 393 Processing helix chain 'B' and resid 397 through 399 No H-bonds generated for 'chain 'B' and resid 397 through 399' Processing helix chain 'B' and resid 414 through 420 Processing helix chain 'B' and resid 423 through 426 No H-bonds generated for 'chain 'B' and resid 423 through 426' Processing helix chain 'B' and resid 439 through 444 Processing helix chain 'B' and resid 464 through 481 Processing helix chain 'B' and resid 494 through 498 removed outlier: 4.338A pdb=" N PHE B 498 " --> pdb=" O GLU B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 522 Processing helix chain 'B' and resid 526 through 533 Processing helix chain 'B' and resid 548 through 558 removed outlier: 4.057A pdb=" N GLY B 558 " --> pdb=" O GLY B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 575 No H-bonds generated for 'chain 'B' and resid 573 through 575' Processing helix chain 'B' and resid 580 through 590 Processing helix chain 'B' and resid 634 through 643 Processing helix chain 'B' and resid 793 through 796 No H-bonds generated for 'chain 'B' and resid 793 through 796' Processing helix chain 'B' and resid 812 through 822 Proline residue: B 820 - end of helix Processing helix chain 'B' and resid 844 through 850 Processing helix chain 'B' and resid 866 through 872 Processing helix chain 'B' and resid 887 through 890 removed outlier: 3.570A pdb=" N SER B 890 " --> pdb=" O SER B 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 887 through 890' Processing helix chain 'B' and resid 894 through 911 removed outlier: 4.056A pdb=" N ASP B 898 " --> pdb=" O TYR B 895 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LYS B 900 " --> pdb=" O ALA B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 929 removed outlier: 4.329A pdb=" N ARG B 928 " --> pdb=" O SER B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 937 through 951 removed outlier: 3.713A pdb=" N SER B 943 " --> pdb=" O SER B 939 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS B 944 " --> pdb=" O LEU B 940 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 960 No H-bonds generated for 'chain 'B' and resid 958 through 960' Processing helix chain 'B' and resid 962 through 965 No H-bonds generated for 'chain 'B' and resid 962 through 965' Processing helix chain 'B' and resid 972 through 983 Processing helix chain 'B' and resid 988 through 996 Processing helix chain 'B' and resid 1014 through 1016 No H-bonds generated for 'chain 'B' and resid 1014 through 1016' Processing helix chain 'B' and resid 1022 through 1032 Processing helix chain 'B' and resid 1130 through 1142 Processing helix chain 'B' and resid 1145 through 1160 Processing sheet with id= A, first strand: chain 'D' and resid 505 through 508 removed outlier: 6.588A pdb=" N CYS D 453 " --> pdb=" O TYR D 488 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N GLN D 490 " --> pdb=" O CYS D 453 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ILE D 455 " --> pdb=" O GLN D 490 " (cutoff:3.500A) removed outlier: 8.954A pdb=" N PHE D 454 " --> pdb=" O HIS D 373 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL D 375 " --> pdb=" O PHE D 454 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N TYR D 403 " --> pdb=" O VAL D 374 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N LEU D 376 " --> pdb=" O TYR D 403 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL D 405 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL D 378 " --> pdb=" O VAL D 405 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LEU D 407 " --> pdb=" O VAL D 378 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 560 through 565 removed outlier: 6.665A pdb=" N ILE D 625 " --> pdb=" O LEU D 595 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LEU D 595 " --> pdb=" O ILE D 625 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 749 through 753 Processing sheet with id= D, first strand: chain 'D' and resid 856 through 860 removed outlier: 6.003A pdb=" N ILE D 834 " --> pdb=" O TYR D 857 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N MET D 859 " --> pdb=" O ILE D 834 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N LEU D 836 " --> pdb=" O MET D 859 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE D 803 " --> pdb=" O VAL D 835 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LEU D 837 " --> pdb=" O ILE D 803 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL D 805 " --> pdb=" O LEU D 837 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N ILE D 804 " --> pdb=" O ASP D 878 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LEU D 880 " --> pdb=" O ILE D 804 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N SER D 806 " --> pdb=" O LEU D 880 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N VAL D 882 " --> pdb=" O SER D 806 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N SER D 916 " --> pdb=" O LEU D 880 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N VAL D 882 " --> pdb=" O SER D 916 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N THR D 918 " --> pdb=" O VAL D 882 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 1006 through 1012 removed outlier: 4.051A pdb=" N ASP D1194 " --> pdb=" O ILE D1012 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 1039 through 1045 Processing sheet with id= G, first strand: chain 'A' and resid 505 through 508 removed outlier: 6.599A pdb=" N CYS A 453 " --> pdb=" O TYR A 488 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N GLN A 490 " --> pdb=" O CYS A 453 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ILE A 455 " --> pdb=" O GLN A 490 " (cutoff:3.500A) removed outlier: 8.962A pdb=" N PHE A 454 " --> pdb=" O HIS A 373 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N VAL A 375 " --> pdb=" O PHE A 454 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N TYR A 403 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N LEU A 376 " --> pdb=" O TYR A 403 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL A 405 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N VAL A 378 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N LEU A 407 " --> pdb=" O VAL A 378 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 560 through 565 removed outlier: 6.661A pdb=" N ILE A 625 " --> pdb=" O LEU A 595 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N LEU A 595 " --> pdb=" O ILE A 625 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 749 through 753 Processing sheet with id= J, first strand: chain 'A' and resid 856 through 860 removed outlier: 6.015A pdb=" N ILE A 834 " --> pdb=" O TYR A 857 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N MET A 859 " --> pdb=" O ILE A 834 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N LEU A 836 " --> pdb=" O MET A 859 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE A 803 " --> pdb=" O VAL A 835 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LEU A 837 " --> pdb=" O ILE A 803 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL A 805 " --> pdb=" O LEU A 837 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ILE A 804 " --> pdb=" O ASP A 878 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU A 880 " --> pdb=" O ILE A 804 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N SER A 806 " --> pdb=" O LEU A 880 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N VAL A 882 " --> pdb=" O SER A 806 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N SER A 916 " --> pdb=" O LEU A 880 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N VAL A 882 " --> pdb=" O SER A 916 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N THR A 918 " --> pdb=" O VAL A 882 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 1006 through 1012 removed outlier: 4.033A pdb=" N ASP A1194 " --> pdb=" O ILE A1012 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 1039 through 1045 Processing sheet with id= M, first strand: chain 'C' and resid 505 through 508 removed outlier: 6.598A pdb=" N CYS C 453 " --> pdb=" O TYR C 488 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N GLN C 490 " --> pdb=" O CYS C 453 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE C 455 " --> pdb=" O GLN C 490 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N PHE C 454 " --> pdb=" O HIS C 373 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL C 375 " --> pdb=" O PHE C 454 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N TYR C 403 " --> pdb=" O VAL C 374 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N LEU C 376 " --> pdb=" O TYR C 403 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL C 405 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N VAL C 378 " --> pdb=" O VAL C 405 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N LEU C 407 " --> pdb=" O VAL C 378 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 560 through 565 removed outlier: 6.653A pdb=" N ILE C 625 " --> pdb=" O LEU C 595 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LEU C 595 " --> pdb=" O ILE C 625 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 749 through 753 Processing sheet with id= P, first strand: chain 'C' and resid 856 through 860 removed outlier: 6.000A pdb=" N ILE C 834 " --> pdb=" O TYR C 857 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N MET C 859 " --> pdb=" O ILE C 834 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N LEU C 836 " --> pdb=" O MET C 859 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE C 803 " --> pdb=" O VAL C 835 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LEU C 837 " --> pdb=" O ILE C 803 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL C 805 " --> pdb=" O LEU C 837 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ILE C 804 " --> pdb=" O ASP C 878 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU C 880 " --> pdb=" O ILE C 804 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N SER C 806 " --> pdb=" O LEU C 880 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N VAL C 882 " --> pdb=" O SER C 806 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N SER C 916 " --> pdb=" O LEU C 880 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N VAL C 882 " --> pdb=" O SER C 916 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR C 918 " --> pdb=" O VAL C 882 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 1006 through 1012 removed outlier: 4.148A pdb=" N ASP C1194 " --> pdb=" O ILE C1012 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 1039 through 1045 Processing sheet with id= S, first strand: chain 'B' and resid 505 through 508 removed outlier: 6.600A pdb=" N CYS B 453 " --> pdb=" O TYR B 488 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N GLN B 490 " --> pdb=" O CYS B 453 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ILE B 455 " --> pdb=" O GLN B 490 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N PHE B 454 " --> pdb=" O HIS B 373 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL B 375 " --> pdb=" O PHE B 454 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N TYR B 403 " --> pdb=" O VAL B 374 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LEU B 376 " --> pdb=" O TYR B 403 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL B 405 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N VAL B 378 " --> pdb=" O VAL B 405 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N LEU B 407 " --> pdb=" O VAL B 378 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 560 through 565 removed outlier: 6.661A pdb=" N ILE B 625 " --> pdb=" O LEU B 595 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N LEU B 595 " --> pdb=" O ILE B 625 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 749 through 753 Processing sheet with id= V, first strand: chain 'B' and resid 856 through 860 removed outlier: 6.005A pdb=" N ILE B 834 " --> pdb=" O TYR B 857 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N MET B 859 " --> pdb=" O ILE B 834 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LEU B 836 " --> pdb=" O MET B 859 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE B 803 " --> pdb=" O VAL B 835 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LEU B 837 " --> pdb=" O ILE B 803 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL B 805 " --> pdb=" O LEU B 837 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ILE B 804 " --> pdb=" O ASP B 878 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LEU B 880 " --> pdb=" O ILE B 804 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N SER B 806 " --> pdb=" O LEU B 880 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VAL B 882 " --> pdb=" O SER B 806 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N SER B 916 " --> pdb=" O LEU B 880 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N VAL B 882 " --> pdb=" O SER B 916 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N THR B 918 " --> pdb=" O VAL B 882 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 1006 through 1012 removed outlier: 4.035A pdb=" N ASP B1194 " --> pdb=" O ILE B1012 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 1039 through 1045 1159 hydrogen bonds defined for protein. 2943 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: 10.76 Time building geometry restraints manager: 12.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.52 - 0.82: 1 0.82 - 1.12: 0 1.12 - 1.42: 12107 1.42 - 1.71: 16935 1.71 - 2.01: 297 Bond restraints: 29340 Sorted by residual: bond pdb=" CG PRO C 229 " pdb=" CD PRO C 229 " ideal model delta sigma weight residual 1.503 0.520 0.983 3.40e-02 8.65e+02 8.36e+02 bond pdb=" CB PRO C 229 " pdb=" CG PRO C 229 " ideal model delta sigma weight residual 1.492 2.013 -0.521 5.00e-02 4.00e+02 1.09e+02 bond pdb=" C27 LQ9 C1301 " pdb=" N12 LQ9 C1301 " ideal model delta sigma weight residual 1.326 1.494 -0.168 2.00e-02 2.50e+03 7.08e+01 bond pdb=" C27 LQ9 A1301 " pdb=" N12 LQ9 A1301 " ideal model delta sigma weight residual 1.326 1.493 -0.167 2.00e-02 2.50e+03 6.94e+01 bond pdb=" C27 LQ9 D1301 " pdb=" N12 LQ9 D1301 " ideal model delta sigma weight residual 1.326 1.493 -0.167 2.00e-02 2.50e+03 6.93e+01 ... (remaining 29335 not shown) Histogram of bond angle deviations from ideal: 44.69 - 63.00: 1 63.00 - 81.31: 1 81.31 - 99.62: 4 99.62 - 117.93: 21891 117.93 - 136.24: 17987 Bond angle restraints: 39884 Sorted by residual: angle pdb=" N PRO C 229 " pdb=" CD PRO C 229 " pdb=" CG PRO C 229 " ideal model delta sigma weight residual 103.20 44.69 58.51 1.50e+00 4.44e-01 1.52e+03 angle pdb=" CA PRO C 229 " pdb=" CB PRO C 229 " pdb=" CG PRO C 229 " ideal model delta sigma weight residual 104.50 73.07 31.43 1.90e+00 2.77e-01 2.74e+02 angle pdb=" N PRO C 229 " pdb=" CA PRO C 229 " pdb=" CB PRO C 229 " ideal model delta sigma weight residual 103.08 93.54 9.54 9.70e-01 1.06e+00 9.68e+01 angle pdb=" CB PRO C 229 " pdb=" CG PRO C 229 " pdb=" CD PRO C 229 " ideal model delta sigma weight residual 106.10 83.98 22.12 3.20e+00 9.77e-02 4.78e+01 angle pdb=" CA PRO C 229 " pdb=" N PRO C 229 " pdb=" CD PRO C 229 " ideal model delta sigma weight residual 112.00 103.86 8.14 1.40e+00 5.10e-01 3.38e+01 ... (remaining 39879 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.23: 15872 21.23 - 42.46: 1401 42.46 - 63.68: 216 63.68 - 84.91: 36 84.91 - 106.14: 7 Dihedral angle restraints: 17532 sinusoidal: 6880 harmonic: 10652 Sorted by residual: dihedral pdb=" CA CYS B 148 " pdb=" C CYS B 148 " pdb=" N PRO B 149 " pdb=" CA PRO B 149 " ideal model delta harmonic sigma weight residual 180.00 146.11 33.89 0 5.00e+00 4.00e-02 4.59e+01 dihedral pdb=" CA CYS C 148 " pdb=" C CYS C 148 " pdb=" N PRO C 149 " pdb=" CA PRO C 149 " ideal model delta harmonic sigma weight residual 180.00 146.43 33.57 0 5.00e+00 4.00e-02 4.51e+01 dihedral pdb=" CA CYS A 148 " pdb=" C CYS A 148 " pdb=" N PRO A 149 " pdb=" CA PRO A 149 " ideal model delta harmonic sigma weight residual 180.00 147.80 32.20 0 5.00e+00 4.00e-02 4.15e+01 ... (remaining 17529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3576 0.046 - 0.093: 729 0.093 - 0.139: 233 0.139 - 0.185: 15 0.185 - 0.232: 3 Chirality restraints: 4556 Sorted by residual: chirality pdb=" CA SER C 313 " pdb=" N SER C 313 " pdb=" C SER C 313 " pdb=" CB SER C 313 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA MET A 192 " pdb=" N MET A 192 " pdb=" C MET A 192 " pdb=" CB MET A 192 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" C13 LQ9 D1301 " pdb=" C15 LQ9 D1301 " pdb=" C17 LQ9 D1301 " pdb=" N07 LQ9 D1301 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.19 2.00e-01 2.50e+01 8.83e-01 ... (remaining 4553 not shown) Planarity restraints: 5008 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP B 325 " 0.064 5.00e-02 4.00e+02 9.31e-02 1.39e+01 pdb=" N PRO B 326 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO B 326 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 326 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 325 " 0.017 2.00e-02 2.50e+03 1.77e-02 7.84e+00 pdb=" CG TRP C 325 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP C 325 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP C 325 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 325 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 325 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 325 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 325 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 325 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 325 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS C 148 " 0.043 5.00e-02 4.00e+02 6.56e-02 6.87e+00 pdb=" N PRO C 149 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 149 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 149 " 0.037 5.00e-02 4.00e+02 ... (remaining 5005 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.25: 16 2.25 - 2.98: 13982 2.98 - 3.70: 50929 3.70 - 4.42: 83578 4.42 - 5.14: 139346 Nonbonded interactions: 287851 Sorted by model distance: nonbonded pdb=" CG MET D 334 " pdb=" F02 LQ9 D1301 " model vdw 1.532 3.390 nonbonded pdb=" CG MET A 334 " pdb=" F02 LQ9 A1301 " model vdw 1.640 3.390 nonbonded pdb=" CG MET B 334 " pdb=" F02 LQ9 B1301 " model vdw 1.900 3.390 nonbonded pdb=" OG SER C 426 " pdb=" OE1 GLN C 427 " model vdw 2.096 2.440 nonbonded pdb=" O VAL D 183 " pdb=" OG SER D 187 " model vdw 2.125 2.440 ... (remaining 287846 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 110 through 1205 or resid 1301 through 1302 or resid 1304 \ through 1305)) selection = (chain 'B' and (resid 110 through 1205 or resid 1301 through 1302 or resid 1304 \ through 1305)) selection = (chain 'C' and (resid 110 through 1205 or resid 1301 through 1302 or resid 1304 \ through 1305)) selection = (chain 'D' and (resid 110 through 1205 or resid 1301 through 1302 or resid 1304 \ through 1305)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.740 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: 0.020 Extract box with map and model: 5.390 Check model and map are aligned: 0.420 Set scattering table: 0.350 Process input model: 81.990 Find NCS groups from input model: 2.380 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6439 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 : 0.008 0.983 29340 Z= 0.564 Angle : 0.762 58.508 39884 Z= 0.407 Chirality : 0.041 0.232 4556 Planarity : 0.004 0.093 5008 Dihedral : 16.067 106.141 10620 Min Nonbonded Distance : 1.532 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.19 % Allowed : 22.22 % Favored : 77.59 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.14), residues: 3552 helix: 0.65 (0.13), residues: 1720 sheet: -0.38 (0.28), residues: 308 loop : -0.30 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP C 325 HIS 0.005 0.001 HIS C 291 PHE 0.030 0.001 PHE B 268 TYR 0.019 0.001 TYR D 553 ARG 0.007 0.000 ARG B 600 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 508 time to evaluate : 3.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 216 MET cc_start: 0.7004 (tpt) cc_final: 0.6790 (tpp) REVERT: D 387 MET cc_start: 0.8327 (mmm) cc_final: 0.7888 (mmp) REVERT: C 174 MET cc_start: 0.5294 (mmm) cc_final: 0.4987 (pmm) outliers start: 6 outliers final: 4 residues processed: 513 average time/residue: 1.2369 time to fit residues: 757.2840 Evaluate side-chains 302 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 298 time to evaluate : 3.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 155 PHE Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain B residue 212 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 0.9990 chunk 272 optimal weight: 9.9990 chunk 151 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 184 optimal weight: 30.0000 chunk 145 optimal weight: 0.0070 chunk 282 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 171 optimal weight: 4.9990 chunk 210 optimal weight: 8.9990 chunk 326 optimal weight: 3.9990 overall best weight: 2.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 119 ASN ** D 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 400 GLN D 470 GLN D 505 HIS D 800 ASN D1136 GLN A 251 ASN A 254 ASN ** A 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 GLN A 470 GLN A 505 HIS ** A 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 768 HIS A 800 ASN A 816 ASN A 879 ASN A1159 HIS C 251 ASN C 254 ASN C 400 GLN C 470 GLN C 505 HIS C 540 GLN C 632 ASN C 800 ASN C 816 ASN ** C1155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 ASN ** B 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 GLN B 470 GLN B 484 ASN B 505 HIS ** B 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 HIS B 632 ASN B 800 ASN B 816 ASN B 879 ASN B1155 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.5429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.126 29340 Z= 0.453 Angle : 0.853 15.085 39884 Z= 0.428 Chirality : 0.050 0.287 4556 Planarity : 0.007 0.079 5008 Dihedral : 7.601 81.620 3992 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 5.15 % Allowed : 22.02 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.13), residues: 3552 helix: -0.19 (0.12), residues: 1704 sheet: -0.73 (0.28), residues: 312 loop : -0.43 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP A 243 HIS 0.013 0.002 HIS C 291 PHE 0.055 0.004 PHE B 222 TYR 0.032 0.003 TYR A 317 ARG 0.016 0.001 ARG C 780 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 432 time to evaluate : 3.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 566 MET cc_start: 0.8075 (tmm) cc_final: 0.7717 (tmt) REVERT: D 1157 MET cc_start: 0.7811 (mtp) cc_final: 0.7557 (mtt) REVERT: A 163 ASN cc_start: 0.8026 (OUTLIER) cc_final: 0.7311 (p0) REVERT: A 180 GLN cc_start: 0.6999 (mt0) cc_final: 0.6776 (mm-40) REVERT: A 846 PHE cc_start: 0.7788 (t80) cc_final: 0.7503 (t80) REVERT: C 119 ASN cc_start: 0.7225 (t0) cc_final: 0.6918 (t0) REVERT: C 174 MET cc_start: 0.5958 (mmm) cc_final: 0.5568 (pmm) REVERT: C 447 MET cc_start: 0.7679 (mmm) cc_final: 0.7478 (mmm) REVERT: C 844 HIS cc_start: 0.6738 (OUTLIER) cc_final: 0.6472 (p-80) REVERT: C 1136 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7728 (tt0) REVERT: B 204 TRP cc_start: 0.5208 (t-100) cc_final: 0.4986 (t60) REVERT: B 473 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8856 (mp) outliers start: 159 outliers final: 31 residues processed: 536 average time/residue: 1.1500 time to fit residues: 745.8137 Evaluate side-chains 355 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 320 time to evaluate : 3.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 155 PHE Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 356 ARG Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 883 VAL Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 325 TRP Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 844 HIS Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain C residue 973 SER Chi-restraints excluded: chain C residue 1136 GLN Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 627 ILE Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 1162 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 5.9990 chunk 101 optimal weight: 8.9990 chunk 272 optimal weight: 5.9990 chunk 222 optimal weight: 3.9990 chunk 90 optimal weight: 20.0000 chunk 327 optimal weight: 6.9990 chunk 353 optimal weight: 6.9990 chunk 291 optimal weight: 0.7980 chunk 324 optimal weight: 0.2980 chunk 111 optimal weight: 7.9990 chunk 262 optimal weight: 2.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 254 ASN D 369 GLN D 535 HIS D 816 ASN D1159 HIS ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 ASN A 460 ASN A 469 HIS A1159 HIS C 180 GLN C 247 HIS C 469 HIS C1155 ASN C1159 HIS B 119 ASN ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 ASN B 469 HIS B 588 HIS B1159 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.6604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 29340 Z= 0.354 Angle : 0.684 12.565 39884 Z= 0.335 Chirality : 0.045 0.250 4556 Planarity : 0.005 0.076 5008 Dihedral : 7.206 86.014 3990 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.70 % Allowed : 24.29 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.14), residues: 3552 helix: 0.28 (0.13), residues: 1688 sheet: -0.59 (0.29), residues: 300 loop : -0.14 (0.15), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 325 HIS 0.015 0.002 HIS C 291 PHE 0.030 0.002 PHE D 846 TYR 0.022 0.002 TYR B 351 ARG 0.008 0.001 ARG B1142 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 371 time to evaluate : 3.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 216 MET cc_start: 0.7018 (tpp) cc_final: 0.6765 (tpp) REVERT: D 329 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7800 (tp) REVERT: D 447 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7635 (mmt) REVERT: D 545 SER cc_start: 0.8388 (OUTLIER) cc_final: 0.8145 (p) REVERT: D 566 MET cc_start: 0.8244 (tmm) cc_final: 0.7864 (tmt) REVERT: D 1010 MET cc_start: 0.8558 (ptm) cc_final: 0.8319 (ttp) REVERT: A 127 CYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8183 (m) REVERT: A 222 PHE cc_start: 0.7861 (OUTLIER) cc_final: 0.7544 (t80) REVERT: A 356 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7412 (ppp80) REVERT: A 447 MET cc_start: 0.8481 (mmm) cc_final: 0.8281 (mmm) REVERT: A 839 ASP cc_start: 0.7481 (OUTLIER) cc_final: 0.7228 (m-30) REVERT: C 119 ASN cc_start: 0.7457 (t0) cc_final: 0.7023 (t0) REVERT: C 213 VAL cc_start: 0.7807 (OUTLIER) cc_final: 0.7572 (t) REVERT: C 351 TYR cc_start: 0.7799 (t80) cc_final: 0.6700 (t80) REVERT: C 631 GLU cc_start: 0.7696 (mp0) cc_final: 0.7453 (mp0) REVERT: C 773 LYS cc_start: 0.8240 (mtmt) cc_final: 0.8035 (ptmt) REVERT: C 844 HIS cc_start: 0.6988 (OUTLIER) cc_final: 0.6679 (p-80) REVERT: B 555 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.7395 (tpm-80) REVERT: B 757 SER cc_start: 0.8513 (OUTLIER) cc_final: 0.8311 (m) REVERT: B 829 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.8001 (ptpp) REVERT: B 839 ASP cc_start: 0.7642 (OUTLIER) cc_final: 0.7396 (m-30) outliers start: 145 outliers final: 42 residues processed: 465 average time/residue: 1.2143 time to fit residues: 678.3896 Evaluate side-chains 383 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 328 time to evaluate : 3.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 155 PHE Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 325 TRP Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 356 ARG Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 545 SER Chi-restraints excluded: chain D residue 714 LEU Chi-restraints excluded: chain D residue 884 ASP Chi-restraints excluded: chain D residue 1164 THR Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 839 ASP Chi-restraints excluded: chain A residue 844 HIS Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain C residue 155 PHE Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 325 TRP Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 844 HIS Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain C residue 1001 THR Chi-restraints excluded: chain C residue 1010 MET Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 555 ARG Chi-restraints excluded: chain B residue 627 ILE Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 829 LYS Chi-restraints excluded: chain B residue 839 ASP Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 1159 HIS Chi-restraints excluded: chain B residue 1162 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 5.9990 chunk 246 optimal weight: 2.9990 chunk 169 optimal weight: 0.5980 chunk 36 optimal weight: 6.9990 chunk 156 optimal weight: 0.8980 chunk 219 optimal weight: 0.5980 chunk 328 optimal weight: 5.9990 chunk 347 optimal weight: 0.9990 chunk 171 optimal weight: 0.0060 chunk 311 optimal weight: 7.9990 chunk 93 optimal weight: 20.0000 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 HIS D 632 ASN ** D1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 ASN A1159 HIS C 247 HIS B 119 ASN B 460 ASN B 586 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.6813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29340 Z= 0.163 Angle : 0.600 10.907 39884 Z= 0.288 Chirality : 0.041 0.255 4556 Planarity : 0.004 0.064 5008 Dihedral : 6.612 86.512 3986 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.50 % Allowed : 26.04 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.14), residues: 3552 helix: 0.43 (0.13), residues: 1708 sheet: -0.50 (0.28), residues: 336 loop : -0.04 (0.16), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 325 HIS 0.022 0.001 HIS B1159 PHE 0.034 0.001 PHE D 305 TYR 0.024 0.001 TYR B 553 ARG 0.010 0.000 ARG B 565 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 345 time to evaluate : 3.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 216 MET cc_start: 0.6996 (tpp) cc_final: 0.6744 (tpp) REVERT: D 356 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.7314 (ttp80) REVERT: D 566 MET cc_start: 0.8182 (tmm) cc_final: 0.7826 (tmt) REVERT: D 1017 LEU cc_start: 0.8727 (mt) cc_final: 0.8336 (mt) REVERT: A 127 CYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8220 (m) REVERT: A 163 ASN cc_start: 0.8354 (OUTLIER) cc_final: 0.7646 (p0) REVERT: A 356 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7434 (ppp80) REVERT: A 447 MET cc_start: 0.8389 (mmm) cc_final: 0.8174 (tpt) REVERT: C 930 MET cc_start: 0.7214 (tpt) cc_final: 0.6873 (tpt) REVERT: B 143 ILE cc_start: 0.8023 (pt) cc_final: 0.7696 (pp) REVERT: B 555 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.7349 (tpm-80) REVERT: B 566 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7984 (tmm) REVERT: B 829 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7896 (ptpp) REVERT: B 855 MET cc_start: 0.8681 (mtm) cc_final: 0.8331 (mtp) REVERT: B 1017 LEU cc_start: 0.8061 (tp) cc_final: 0.7773 (mm) outliers start: 108 outliers final: 44 residues processed: 414 average time/residue: 1.1697 time to fit residues: 587.4326 Evaluate side-chains 377 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 326 time to evaluate : 3.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 356 ARG Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 714 LEU Chi-restraints excluded: chain D residue 876 TYR Chi-restraints excluded: chain D residue 1159 HIS Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 844 HIS Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 325 TRP Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 783 LYS Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 1043 THR Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 204 TRP Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 555 ARG Chi-restraints excluded: chain B residue 566 MET Chi-restraints excluded: chain B residue 787 HIS Chi-restraints excluded: chain B residue 829 LYS Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1162 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 chunk 5 optimal weight: 0.0570 chunk 259 optimal weight: 10.0000 chunk 143 optimal weight: 3.9990 chunk 296 optimal weight: 6.9990 chunk 240 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 177 optimal weight: 4.9990 chunk 312 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 overall best weight: 3.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 151 GLN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 490 GLN D1159 HIS ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1159 HIS C 247 HIS ** C 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 535 HIS C1159 HIS B 247 HIS B 460 ASN ** B 981 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.7641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 29340 Z= 0.391 Angle : 0.660 10.487 39884 Z= 0.317 Chirality : 0.045 0.273 4556 Planarity : 0.005 0.071 5008 Dihedral : 6.463 77.719 3984 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.08 % Allowed : 26.23 % Favored : 69.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.14), residues: 3552 helix: 0.34 (0.13), residues: 1692 sheet: -0.24 (0.30), residues: 300 loop : 0.05 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 325 HIS 0.019 0.002 HIS C 291 PHE 0.032 0.002 PHE B 212 TYR 0.025 0.002 TYR C 351 ARG 0.016 0.001 ARG B1142 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 370 time to evaluate : 3.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 216 MET cc_start: 0.7037 (tpp) cc_final: 0.6825 (tpp) REVERT: D 356 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.7430 (ttp80) REVERT: D 448 ASP cc_start: 0.7849 (OUTLIER) cc_final: 0.7616 (p0) REVERT: D 566 MET cc_start: 0.8219 (tmm) cc_final: 0.7887 (tmt) REVERT: D 1017 LEU cc_start: 0.8836 (mt) cc_final: 0.8473 (mt) REVERT: A 447 MET cc_start: 0.8505 (mmm) cc_final: 0.8267 (tpt) REVERT: C 418 ARG cc_start: 0.8470 (ttm-80) cc_final: 0.8177 (mtt180) REVERT: C 844 HIS cc_start: 0.7186 (OUTLIER) cc_final: 0.6924 (t70) REVERT: B 143 ILE cc_start: 0.8156 (pt) cc_final: 0.7827 (pp) REVERT: B 204 TRP cc_start: 0.3935 (OUTLIER) cc_final: 0.3348 (t60) REVERT: B 220 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7710 (pp) REVERT: B 555 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.7384 (tpm-80) REVERT: B 772 VAL cc_start: 0.8893 (p) cc_final: 0.8683 (t) REVERT: B 1033 SER cc_start: 0.8487 (OUTLIER) cc_final: 0.8284 (p) REVERT: B 1141 TYR cc_start: 0.8167 (t80) cc_final: 0.7870 (t80) REVERT: B 1174 GLN cc_start: 0.6287 (OUTLIER) cc_final: 0.5520 (mp10) REVERT: B 1189 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.7281 (mtm-85) outliers start: 126 outliers final: 58 residues processed: 447 average time/residue: 1.1752 time to fit residues: 637.0742 Evaluate side-chains 410 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 343 time to evaluate : 3.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 325 TRP Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 354 MET Chi-restraints excluded: chain D residue 356 ARG Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 714 LEU Chi-restraints excluded: chain D residue 883 VAL Chi-restraints excluded: chain D residue 884 ASP Chi-restraints excluded: chain D residue 1001 THR Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 844 HIS Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 981 GLN Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 783 LYS Chi-restraints excluded: chain C residue 844 HIS Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 1021 THR Chi-restraints excluded: chain C residue 1043 THR Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 204 TRP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain B residue 555 ARG Chi-restraints excluded: chain B residue 787 HIS Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 1033 SER Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1174 GLN Chi-restraints excluded: chain B residue 1189 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 0.0770 chunk 313 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 204 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 348 optimal weight: 0.9980 chunk 289 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 chunk 28 optimal weight: 0.0000 chunk 115 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 overall best weight: 0.5142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 ASN A 490 GLN ** C 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 369 GLN ** C 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN B 247 HIS B 254 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.7708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 29340 Z= 0.158 Angle : 0.606 10.102 39884 Z= 0.288 Chirality : 0.041 0.248 4556 Planarity : 0.004 0.058 5008 Dihedral : 5.997 71.258 3984 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.30 % Allowed : 27.36 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.14), residues: 3552 helix: 0.55 (0.13), residues: 1680 sheet: -0.13 (0.30), residues: 300 loop : 0.23 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 325 HIS 0.020 0.001 HIS A 291 PHE 0.057 0.001 PHE A 235 TYR 0.023 0.001 TYR C 553 ARG 0.012 0.000 ARG D 948 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 359 time to evaluate : 3.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 216 MET cc_start: 0.7075 (tpp) cc_final: 0.6749 (tpp) REVERT: D 329 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7946 (tp) REVERT: D 356 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.7302 (ttp80) REVERT: D 959 MET cc_start: 0.8518 (ptm) cc_final: 0.8075 (ttp) REVERT: D 1017 LEU cc_start: 0.8812 (mt) cc_final: 0.8502 (mt) REVERT: A 163 ASN cc_start: 0.8530 (OUTLIER) cc_final: 0.7732 (p0) REVERT: A 356 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7604 (ppp80) REVERT: A 566 MET cc_start: 0.7984 (OUTLIER) cc_final: 0.7145 (tmm) REVERT: A 1138 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7450 (mm) REVERT: C 427 GLN cc_start: 0.8263 (pm20) cc_final: 0.8016 (pm20) REVERT: C 844 HIS cc_start: 0.7149 (OUTLIER) cc_final: 0.6932 (t70) REVERT: C 930 MET cc_start: 0.7330 (tpt) cc_final: 0.6970 (tpt) REVERT: C 1204 LEU cc_start: 0.8320 (mt) cc_final: 0.8116 (mp) REVERT: B 143 ILE cc_start: 0.8149 (pt) cc_final: 0.7857 (pp) REVERT: B 772 VAL cc_start: 0.8863 (p) cc_final: 0.8650 (t) REVERT: B 930 MET cc_start: 0.7005 (OUTLIER) cc_final: 0.6670 (tpt) REVERT: B 1017 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7986 (mm) REVERT: B 1138 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7789 (mm) REVERT: B 1174 GLN cc_start: 0.6278 (OUTLIER) cc_final: 0.5510 (mp10) outliers start: 102 outliers final: 46 residues processed: 422 average time/residue: 1.2499 time to fit residues: 634.2711 Evaluate side-chains 392 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 335 time to evaluate : 3.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 325 TRP Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 356 ARG Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 716 LEU Chi-restraints excluded: chain D residue 876 TYR Chi-restraints excluded: chain D residue 884 ASP Chi-restraints excluded: chain D residue 936 ASP Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 325 TRP Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 844 HIS Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 981 GLN Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 325 TRP Chi-restraints excluded: chain C residue 844 HIS Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 1043 THR Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 204 TRP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 787 HIS Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 930 MET Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1138 LEU Chi-restraints excluded: chain B residue 1174 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 198 optimal weight: 1.9990 chunk 254 optimal weight: 1.9990 chunk 197 optimal weight: 5.9990 chunk 293 optimal weight: 6.9990 chunk 194 optimal weight: 0.9980 chunk 346 optimal weight: 0.0270 chunk 217 optimal weight: 3.9990 chunk 211 optimal weight: 0.8980 chunk 160 optimal weight: 0.9990 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 ASN ** C 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 369 GLN C 550 GLN C1159 HIS B 180 GLN B 247 HIS B 254 ASN B 540 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.7878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29340 Z= 0.168 Angle : 0.595 10.034 39884 Z= 0.283 Chirality : 0.041 0.250 4556 Planarity : 0.004 0.067 5008 Dihedral : 5.552 59.724 3984 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.04 % Allowed : 28.08 % Favored : 68.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.14), residues: 3552 helix: 0.63 (0.13), residues: 1680 sheet: 0.06 (0.31), residues: 300 loop : 0.30 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 204 HIS 0.027 0.001 HIS A 291 PHE 0.044 0.002 PHE A 222 TYR 0.016 0.001 TYR C 553 ARG 0.013 0.000 ARG B 418 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 357 time to evaluate : 3.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 329 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7934 (tp) REVERT: D 356 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.7229 (ttp80) REVERT: D 844 HIS cc_start: 0.6997 (OUTLIER) cc_final: 0.6743 (t-90) REVERT: D 959 MET cc_start: 0.8511 (ptm) cc_final: 0.8103 (ttp) REVERT: D 1017 LEU cc_start: 0.8725 (mt) cc_final: 0.8396 (mt) REVERT: D 1162 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8103 (mm) REVERT: A 163 ASN cc_start: 0.8526 (OUTLIER) cc_final: 0.7736 (p0) REVERT: C 119 ASN cc_start: 0.7661 (t0) cc_final: 0.7296 (m-40) REVERT: C 127 CYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7498 (m) REVERT: C 603 ASN cc_start: 0.6948 (OUTLIER) cc_final: 0.6437 (m-40) REVERT: B 143 ILE cc_start: 0.8258 (pt) cc_final: 0.8011 (pp) REVERT: B 192 MET cc_start: 0.7707 (mpt) cc_final: 0.7459 (mpt) REVERT: B 930 MET cc_start: 0.7012 (OUTLIER) cc_final: 0.6645 (tpt) REVERT: B 1138 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7716 (mm) REVERT: B 1174 GLN cc_start: 0.6279 (OUTLIER) cc_final: 0.5500 (mp10) outliers start: 94 outliers final: 38 residues processed: 418 average time/residue: 1.2248 time to fit residues: 616.2660 Evaluate side-chains 381 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 333 time to evaluate : 3.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 325 TRP Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 356 ARG Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 716 LEU Chi-restraints excluded: chain D residue 844 HIS Chi-restraints excluded: chain D residue 876 TYR Chi-restraints excluded: chain D residue 884 ASP Chi-restraints excluded: chain D residue 936 ASP Chi-restraints excluded: chain D residue 1162 LEU Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 844 HIS Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 981 GLN Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 1043 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 787 HIS Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 930 MET Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1138 LEU Chi-restraints excluded: chain B residue 1174 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 214 optimal weight: 0.9980 chunk 138 optimal weight: 0.6980 chunk 207 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 220 optimal weight: 1.9990 chunk 236 optimal weight: 4.9990 chunk 171 optimal weight: 0.0020 chunk 32 optimal weight: 7.9990 chunk 272 optimal weight: 8.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 415 GLN D 540 GLN ** D1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 ASN ** C 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 369 GLN C1159 HIS ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 HIS B 415 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.7972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29340 Z= 0.178 Angle : 0.614 11.093 39884 Z= 0.289 Chirality : 0.041 0.264 4556 Planarity : 0.004 0.054 5008 Dihedral : 5.446 59.323 3984 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.62 % Allowed : 28.72 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.14), residues: 3552 helix: 0.63 (0.13), residues: 1680 sheet: 0.13 (0.30), residues: 300 loop : 0.33 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 204 HIS 0.035 0.001 HIS A 291 PHE 0.041 0.001 PHE B 235 TYR 0.015 0.001 TYR C 553 ARG 0.009 0.000 ARG C 600 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 343 time to evaluate : 3.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 188 PHE cc_start: 0.7757 (t80) cc_final: 0.7555 (t80) REVERT: D 329 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7938 (tp) REVERT: D 356 ARG cc_start: 0.7439 (ttt180) cc_final: 0.7197 (ttp80) REVERT: D 780 ARG cc_start: 0.8154 (ttt90) cc_final: 0.7904 (ttt-90) REVERT: D 844 HIS cc_start: 0.6990 (OUTLIER) cc_final: 0.6733 (t-90) REVERT: D 959 MET cc_start: 0.8539 (ptm) cc_final: 0.8081 (ttp) REVERT: D 1017 LEU cc_start: 0.8726 (mt) cc_final: 0.8430 (mt) REVERT: D 1162 LEU cc_start: 0.8550 (mp) cc_final: 0.8130 (mm) REVERT: A 163 ASN cc_start: 0.8521 (OUTLIER) cc_final: 0.7771 (p0) REVERT: A 192 MET cc_start: 0.7090 (mpm) cc_final: 0.6680 (mpt) REVERT: C 127 CYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7514 (m) REVERT: C 930 MET cc_start: 0.7333 (tpt) cc_final: 0.6952 (tpt) REVERT: C 1204 LEU cc_start: 0.8327 (mt) cc_final: 0.8116 (mp) REVERT: B 143 ILE cc_start: 0.8265 (pt) cc_final: 0.7886 (mm) REVERT: B 204 TRP cc_start: 0.3962 (OUTLIER) cc_final: 0.3568 (t-100) REVERT: B 930 MET cc_start: 0.6992 (OUTLIER) cc_final: 0.6648 (tpt) REVERT: B 1138 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7751 (mm) REVERT: B 1174 GLN cc_start: 0.6287 (OUTLIER) cc_final: 0.5511 (mp10) outliers start: 81 outliers final: 45 residues processed: 397 average time/residue: 1.2260 time to fit residues: 587.1598 Evaluate side-chains 381 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 328 time to evaluate : 3.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 716 LEU Chi-restraints excluded: chain D residue 844 HIS Chi-restraints excluded: chain D residue 876 TYR Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 844 HIS Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 981 GLN Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 383 ILE Chi-restraints excluded: chain C residue 783 LYS Chi-restraints excluded: chain C residue 841 LYS Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 1043 THR Chi-restraints excluded: chain B residue 204 TRP Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 787 HIS Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 930 MET Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1138 LEU Chi-restraints excluded: chain B residue 1174 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 3.9990 chunk 332 optimal weight: 0.9990 chunk 303 optimal weight: 0.9990 chunk 323 optimal weight: 0.2980 chunk 194 optimal weight: 30.0000 chunk 140 optimal weight: 4.9990 chunk 253 optimal weight: 0.9990 chunk 99 optimal weight: 7.9990 chunk 292 optimal weight: 7.9990 chunk 305 optimal weight: 0.9980 chunk 322 optimal weight: 5.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1159 HIS B 247 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.8051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29340 Z= 0.174 Angle : 0.610 11.111 39884 Z= 0.287 Chirality : 0.041 0.295 4556 Planarity : 0.004 0.063 5008 Dihedral : 5.358 58.819 3984 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.43 % Allowed : 29.37 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.14), residues: 3552 helix: 0.67 (0.13), residues: 1676 sheet: 0.19 (0.31), residues: 300 loop : 0.34 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 204 HIS 0.038 0.001 HIS A 291 PHE 0.053 0.002 PHE B 235 TYR 0.024 0.001 TYR C 351 ARG 0.012 0.000 ARG C 418 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 338 time to evaluate : 3.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 329 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7926 (tp) REVERT: D 356 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.7274 (ttp80) REVERT: D 780 ARG cc_start: 0.8155 (ttt90) cc_final: 0.7910 (ttt-90) REVERT: D 844 HIS cc_start: 0.6993 (OUTLIER) cc_final: 0.6736 (t-90) REVERT: D 959 MET cc_start: 0.8538 (ptm) cc_final: 0.8098 (ttp) REVERT: D 1017 LEU cc_start: 0.8707 (mt) cc_final: 0.8434 (mt) REVERT: D 1162 LEU cc_start: 0.8563 (mp) cc_final: 0.8151 (mm) REVERT: A 163 ASN cc_start: 0.8521 (OUTLIER) cc_final: 0.7722 (p0) REVERT: A 192 MET cc_start: 0.7143 (mpm) cc_final: 0.6761 (mpt) REVERT: A 308 CYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7620 (m) REVERT: C 127 CYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7628 (m) REVERT: C 351 TYR cc_start: 0.7619 (t80) cc_final: 0.7375 (t80) REVERT: C 603 ASN cc_start: 0.6969 (OUTLIER) cc_final: 0.6438 (m-40) REVERT: C 844 HIS cc_start: 0.7187 (OUTLIER) cc_final: 0.6899 (p-80) REVERT: C 930 MET cc_start: 0.7322 (tpt) cc_final: 0.6971 (tpt) REVERT: B 143 ILE cc_start: 0.8268 (pt) cc_final: 0.7897 (mm) REVERT: B 192 MET cc_start: 0.7676 (mpt) cc_final: 0.7472 (mpt) REVERT: B 204 TRP cc_start: 0.3949 (OUTLIER) cc_final: 0.3533 (t-100) REVERT: B 930 MET cc_start: 0.6991 (OUTLIER) cc_final: 0.6635 (tpt) REVERT: B 1017 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8053 (mm) REVERT: B 1138 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7802 (mm) outliers start: 75 outliers final: 44 residues processed: 382 average time/residue: 1.1911 time to fit residues: 549.9462 Evaluate side-chains 381 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 325 time to evaluate : 3.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 356 ARG Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 844 HIS Chi-restraints excluded: chain D residue 876 TYR Chi-restraints excluded: chain D residue 884 ASP Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 844 HIS Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 981 GLN Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 841 LYS Chi-restraints excluded: chain C residue 844 HIS Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 1043 THR Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 204 TRP Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 787 HIS Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 930 MET Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1138 LEU Chi-restraints excluded: chain B residue 1162 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 2.9990 chunk 341 optimal weight: 0.9990 chunk 208 optimal weight: 0.2980 chunk 162 optimal weight: 8.9990 chunk 237 optimal weight: 4.9990 chunk 358 optimal weight: 0.9980 chunk 330 optimal weight: 4.9990 chunk 285 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 220 optimal weight: 0.9980 chunk 175 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1159 HIS B 247 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.8122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29340 Z= 0.175 Angle : 0.618 11.599 39884 Z= 0.290 Chirality : 0.042 0.288 4556 Planarity : 0.004 0.054 5008 Dihedral : 5.270 57.768 3984 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.01 % Allowed : 29.76 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.14), residues: 3552 helix: 0.66 (0.13), residues: 1684 sheet: 0.22 (0.31), residues: 300 loop : 0.36 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 204 HIS 0.036 0.001 HIS A 291 PHE 0.036 0.001 PHE C 155 TYR 0.023 0.001 TYR C 351 ARG 0.007 0.000 ARG D 418 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 327 time to evaluate : 3.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 216 MET cc_start: 0.6840 (mmm) cc_final: 0.6488 (mmp) REVERT: D 329 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7853 (tp) REVERT: D 356 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.7290 (ttp80) REVERT: D 780 ARG cc_start: 0.8160 (ttt90) cc_final: 0.7922 (ttt-90) REVERT: D 844 HIS cc_start: 0.6995 (OUTLIER) cc_final: 0.6724 (t-90) REVERT: D 948 ARG cc_start: 0.7755 (ttm110) cc_final: 0.7538 (ptp-110) REVERT: D 959 MET cc_start: 0.8538 (ptm) cc_final: 0.8104 (ttp) REVERT: D 1017 LEU cc_start: 0.8696 (mt) cc_final: 0.8419 (mt) REVERT: D 1162 LEU cc_start: 0.8541 (mp) cc_final: 0.8128 (mm) REVERT: A 163 ASN cc_start: 0.8517 (OUTLIER) cc_final: 0.7717 (p0) REVERT: A 192 MET cc_start: 0.7229 (mpm) cc_final: 0.6844 (mpt) REVERT: A 308 CYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7625 (m) REVERT: C 127 CYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7584 (m) REVERT: C 603 ASN cc_start: 0.7052 (OUTLIER) cc_final: 0.6539 (m-40) REVERT: C 844 HIS cc_start: 0.7181 (OUTLIER) cc_final: 0.6896 (p-80) REVERT: C 930 MET cc_start: 0.7335 (tpt) cc_final: 0.6981 (tpt) REVERT: B 192 MET cc_start: 0.7675 (mpt) cc_final: 0.7435 (mpt) REVERT: B 204 TRP cc_start: 0.3914 (OUTLIER) cc_final: 0.3435 (t-100) REVERT: B 566 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.7333 (tmm) REVERT: B 930 MET cc_start: 0.6987 (OUTLIER) cc_final: 0.6615 (tpt) REVERT: B 1017 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8077 (mm) REVERT: B 1138 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7777 (mm) outliers start: 62 outliers final: 45 residues processed: 367 average time/residue: 1.2879 time to fit residues: 566.3871 Evaluate side-chains 381 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 323 time to evaluate : 3.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 356 ARG Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 844 HIS Chi-restraints excluded: chain D residue 876 TYR Chi-restraints excluded: chain D residue 884 ASP Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 844 HIS Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 981 GLN Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 317 TYR Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 383 ILE Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 844 HIS Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 974 MET Chi-restraints excluded: chain C residue 1043 THR Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 204 TRP Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 566 MET Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 787 HIS Chi-restraints excluded: chain B residue 799 LYS Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 930 MET Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1138 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 7.9990 chunk 304 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 263 optimal weight: 6.9990 chunk 42 optimal weight: 0.0770 chunk 79 optimal weight: 20.0000 chunk 286 optimal weight: 10.0000 chunk 119 optimal weight: 6.9990 chunk 293 optimal weight: 10.0000 chunk 36 optimal weight: 0.0070 chunk 52 optimal weight: 0.6980 overall best weight: 0.9358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1159 HIS B 247 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.103083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.079876 restraints weight = 67794.129| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 3.21 r_work: 0.3204 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.8182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29340 Z= 0.178 Angle : 0.617 11.888 39884 Z= 0.289 Chirality : 0.042 0.280 4556 Planarity : 0.004 0.059 5008 Dihedral : 5.210 56.548 3984 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.07 % Allowed : 29.76 % Favored : 68.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.14), residues: 3552 helix: 0.70 (0.13), residues: 1684 sheet: 0.27 (0.31), residues: 300 loop : 0.38 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 204 HIS 0.033 0.001 HIS A 291 PHE 0.030 0.001 PHE D 275 TYR 0.035 0.001 TYR C 317 ARG 0.014 0.000 ARG C 418 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10091.90 seconds wall clock time: 181 minutes 38.63 seconds (10898.63 seconds total)