Starting phenix.real_space_refine on Thu Mar 21 16:28:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mke_23893/03_2024/7mke_23893_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mke_23893/03_2024/7mke_23893.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mke_23893/03_2024/7mke_23893.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mke_23893/03_2024/7mke_23893.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mke_23893/03_2024/7mke_23893_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mke_23893/03_2024/7mke_23893_updated.pdb" } resolution = 3.7 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= 0.014 sd= 0.070 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 79 5.49 5 Mg 1 5.21 5 S 128 5.16 5 C 18989 2.51 5 N 5413 2.21 5 O 6029 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "H TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 181": "OE1" <-> "OE2" Residue "H TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 44": "OE1" <-> "OE2" Residue "I GLU 77": "OE1" <-> "OE2" Residue "I GLU 226": "OE1" <-> "OE2" Residue "I ASP 254": "OD1" <-> "OD2" Residue "I ARG 268": "NH1" <-> "NH2" Residue "I ARG 332": "NH1" <-> "NH2" Residue "I PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 516": "OD1" <-> "OD2" Residue "I TYR 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 813": "OE1" <-> "OE2" Residue "I GLU 898": "OE1" <-> "OE2" Residue "I GLU 968": "OE1" <-> "OE2" Residue "I PHE 972": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 1147": "NH1" <-> "NH2" Residue "I PHE 1187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 1192": "OE1" <-> "OE2" Residue "I TYR 1251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 1274": "OE1" <-> "OE2" Residue "J TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 52": "OE1" <-> "OE2" Residue "J PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 163": "OE1" <-> "OE2" Residue "J TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 532": "OE1" <-> "OE2" Residue "J GLU 556": "OE1" <-> "OE2" Residue "J TYR 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 811": "OE1" <-> "OE2" Residue "J PHE 988": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 1143": "OD1" <-> "OD2" Residue "J PHE 1199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 1200": "OE1" <-> "OE2" Residue "J GLU 1205": "OE1" <-> "OE2" Residue "J PHE 1274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 1317": "OE1" <-> "OE2" Residue "J GLU 1334": "OE1" <-> "OE2" Residue "K ARG 16": "NH1" <-> "NH2" Residue "K ASP 36": "OD1" <-> "OD2" Residue "K ASP 44": "OD1" <-> "OD2" Residue "K GLU 74": "OE1" <-> "OE2" Residue "L PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 481": "OE1" <-> "OE2" Residue "L GLU 491": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 30641 Number of models: 1 Model: "" Number of chains: 11 Chain: "G" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1808 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 9, 'TRANS': 223} Chain: "H" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1714 Classifications: {'peptide': 223} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 8, 'TRANS': 212} Chain breaks: 1 Chain: "I" Number of atoms: 10567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10567 Classifications: {'peptide': 1340} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1281} Chain: "J" Number of atoms: 10377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1335, 10377 Classifications: {'peptide': 1335} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 1278} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "L" Number of atoms: 3781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3781 Classifications: {'peptide': 465} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 451} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "P" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 907 Classifications: {'DNA': 44} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 43} Chain breaks: 1 Chain: "Q" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 749 Classifications: {'DNA': 37} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 36} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'1N7': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'1N7:plan-1': 2} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'1N7': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'1N7:plan-1': 2} Unresolved non-hydrogen planarities: 6 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14538 SG CYS J 70 100.691 52.642 74.134 1.00 96.23 S ATOM 14552 SG CYS J 72 99.702 50.812 72.593 1.00 96.96 S ATOM 14660 SG CYS J 85 102.572 51.997 70.782 1.00103.27 S ATOM 14684 SG CYS J 88 101.419 54.865 72.505 1.00104.22 S ATOM 20367 SG CYS J 814 124.499 107.404 109.180 1.00 80.68 S ATOM 20932 SG CYS J 888 121.489 105.813 107.397 1.00 74.16 S ATOM 20983 SG CYS J 895 122.663 104.491 110.686 1.00 68.11 S ATOM 21004 SG CYS J 898 121.210 107.972 110.653 1.00 69.90 S Time building chain proxies: 15.13, per 1000 atoms: 0.49 Number of scatterers: 30641 At special positions: 0 Unit cell: (152.64, 182.32, 193.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 128 16.00 P 79 15.00 Mg 1 11.99 O 6029 8.00 N 5413 7.00 C 18989 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: 13.91 Conformation dependent library (CDL) restraints added in 5.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " Number of angles added : 12 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6818 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 129 helices and 36 sheets defined 36.8% alpha, 9.0% beta 37 base pairs and 60 stacking pairs defined. Time for finding SS restraints: 15.77 Creating SS restraints... Processing helix chain 'G' and resid 35 through 49 Processing helix chain 'G' and resid 78 through 86 Processing helix chain 'G' and resid 112 through 114 No H-bonds generated for 'chain 'G' and resid 112 through 114' Processing helix chain 'G' and resid 155 through 158 No H-bonds generated for 'chain 'G' and resid 155 through 158' Processing helix chain 'G' and resid 213 through 232 removed outlier: 3.718A pdb=" N GLU G 229 " --> pdb=" O ALA G 225 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N PHE G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 49 Processing helix chain 'H' and resid 78 through 86 Processing helix chain 'H' and resid 112 through 114 No H-bonds generated for 'chain 'H' and resid 112 through 114' Processing helix chain 'H' and resid 155 through 157 No H-bonds generated for 'chain 'H' and resid 155 through 157' Processing helix chain 'H' and resid 213 through 228 removed outlier: 3.718A pdb=" N LEU H 228 " --> pdb=" O LEU H 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 38 Processing helix chain 'I' and resid 49 through 56 Processing helix chain 'I' and resid 82 through 88 Processing helix chain 'I' and resid 207 through 212 Processing helix chain 'I' and resid 217 through 224 Processing helix chain 'I' and resid 243 through 246 removed outlier: 3.558A pdb=" N LEU I 246 " --> pdb=" O PRO I 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 243 through 246' Processing helix chain 'I' and resid 271 through 280 Processing helix chain 'I' and resid 289 through 294 removed outlier: 3.823A pdb=" N ALA I 293 " --> pdb=" O VAL I 289 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLY I 294 " --> pdb=" O GLU I 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 289 through 294' Processing helix chain 'I' and resid 319 through 327 Processing helix chain 'I' and resid 346 through 353 Processing helix chain 'I' and resid 359 through 370 Processing helix chain 'I' and resid 378 through 388 Processing helix chain 'I' and resid 399 through 408 Processing helix chain 'I' and resid 422 through 437 Processing helix chain 'I' and resid 456 through 480 removed outlier: 3.690A pdb=" N ARG I 470 " --> pdb=" O VAL I 466 " (cutoff:3.500A) Processing helix chain 'I' and resid 496 through 507 removed outlier: 4.878A pdb=" N ALA I 501 " --> pdb=" O PRO I 497 " (cutoff:3.500A) Processing helix chain 'I' and resid 520 through 527 Processing helix chain 'I' and resid 540 through 542 No H-bonds generated for 'chain 'I' and resid 540 through 542' Processing helix chain 'I' and resid 545 through 548 No H-bonds generated for 'chain 'I' and resid 545 through 548' Processing helix chain 'I' and resid 552 through 554 No H-bonds generated for 'chain 'I' and resid 552 through 554' Processing helix chain 'I' and resid 610 through 613 No H-bonds generated for 'chain 'I' and resid 610 through 613' Processing helix chain 'I' and resid 664 through 667 removed outlier: 3.802A pdb=" N LEU I 667 " --> pdb=" O GLY I 664 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 664 through 667' Processing helix chain 'I' and resid 671 through 673 No H-bonds generated for 'chain 'I' and resid 671 through 673' Processing helix chain 'I' and resid 676 through 688 removed outlier: 4.478A pdb=" N ARG I 687 " --> pdb=" O ALA I 683 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLN I 688 " --> pdb=" O ASN I 684 " (cutoff:3.500A) Processing helix chain 'I' and resid 705 through 711 Processing helix chain 'I' and resid 820 through 824 Processing helix chain 'I' and resid 861 through 864 removed outlier: 3.713A pdb=" N LYS I 864 " --> pdb=" O ALA I 861 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 861 through 864' Processing helix chain 'I' and resid 899 through 906 Processing helix chain 'I' and resid 943 through 980 removed outlier: 3.650A pdb=" N VAL I 980 " --> pdb=" O ARG I 976 " (cutoff:3.500A) Processing helix chain 'I' and resid 987 through 991 removed outlier: 3.686A pdb=" N LYS I 991 " --> pdb=" O GLU I 987 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 987 through 991' Processing helix chain 'I' and resid 997 through 999 No H-bonds generated for 'chain 'I' and resid 997 through 999' Processing helix chain 'I' and resid 1008 through 1037 removed outlier: 3.927A pdb=" N GLU I1012 " --> pdb=" O GLN I1008 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N GLN I1013 " --> pdb=" O ASN I1009 " (cutoff:3.500A) Processing helix chain 'I' and resid 1100 through 1106 Proline residue: I1104 - end of helix Processing helix chain 'I' and resid 1110 through 1133 Processing helix chain 'I' and resid 1138 through 1150 Processing helix chain 'I' and resid 1168 through 1176 Processing helix chain 'I' and resid 1192 through 1201 Processing helix chain 'I' and resid 1272 through 1280 Processing helix chain 'I' and resid 1285 through 1291 Processing helix chain 'I' and resid 1300 through 1309 Processing helix chain 'I' and resid 1321 through 1332 Processing helix chain 'J' and resid 27 through 33 Processing helix chain 'J' and resid 78 through 80 No H-bonds generated for 'chain 'J' and resid 78 through 80' Processing helix chain 'J' and resid 96 through 99 removed outlier: 3.541A pdb=" N ARG J 99 " --> pdb=" O LYS J 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 96 through 99' Processing helix chain 'J' and resid 114 through 118 Processing helix chain 'J' and resid 123 through 128 Processing helix chain 'J' and resid 132 through 139 Processing helix chain 'J' and resid 162 through 171 Processing helix chain 'J' and resid 182 through 191 Processing helix chain 'J' and resid 194 through 207 Processing helix chain 'J' and resid 211 through 229 Processing helix chain 'J' and resid 235 through 237 No H-bonds generated for 'chain 'J' and resid 235 through 237' Processing helix chain 'J' and resid 247 through 249 No H-bonds generated for 'chain 'J' and resid 247 through 249' Processing helix chain 'J' and resid 264 through 285 Processing helix chain 'J' and resid 289 through 300 Processing helix chain 'J' and resid 304 through 308 Processing helix chain 'J' and resid 327 through 331 Processing helix chain 'J' and resid 337 through 340 No H-bonds generated for 'chain 'J' and resid 337 through 340' Processing helix chain 'J' and resid 370 through 376 Processing helix chain 'J' and resid 378 through 388 Processing helix chain 'J' and resid 394 through 403 Processing helix chain 'J' and resid 406 through 415 removed outlier: 3.738A pdb=" N TRP J 409 " --> pdb=" O ALA J 406 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP J 410 " --> pdb=" O VAL J 407 " (cutoff:3.500A) Processing helix chain 'J' and resid 431 through 433 No H-bonds generated for 'chain 'J' and resid 431 through 433' Processing helix chain 'J' and resid 451 through 453 No H-bonds generated for 'chain 'J' and resid 451 through 453' Processing helix chain 'J' and resid 474 through 482 Processing helix chain 'J' and resid 486 through 488 No H-bonds generated for 'chain 'J' and resid 486 through 488' Processing helix chain 'J' and resid 505 through 513 Processing helix chain 'J' and resid 530 through 538 Processing helix chain 'J' and resid 574 through 581 removed outlier: 4.127A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 589 through 592 Processing helix chain 'J' and resid 599 through 612 Processing helix chain 'J' and resid 615 through 635 Processing helix chain 'J' and resid 641 through 643 No H-bonds generated for 'chain 'J' and resid 641 through 643' Processing helix chain 'J' and resid 650 through 669 Processing helix chain 'J' and resid 675 through 701 Processing helix chain 'J' and resid 721 through 727 Processing helix chain 'J' and resid 769 through 803 removed outlier: 4.313A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA J 779 " --> pdb=" O SER J 775 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N THR J 790 " --> pdb=" O THR J 786 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) Processing helix chain 'J' and resid 835 through 837 No H-bonds generated for 'chain 'J' and resid 835 through 837' Processing helix chain 'J' and resid 866 through 873 Processing helix chain 'J' and resid 885 through 887 No H-bonds generated for 'chain 'J' and resid 885 through 887' Processing helix chain 'J' and resid 915 through 929 Proline residue: J 926 - end of helix removed outlier: 5.639A pdb=" N GLN J 929 " --> pdb=" O GLU J 925 " (cutoff:3.500A) Processing helix chain 'J' and resid 1138 through 1145 Processing helix chain 'J' and resid 1217 through 1224 Processing helix chain 'J' and resid 1226 through 1244 removed outlier: 4.251A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1250 through 1260 Processing helix chain 'J' and resid 1282 through 1294 Processing helix chain 'J' and resid 1309 through 1312 No H-bonds generated for 'chain 'J' and resid 1309 through 1312' Processing helix chain 'J' and resid 1320 through 1323 No H-bonds generated for 'chain 'J' and resid 1320 through 1323' Processing helix chain 'J' and resid 1328 through 1338 Processing helix chain 'J' and resid 1348 through 1352 Processing helix chain 'J' and resid 1361 through 1372 removed outlier: 3.876A pdb=" N ALA J1364 " --> pdb=" O THR J1361 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 12 Processing helix chain 'K' and resid 18 through 31 Processing helix chain 'K' and resid 46 through 55 Processing helix chain 'K' and resid 61 through 79 removed outlier: 4.078A pdb=" N GLU K 79 " --> pdb=" O GLN K 75 " (cutoff:3.500A) Processing helix chain 'L' and resid 97 through 107 removed outlier: 3.870A pdb=" N THR L 107 " --> pdb=" O ARG L 103 " (cutoff:3.500A) Processing helix chain 'L' and resid 113 through 136 removed outlier: 3.742A pdb=" N GLU L 136 " --> pdb=" O CYS L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 138 through 152 Processing helix chain 'L' and resid 158 through 161 No H-bonds generated for 'chain 'L' and resid 158 through 161' Processing helix chain 'L' and resid 216 through 233 Processing helix chain 'L' and resid 245 through 257 Processing helix chain 'L' and resid 263 through 291 removed outlier: 4.138A pdb=" N LEU L 290 " --> pdb=" O LEU L 286 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS L 291 " --> pdb=" O ILE L 287 " (cutoff:3.500A) Processing helix chain 'L' and resid 300 through 306 removed outlier: 3.783A pdb=" N THR L 304 " --> pdb=" O LYS L 300 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU L 305 " --> pdb=" O ASN L 301 " (cutoff:3.500A) Processing helix chain 'L' and resid 320 through 322 No H-bonds generated for 'chain 'L' and resid 320 through 322' Processing helix chain 'L' and resid 325 through 332 removed outlier: 3.857A pdb=" N LYS L 329 " --> pdb=" O PRO L 325 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N HIS L 331 " --> pdb=" O SER L 327 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASP L 332 " --> pdb=" O GLU L 328 " (cutoff:3.500A) Processing helix chain 'L' and resid 334 through 351 removed outlier: 3.535A pdb=" N THR L 351 " --> pdb=" O ILE L 347 " (cutoff:3.500A) Processing helix chain 'L' and resid 355 through 393 removed outlier: 5.729A pdb=" N ARG L 385 " --> pdb=" O GLU L 381 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N LEU L 386 " --> pdb=" O ALA L 382 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL L 387 " --> pdb=" O ASN L 383 " (cutoff:3.500A) Processing helix chain 'L' and resid 401 through 417 Processing helix chain 'L' and resid 421 through 423 No H-bonds generated for 'chain 'L' and resid 421 through 423' Processing helix chain 'L' and resid 427 through 445 Processing helix chain 'L' and resid 454 through 474 removed outlier: 3.806A pdb=" N GLN L 472 " --> pdb=" O ARG L 468 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU L 473 " --> pdb=" O GLN L 469 " (cutoff:3.500A) Processing helix chain 'L' and resid 480 through 486 Processing helix chain 'L' and resid 493 through 500 Processing helix chain 'L' and resid 519 through 522 No H-bonds generated for 'chain 'L' and resid 519 through 522' Processing helix chain 'L' and resid 531 through 549 Processing helix chain 'L' and resid 553 through 562 Processing helix chain 'L' and resid 573 through 580 Processing helix chain 'L' and resid 584 through 598 Processing helix chain 'L' and resid 604 through 610 removed outlier: 4.148A pdb=" N PHE L 610 " --> pdb=" O VAL L 606 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'G' and resid 23 through 28 removed outlier: 3.817A pdb=" N ARG G 182 " --> pdb=" O GLU G 206 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'G' and resid 90 through 92 Processing sheet with id= C, first strand: chain 'G' and resid 98 through 105 Processing sheet with id= D, first strand: chain 'G' and resid 188 through 190 removed outlier: 4.120A pdb=" N LEU G 198 " --> pdb=" O ALA G 190 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.541A pdb=" N GLY G 108 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 24 through 28 Processing sheet with id= G, first strand: chain 'H' and resid 97 through 101 removed outlier: 3.789A pdb=" N VAL H 98 " --> pdb=" O VAL H 146 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU H 58 " --> pdb=" O LYS H 145 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLY H 149 " --> pdb=" O CYS H 54 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N CYS H 54 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 188 through 190 Processing sheet with id= I, first strand: chain 'H' and resid 109 through 111 Processing sheet with id= J, first strand: chain 'I' and resid 93 through 95 Processing sheet with id= K, first strand: chain 'I' and resid 143 through 145 Processing sheet with id= L, first strand: chain 'I' and resid 148 through 151 removed outlier: 3.593A pdb=" N HIS I 150 " --> pdb=" O ARG I 452 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'I' and resid 154 through 156 Processing sheet with id= N, first strand: chain 'I' and resid 185 through 188 removed outlier: 3.737A pdb=" N GLU I 187 " --> pdb=" O PHE I 195 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'I' and resid 227 through 231 Processing sheet with id= P, first strand: chain 'I' and resid 633 through 635 Processing sheet with id= Q, first strand: chain 'I' and resid 748 through 752 removed outlier: 3.686A pdb=" N TYR I 726 " --> pdb=" O VAL I 733 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 1227 through 1232 removed outlier: 6.328A pdb=" N ILE I1096 " --> pdb=" O ALA I 803 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 830 through 839 removed outlier: 3.946A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 887 through 889 Processing sheet with id= U, first strand: chain 'I' and resid 66 through 75 removed outlier: 7.043A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE I 104 " --> pdb=" O ASP I 116 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.865A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'I' and resid 301 through 303 removed outlier: 5.413A pdb=" N ASP I 303 " --> pdb=" O LEU I 309 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LEU I 309 " --> pdb=" O ASP I 303 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'I' and resid 589 through 594 removed outlier: 5.637A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'J' and resid 103 through 106 removed outlier: 3.804A pdb=" N GLY J 103 " --> pdb=" O VAL J 244 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'J' and resid 252 through 255 removed outlier: 3.642A pdb=" N ARG J 259 " --> pdb=" O LEU J 255 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'J' and resid 350 through 354 Processing sheet with id= AB, first strand: chain 'J' and resid 547 through 549 Processing sheet with id= AC, first strand: chain 'J' and resid 552 through 556 Processing sheet with id= AD, first strand: chain 'J' and resid 820 through 823 removed outlier: 3.630A pdb=" N VAL J 880 " --> pdb=" O MET J 822 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'J' and resid 957 through 961 removed outlier: 3.520A pdb=" N THR J 980 " --> pdb=" O VAL J 997 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'J' and resid 965 through 967 Processing sheet with id= AG, first strand: chain 'J' and resid 1162 through 1165 Processing sheet with id= AH, first strand: chain 'J' and resid 1172 through 1174 Processing sheet with id= AI, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 6.512A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'J' and resid 949 through 951 removed outlier: 3.735A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) 980 hydrogen bonds defined for protein. 2832 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 91 hydrogen bonds 182 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 60 stacking parallelities Total time for adding SS restraints: 13.34 Time building geometry restraints manager: 14.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9847 1.34 - 1.46: 5954 1.46 - 1.58: 15063 1.58 - 1.70: 171 1.70 - 1.82: 234 Bond restraints: 31269 Sorted by residual: bond pdb=" C19 1N7 L 701 " pdb=" C3 1N7 L 701 " ideal model delta sigma weight residual 1.532 1.824 -0.292 2.00e-02 2.50e+03 2.13e+02 bond pdb=" C19 1N7 I1402 " pdb=" C3 1N7 I1402 " ideal model delta sigma weight residual 1.532 1.821 -0.289 2.00e-02 2.50e+03 2.08e+02 bond pdb=" C19 1N7 L 702 " pdb=" C3 1N7 L 702 " ideal model delta sigma weight residual 1.532 1.820 -0.288 2.00e-02 2.50e+03 2.08e+02 bond pdb=" C19 1N7 I1401 " pdb=" C3 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.818 -0.286 2.00e-02 2.50e+03 2.05e+02 bond pdb=" C3 1N7 L 701 " pdb=" C4 1N7 L 701 " ideal model delta sigma weight residual 1.532 1.729 -0.197 2.00e-02 2.50e+03 9.68e+01 ... (remaining 31264 not shown) Histogram of bond angle deviations from ideal: 97.30 - 105.63: 965 105.63 - 113.97: 18664 113.97 - 122.31: 18087 122.31 - 130.64: 4756 130.64 - 138.98: 111 Bond angle restraints: 42583 Sorted by residual: angle pdb=" C LEU I 487 " pdb=" N MET I 488 " pdb=" CA MET I 488 " ideal model delta sigma weight residual 120.67 138.98 -18.31 1.34e+00 5.57e-01 1.87e+02 angle pdb=" C ILE H 168 " pdb=" N GLY H 169 " pdb=" CA GLY H 169 " ideal model delta sigma weight residual 121.70 132.49 -10.79 1.80e+00 3.09e-01 3.59e+01 angle pdb=" C LEU I 484 " pdb=" N ASP I 485 " pdb=" CA ASP I 485 " ideal model delta sigma weight residual 121.70 131.01 -9.31 1.80e+00 3.09e-01 2.68e+01 angle pdb=" N ASP I 516 " pdb=" CA ASP I 516 " pdb=" C ASP I 516 " ideal model delta sigma weight residual 109.96 102.78 7.18 1.49e+00 4.50e-01 2.32e+01 angle pdb=" C LEU I 397 " pdb=" N SER I 398 " pdb=" CA SER I 398 " ideal model delta sigma weight residual 121.54 130.25 -8.71 1.91e+00 2.74e-01 2.08e+01 ... (remaining 42578 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.44: 18412 34.44 - 68.88: 830 68.88 - 103.31: 37 103.31 - 137.75: 1 137.75 - 172.19: 3 Dihedral angle restraints: 19283 sinusoidal: 8706 harmonic: 10577 Sorted by residual: dihedral pdb=" CA PRO I 897 " pdb=" C PRO I 897 " pdb=" N GLU I 898 " pdb=" CA GLU I 898 " ideal model delta harmonic sigma weight residual -180.00 -138.69 -41.31 0 5.00e+00 4.00e-02 6.83e+01 dihedral pdb=" CA ASP J1184 " pdb=" C ASP J1184 " pdb=" N PRO J1185 " pdb=" CA PRO J1185 " ideal model delta harmonic sigma weight residual -180.00 -140.53 -39.47 0 5.00e+00 4.00e-02 6.23e+01 dihedral pdb=" CA ARG G 235 " pdb=" C ARG G 235 " pdb=" N ASP G 236 " pdb=" CA ASP G 236 " ideal model delta harmonic sigma weight residual 180.00 -143.98 -36.02 0 5.00e+00 4.00e-02 5.19e+01 ... (remaining 19280 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 4507 0.094 - 0.188: 354 0.188 - 0.282: 13 0.282 - 0.376: 1 0.376 - 0.469: 4 Chirality restraints: 4879 Sorted by residual: chirality pdb=" C19 1N7 L 701 " pdb=" C18 1N7 L 701 " pdb=" C2 1N7 L 701 " pdb=" C3 1N7 L 701 " both_signs ideal model delta sigma weight residual False -2.53 -3.00 0.47 2.00e-01 2.50e+01 5.51e+00 chirality pdb=" C19 1N7 I1402 " pdb=" C18 1N7 I1402 " pdb=" C2 1N7 I1402 " pdb=" C3 1N7 I1402 " both_signs ideal model delta sigma weight residual False -2.53 -2.99 0.46 2.00e-01 2.50e+01 5.20e+00 chirality pdb=" C19 1N7 I1401 " pdb=" C18 1N7 I1401 " pdb=" C2 1N7 I1401 " pdb=" C3 1N7 I1401 " both_signs ideal model delta sigma weight residual False -2.53 -2.98 0.45 2.00e-01 2.50e+01 5.08e+00 ... (remaining 4876 not shown) Planarity restraints: 5259 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP I 485 " 0.015 2.00e-02 2.50e+03 3.05e-02 9.32e+00 pdb=" C ASP I 485 " -0.053 2.00e-02 2.50e+03 pdb=" O ASP I 485 " 0.020 2.00e-02 2.50e+03 pdb=" N THR I 486 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR I 896 " -0.050 5.00e-02 4.00e+02 7.56e-02 9.15e+00 pdb=" N PRO I 897 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO I 897 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO I 897 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE J1325 " 0.015 2.00e-02 2.50e+03 2.98e-02 8.87e+00 pdb=" C PHE J1325 " -0.051 2.00e-02 2.50e+03 pdb=" O PHE J1325 " 0.020 2.00e-02 2.50e+03 pdb=" N GLN J1326 " 0.017 2.00e-02 2.50e+03 ... (remaining 5256 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 634 2.64 - 3.21: 27603 3.21 - 3.77: 49457 3.77 - 4.34: 62852 4.34 - 4.90: 101388 Nonbonded interactions: 241934 Sorted by model distance: nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1501 " model vdw 2.077 2.170 nonbonded pdb=" OE1 GLU J 811 " pdb=" OG1 THR J 890 " model vdw 2.229 2.440 nonbonded pdb=" O THR J 528 " pdb=" OG1 THR J 528 " model vdw 2.247 2.440 nonbonded pdb=" O ASP L 514 " pdb=" OG SER L 517 " model vdw 2.251 2.440 nonbonded pdb=" N ASP H 15 " pdb=" OD1 ASP H 15 " model vdw 2.258 2.520 ... (remaining 241929 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 'G' and (resid 5 through 158 or resid 167 through 233)) selection = (chain 'H' and resid 5 through 233) } 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 group one per residue 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: 0.950 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: 5.160 Check model and map are aligned: 0.470 Set scattering table: 0.260 Process input model: 97.810 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 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 : 0.009 0.292 31269 Z= 0.568 Angle : 0.864 18.306 42583 Z= 0.485 Chirality : 0.052 0.469 4879 Planarity : 0.006 0.076 5259 Dihedral : 17.406 172.190 12465 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.85 % Favored : 91.10 % Rotamer: Outliers : 7.42 % Allowed : 13.21 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.11 % Twisted Proline : 0.70 % Twisted General : 0.17 % 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: -2.11 (0.13), residues: 3651 helix: -0.21 (0.13), residues: 1377 sheet: -1.69 (0.24), residues: 435 loop : -2.30 (0.13), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I1276 HIS 0.007 0.001 HIS J 777 PHE 0.016 0.002 PHE J 620 TYR 0.022 0.002 TYR G 177 ARG 0.009 0.001 ARG I 974 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 148 time to evaluate : 3.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 194 GLN cc_start: 0.8190 (tp40) cc_final: 0.7984 (tp40) REVERT: I 213 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8791 (tt) REVERT: I 240 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7887 (pm20) REVERT: I 315 MET cc_start: 0.8341 (mmm) cc_final: 0.8127 (mmm) REVERT: I 369 MET cc_start: 0.8467 (tmm) cc_final: 0.8051 (tmm) REVERT: I 492 MET cc_start: 0.8533 (pmm) cc_final: 0.7918 (pmm) REVERT: I 515 MET cc_start: 0.8572 (ttp) cc_final: 0.8354 (ttp) REVERT: I 658 GLN cc_start: 0.9265 (OUTLIER) cc_final: 0.7965 (pp30) REVERT: I 697 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8211 (mtmm) REVERT: I 1287 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8836 (tp) REVERT: J 56 LEU cc_start: 0.9456 (OUTLIER) cc_final: 0.9176 (tt) REVERT: J 126 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.8981 (pp) REVERT: J 255 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8563 (mm) REVERT: J 596 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9186 (mm) REVERT: J 697 MET cc_start: 0.8806 (ttp) cc_final: 0.8590 (ttp) REVERT: J 706 VAL cc_start: 0.8739 (OUTLIER) cc_final: 0.8392 (m) REVERT: J 746 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8807 (mt) REVERT: J 1034 PHE cc_start: 0.8190 (OUTLIER) cc_final: 0.7941 (m-80) REVERT: L 365 MET cc_start: 0.9155 (mmt) cc_final: 0.8869 (mmt) REVERT: L 379 MET cc_start: 0.8757 (ppp) cc_final: 0.8517 (ppp) REVERT: L 487 MET cc_start: 0.8510 (mmt) cc_final: 0.8232 (mmt) outliers start: 233 outliers final: 110 residues processed: 370 average time/residue: 0.3695 time to fit residues: 231.8619 Evaluate side-chains 253 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 131 time to evaluate : 3.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 32 GLU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 15 ASP Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 240 GLU Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 391 SER Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 572 ILE Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 643 SER Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 658 GLN Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 781 ASP Chi-restraints excluded: chain I residue 819 SER Chi-restraints excluded: chain I residue 830 THR Chi-restraints excluded: chain I residue 851 THR Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 990 ASP Chi-restraints excluded: chain I residue 1038 GLN Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1287 LEU Chi-restraints excluded: chain I residue 1337 ILE Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 115 TRP Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 353 SER Chi-restraints excluded: chain J residue 394 ILE Chi-restraints excluded: chain J residue 410 ASP Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 536 LEU Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 654 ILE Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 684 ASP Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 806 ASP Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 890 THR Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 962 ASN Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1034 PHE Chi-restraints excluded: chain J residue 1058 SER Chi-restraints excluded: chain J residue 1176 VAL Chi-restraints excluded: chain J residue 1229 VAL Chi-restraints excluded: chain J residue 1250 ASP Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1273 ASP Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 331 HIS Chi-restraints excluded: chain L residue 354 THR Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 558 VAL Chi-restraints excluded: chain L residue 567 MET Chi-restraints excluded: chain L residue 573 LEU Chi-restraints excluded: chain L residue 580 PHE Chi-restraints excluded: chain L residue 606 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 4.9990 chunk 281 optimal weight: 50.0000 chunk 156 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 190 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 291 optimal weight: 8.9990 chunk 112 optimal weight: 0.8980 chunk 177 optimal weight: 2.9990 chunk 217 optimal weight: 4.9990 chunk 337 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 132 HIS H 194 GLN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 808 ASN J 153 ASN ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 266 ASN J 335 GLN J 365 GLN J 465 GLN ** J1289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 75 GLN ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.0828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31269 Z= 0.195 Angle : 0.569 10.165 42583 Z= 0.299 Chirality : 0.041 0.160 4879 Planarity : 0.004 0.070 5259 Dihedral : 15.727 172.725 5398 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.07 % Favored : 92.85 % Rotamer: Outliers : 5.16 % Allowed : 15.98 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.11 % Twisted Proline : 0.70 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.13), residues: 3651 helix: 0.68 (0.14), residues: 1386 sheet: -1.54 (0.23), residues: 465 loop : -2.09 (0.13), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP L 326 HIS 0.003 0.001 HIS J 777 PHE 0.010 0.001 PHE I1144 TYR 0.015 0.001 TYR L 430 ARG 0.004 0.000 ARG L 363 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 149 time to evaluate : 3.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 240 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7847 (pm20) REVERT: I 315 MET cc_start: 0.8307 (mmm) cc_final: 0.8022 (mmm) REVERT: I 369 MET cc_start: 0.8485 (tmm) cc_final: 0.8019 (tmm) REVERT: I 492 MET cc_start: 0.8428 (pmm) cc_final: 0.7687 (pmm) REVERT: I 515 MET cc_start: 0.8496 (ttp) cc_final: 0.8236 (ttp) REVERT: I 658 GLN cc_start: 0.9147 (OUTLIER) cc_final: 0.7279 (pp30) REVERT: I 697 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7791 (ttmm) REVERT: I 800 MET cc_start: 0.7534 (OUTLIER) cc_final: 0.7217 (mtm) REVERT: I 1244 HIS cc_start: 0.8998 (OUTLIER) cc_final: 0.8318 (p-80) REVERT: I 1287 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8593 (tp) REVERT: J 706 VAL cc_start: 0.8700 (OUTLIER) cc_final: 0.8413 (m) REVERT: J 898 CYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7631 (m) REVERT: J 1040 MET cc_start: 0.8336 (mpp) cc_final: 0.7617 (mpp) REVERT: L 291 CYS cc_start: 0.1055 (OUTLIER) cc_final: 0.0505 (m) REVERT: L 365 MET cc_start: 0.9119 (mmt) cc_final: 0.8872 (mmt) REVERT: L 379 MET cc_start: 0.8645 (ppp) cc_final: 0.8280 (ppp) REVERT: L 487 MET cc_start: 0.8443 (mmt) cc_final: 0.8228 (mmt) outliers start: 162 outliers final: 100 residues processed: 302 average time/residue: 0.3572 time to fit residues: 186.3170 Evaluate side-chains 244 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 135 time to evaluate : 3.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 32 GLU Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 15 ASP Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 240 GLU Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 513 GLN Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 606 LEU Chi-restraints excluded: chain I residue 643 SER Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 658 GLN Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 781 ASP Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 808 ASN Chi-restraints excluded: chain I residue 819 SER Chi-restraints excluded: chain I residue 822 VAL Chi-restraints excluded: chain I residue 851 THR Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 990 ASP Chi-restraints excluded: chain I residue 1038 GLN Chi-restraints excluded: chain I residue 1203 ASP Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1287 LEU Chi-restraints excluded: chain I residue 1337 ILE Chi-restraints excluded: chain I residue 1341 ASP Chi-restraints excluded: chain J residue 115 TRP Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 410 ASP Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 516 ASP Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 684 ASP Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 760 THR Chi-restraints excluded: chain J residue 767 LEU Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 806 ASP Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 886 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 898 CYS Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain J residue 1250 ASP Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 291 CYS Chi-restraints excluded: chain L residue 331 HIS Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 573 LEU Chi-restraints excluded: chain L residue 580 PHE Chi-restraints excluded: chain L residue 606 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 187 optimal weight: 8.9990 chunk 104 optimal weight: 9.9990 chunk 281 optimal weight: 50.0000 chunk 230 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 338 optimal weight: 7.9990 chunk 365 optimal weight: 50.0000 chunk 301 optimal weight: 10.0000 chunk 335 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 chunk 271 optimal weight: 20.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 832 HIS I 955 GLN I1038 GLN I1268 GLN ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 266 ASN J 365 GLN J 954 ASN J1010 GLN ** J1289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 75 GLN ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 31269 Z= 0.489 Angle : 0.707 9.467 42583 Z= 0.365 Chirality : 0.044 0.156 4879 Planarity : 0.005 0.085 5259 Dihedral : 15.658 172.733 5329 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.39 % Favored : 90.47 % Rotamer: Outliers : 6.30 % Allowed : 16.96 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.11 % Twisted Proline : 0.70 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.14), residues: 3651 helix: 0.80 (0.14), residues: 1380 sheet: -1.61 (0.23), residues: 473 loop : -2.06 (0.14), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 326 HIS 0.005 0.001 HIS J 545 PHE 0.018 0.002 PHE I1144 TYR 0.017 0.002 TYR I 555 ARG 0.006 0.000 ARG I 974 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 133 time to evaluate : 3.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 27 THR cc_start: 0.9161 (OUTLIER) cc_final: 0.8888 (p) REVERT: G 41 ASN cc_start: 0.8611 (t0) cc_final: 0.8351 (t0) REVERT: G 204 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7839 (tm-30) REVERT: I 213 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8778 (tt) REVERT: I 240 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7990 (tm-30) REVERT: I 315 MET cc_start: 0.8370 (mmm) cc_final: 0.8069 (mmm) REVERT: I 369 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.8002 (tmm) REVERT: I 448 LEU cc_start: 0.9570 (OUTLIER) cc_final: 0.8976 (tt) REVERT: I 492 MET cc_start: 0.8552 (pmm) cc_final: 0.7824 (pmm) REVERT: I 658 GLN cc_start: 0.9275 (OUTLIER) cc_final: 0.7646 (pp30) REVERT: I 800 MET cc_start: 0.7641 (OUTLIER) cc_final: 0.7341 (mtm) REVERT: I 909 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.8113 (ptmm) REVERT: I 1244 HIS cc_start: 0.9058 (OUTLIER) cc_final: 0.8446 (p-80) REVERT: I 1290 MET cc_start: 0.9173 (tpp) cc_final: 0.8808 (tpt) REVERT: J 534 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8513 (tm-30) REVERT: J 706 VAL cc_start: 0.8796 (OUTLIER) cc_final: 0.8523 (m) REVERT: L 291 CYS cc_start: 0.1266 (OUTLIER) cc_final: 0.0911 (m) REVERT: L 477 GLU cc_start: 0.9146 (OUTLIER) cc_final: 0.8836 (tm-30) REVERT: L 567 MET cc_start: 0.8233 (ppp) cc_final: 0.7659 (ppp) outliers start: 198 outliers final: 133 residues processed: 319 average time/residue: 0.3450 time to fit residues: 192.1229 Evaluate side-chains 276 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 129 time to evaluate : 3.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 8 PHE Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 32 GLU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 15 ASP Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 42 ASP Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 240 GLU Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 396 ASP Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 513 GLN Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 553 THR Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 606 LEU Chi-restraints excluded: chain I residue 643 SER Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 658 GLN Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 781 ASP Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 819 SER Chi-restraints excluded: chain I residue 822 VAL Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 851 THR Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 909 LYS Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 990 ASP Chi-restraints excluded: chain I residue 1036 ILE Chi-restraints excluded: chain I residue 1047 LEU Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1203 ASP Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1337 ILE Chi-restraints excluded: chain I residue 1341 ASP Chi-restraints excluded: chain J residue 20 ILE Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 115 TRP Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 353 SER Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 410 ASP Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 449 LEU Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 516 ASP Chi-restraints excluded: chain J residue 534 GLU Chi-restraints excluded: chain J residue 536 LEU Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 654 ILE Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 684 ASP Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 703 THR Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 760 THR Chi-restraints excluded: chain J residue 767 LEU Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 806 ASP Chi-restraints excluded: chain J residue 810 THR Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 886 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 962 ASN Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1046 ILE Chi-restraints excluded: chain J residue 1229 VAL Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain J residue 1250 ASP Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1273 ASP Chi-restraints excluded: chain J residue 1285 VAL Chi-restraints excluded: chain J residue 1325 PHE Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 291 CYS Chi-restraints excluded: chain L residue 331 HIS Chi-restraints excluded: chain L residue 477 GLU Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 573 LEU Chi-restraints excluded: chain L residue 580 PHE Chi-restraints excluded: chain L residue 606 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 334 optimal weight: 30.0000 chunk 254 optimal weight: 0.8980 chunk 175 optimal weight: 0.8980 chunk 37 optimal weight: 10.0000 chunk 161 optimal weight: 2.9990 chunk 227 optimal weight: 4.9990 chunk 339 optimal weight: 7.9990 chunk 359 optimal weight: 30.0000 chunk 177 optimal weight: 2.9990 chunk 321 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 955 GLN J 153 ASN ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 266 ASN J 365 GLN J1010 GLN ** J1289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 75 GLN ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31269 Z= 0.187 Angle : 0.548 8.360 42583 Z= 0.287 Chirality : 0.041 0.143 4879 Planarity : 0.004 0.065 5259 Dihedral : 15.298 171.411 5314 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.33 % Favored : 93.59 % Rotamer: Outliers : 4.93 % Allowed : 18.87 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.11 % Twisted Proline : 0.70 % Twisted General : 0.03 % 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: -0.96 (0.14), residues: 3651 helix: 1.12 (0.14), residues: 1381 sheet: -1.45 (0.24), residues: 468 loop : -1.88 (0.14), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 326 HIS 0.004 0.001 HIS J 777 PHE 0.013 0.001 PHE J1034 TYR 0.014 0.001 TYR L 430 ARG 0.004 0.000 ARG I 637 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 137 time to evaluate : 3.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 27 THR cc_start: 0.9193 (OUTLIER) cc_final: 0.8968 (p) REVERT: I 197 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7632 (ptp-170) REVERT: I 369 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.7976 (tmm) REVERT: I 492 MET cc_start: 0.8498 (pmm) cc_final: 0.7781 (pmm) REVERT: I 658 GLN cc_start: 0.9183 (OUTLIER) cc_final: 0.7168 (pp30) REVERT: I 800 MET cc_start: 0.7600 (OUTLIER) cc_final: 0.7277 (mtm) REVERT: I 1244 HIS cc_start: 0.8943 (OUTLIER) cc_final: 0.8302 (p-80) REVERT: I 1287 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8585 (tp) REVERT: I 1290 MET cc_start: 0.9081 (tpp) cc_final: 0.8636 (tpt) REVERT: J 534 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.7742 (tt0) REVERT: J 706 VAL cc_start: 0.8712 (OUTLIER) cc_final: 0.8466 (m) REVERT: J 898 CYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7672 (m) REVERT: K 43 ASN cc_start: 0.8396 (t0) cc_final: 0.8113 (t0) REVERT: L 291 CYS cc_start: 0.1253 (OUTLIER) cc_final: 0.0830 (m) REVERT: L 567 MET cc_start: 0.8408 (ppp) cc_final: 0.7842 (ppp) outliers start: 155 outliers final: 98 residues processed: 280 average time/residue: 0.3591 time to fit residues: 173.6464 Evaluate side-chains 243 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 134 time to evaluate : 3.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 8 PHE Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 15 ASP Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 42 ASP Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 197 ARG Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 396 ASP Chi-restraints excluded: chain I residue 435 ILE Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 553 THR Chi-restraints excluded: chain I residue 606 LEU Chi-restraints excluded: chain I residue 643 SER Chi-restraints excluded: chain I residue 658 GLN Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 851 THR Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 990 ASP Chi-restraints excluded: chain I residue 1203 ASP Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1287 LEU Chi-restraints excluded: chain I residue 1337 ILE Chi-restraints excluded: chain I residue 1341 ASP Chi-restraints excluded: chain J residue 20 ILE Chi-restraints excluded: chain J residue 70 CYS Chi-restraints excluded: chain J residue 115 TRP Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 410 ASP Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 534 GLU Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 684 ASP Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 760 THR Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 767 LEU Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 806 ASP Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 886 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 898 CYS Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain J residue 1250 ASP Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 291 CYS Chi-restraints excluded: chain L residue 331 HIS Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 561 MET Chi-restraints excluded: chain L residue 573 LEU Chi-restraints excluded: chain L residue 580 PHE Chi-restraints excluded: chain L residue 606 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 299 optimal weight: 10.0000 chunk 204 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 267 optimal weight: 8.9990 chunk 148 optimal weight: 6.9990 chunk 306 optimal weight: 9.9990 chunk 248 optimal weight: 0.0670 chunk 0 optimal weight: 9.9990 chunk 183 optimal weight: 9.9990 chunk 322 optimal weight: 20.0000 chunk 90 optimal weight: 9.9990 overall best weight: 6.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 ASN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 955 GLN ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN ** J1289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 31269 Z= 0.404 Angle : 0.643 8.679 42583 Z= 0.331 Chirality : 0.043 0.154 4879 Planarity : 0.004 0.064 5259 Dihedral : 15.288 171.777 5294 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.07 % Favored : 90.82 % Rotamer: Outliers : 5.70 % Allowed : 18.68 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.11 % Twisted Proline : 0.70 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.14), residues: 3651 helix: 1.08 (0.14), residues: 1383 sheet: -1.49 (0.24), residues: 470 loop : -1.90 (0.14), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 315 HIS 0.004 0.001 HIS J 545 PHE 0.015 0.001 PHE I1144 TYR 0.013 0.001 TYR L 430 ARG 0.006 0.000 ARG I 974 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 133 time to evaluate : 3.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 27 THR cc_start: 0.9203 (OUTLIER) cc_final: 0.8964 (p) REVERT: G 41 ASN cc_start: 0.8559 (t0) cc_final: 0.8255 (t0) REVERT: G 204 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7750 (tm-30) REVERT: I 369 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8057 (tmm) REVERT: I 492 MET cc_start: 0.8528 (pmm) cc_final: 0.7809 (pmm) REVERT: I 658 GLN cc_start: 0.9252 (OUTLIER) cc_final: 0.7593 (pp30) REVERT: I 800 MET cc_start: 0.7621 (OUTLIER) cc_final: 0.7308 (mtm) REVERT: I 909 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.8117 (ptmm) REVERT: I 1085 MET cc_start: 0.8830 (mmt) cc_final: 0.8565 (mmt) REVERT: I 1244 HIS cc_start: 0.9036 (OUTLIER) cc_final: 0.8431 (p-80) REVERT: I 1290 MET cc_start: 0.9084 (tpp) cc_final: 0.8691 (tpt) REVERT: I 1331 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.8302 (ttm170) REVERT: J 180 MET cc_start: 0.6839 (ttt) cc_final: 0.6593 (tpt) REVERT: J 534 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8490 (tm-30) REVERT: J 706 VAL cc_start: 0.8817 (OUTLIER) cc_final: 0.8574 (m) REVERT: J 898 CYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7710 (m) REVERT: K 69 ARG cc_start: 0.9176 (tpp80) cc_final: 0.8685 (tpp80) REVERT: L 291 CYS cc_start: 0.1358 (OUTLIER) cc_final: 0.0833 (m) REVERT: L 567 MET cc_start: 0.8356 (ppp) cc_final: 0.7804 (ppp) outliers start: 179 outliers final: 131 residues processed: 304 average time/residue: 0.3568 time to fit residues: 188.1579 Evaluate side-chains 275 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 132 time to evaluate : 3.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 8 PHE Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 32 GLU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 222 THR Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 15 ASP Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 42 ASP Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 396 ASP Chi-restraints excluded: chain I residue 414 ILE Chi-restraints excluded: chain I residue 435 ILE Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 513 GLN Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 553 THR Chi-restraints excluded: chain I residue 602 GLU Chi-restraints excluded: chain I residue 606 LEU Chi-restraints excluded: chain I residue 643 SER Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 658 GLN Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 781 ASP Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 822 VAL Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 830 THR Chi-restraints excluded: chain I residue 851 THR Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 909 LYS Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 990 ASP Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1203 ASP Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1331 ARG Chi-restraints excluded: chain I residue 1337 ILE Chi-restraints excluded: chain J residue 20 ILE Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 70 CYS Chi-restraints excluded: chain J residue 115 TRP Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 353 SER Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 410 ASP Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 449 LEU Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 516 ASP Chi-restraints excluded: chain J residue 517 CYS Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 534 GLU Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 684 ASP Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 703 THR Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 760 THR Chi-restraints excluded: chain J residue 767 LEU Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 806 ASP Chi-restraints excluded: chain J residue 810 THR Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 884 SER Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 886 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 898 CYS Chi-restraints excluded: chain J residue 962 ASN Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1046 ILE Chi-restraints excluded: chain J residue 1229 VAL Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain J residue 1250 ASP Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1273 ASP Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1326 GLN Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 291 CYS Chi-restraints excluded: chain L residue 331 HIS Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 573 LEU Chi-restraints excluded: chain L residue 580 PHE Chi-restraints excluded: chain L residue 606 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 120 optimal weight: 4.9990 chunk 323 optimal weight: 8.9990 chunk 71 optimal weight: 30.0000 chunk 211 optimal weight: 8.9990 chunk 88 optimal weight: 8.9990 chunk 359 optimal weight: 30.0000 chunk 298 optimal weight: 2.9990 chunk 166 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 188 optimal weight: 0.3980 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 955 GLN ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN ** J1289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31269 Z= 0.187 Angle : 0.541 10.374 42583 Z= 0.282 Chirality : 0.041 0.171 4879 Planarity : 0.004 0.065 5259 Dihedral : 15.116 171.106 5294 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.41 % Favored : 93.51 % Rotamer: Outliers : 5.00 % Allowed : 19.45 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.11 % Twisted Proline : 0.70 % Twisted General : 0.03 % 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: -0.74 (0.14), residues: 3651 helix: 1.31 (0.14), residues: 1381 sheet: -1.37 (0.24), residues: 463 loop : -1.74 (0.14), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 33 HIS 0.004 0.001 HIS J 777 PHE 0.015 0.001 PHE J1199 TYR 0.014 0.001 TYR L 430 ARG 0.003 0.000 ARG I 974 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 142 time to evaluate : 3.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 27 THR cc_start: 0.9262 (OUTLIER) cc_final: 0.9042 (p) REVERT: I 369 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.8043 (tmm) REVERT: I 492 MET cc_start: 0.8443 (pmm) cc_final: 0.7711 (pmm) REVERT: I 658 GLN cc_start: 0.9170 (OUTLIER) cc_final: 0.7177 (pp30) REVERT: I 800 MET cc_start: 0.7587 (OUTLIER) cc_final: 0.7285 (mtm) REVERT: I 1085 MET cc_start: 0.8751 (mmt) cc_final: 0.8448 (mmt) REVERT: I 1244 HIS cc_start: 0.8965 (OUTLIER) cc_final: 0.8326 (p-80) REVERT: I 1290 MET cc_start: 0.9011 (tpp) cc_final: 0.8573 (tpt) REVERT: J 180 MET cc_start: 0.6899 (ttt) cc_final: 0.6461 (tpt) REVERT: J 898 CYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7626 (m) REVERT: J 1215 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7848 (mp0) REVERT: K 25 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.8104 (tmm-80) REVERT: K 43 ASN cc_start: 0.8401 (t0) cc_final: 0.8113 (t0) REVERT: K 69 ARG cc_start: 0.9143 (tpp80) cc_final: 0.8625 (tpp80) REVERT: L 291 CYS cc_start: 0.1282 (OUTLIER) cc_final: 0.0759 (m) REVERT: L 567 MET cc_start: 0.8408 (ppp) cc_final: 0.7867 (ppp) outliers start: 157 outliers final: 112 residues processed: 289 average time/residue: 0.3688 time to fit residues: 183.0699 Evaluate side-chains 257 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 136 time to evaluate : 3.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 8 PHE Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 32 GLU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 15 ASP Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 42 ASP Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 118 LYS Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 396 ASP Chi-restraints excluded: chain I residue 435 ILE Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 513 GLN Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 553 THR Chi-restraints excluded: chain I residue 602 GLU Chi-restraints excluded: chain I residue 606 LEU Chi-restraints excluded: chain I residue 643 SER Chi-restraints excluded: chain I residue 658 GLN Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 781 ASP Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 851 THR Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 990 ASP Chi-restraints excluded: chain I residue 1036 ILE Chi-restraints excluded: chain I residue 1203 ASP Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1337 ILE Chi-restraints excluded: chain J residue 20 ILE Chi-restraints excluded: chain J residue 70 CYS Chi-restraints excluded: chain J residue 115 TRP Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 684 ASP Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 760 THR Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 767 LEU Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 806 ASP Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 886 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 898 CYS Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1046 ILE Chi-restraints excluded: chain J residue 1215 GLU Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain J residue 1250 ASP Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1273 ASP Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1326 GLN Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 25 ARG Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 291 CYS Chi-restraints excluded: chain L residue 331 HIS Chi-restraints excluded: chain L residue 344 LEU Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 558 VAL Chi-restraints excluded: chain L residue 573 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 347 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 chunk 205 optimal weight: 6.9990 chunk 262 optimal weight: 10.0000 chunk 203 optimal weight: 0.8980 chunk 302 optimal weight: 20.0000 chunk 200 optimal weight: 10.0000 chunk 358 optimal weight: 10.0000 chunk 224 optimal weight: 7.9990 chunk 218 optimal weight: 2.9990 chunk 165 optimal weight: 0.3980 overall best weight: 3.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 955 GLN J 153 ASN ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 31269 Z= 0.278 Angle : 0.577 10.338 42583 Z= 0.298 Chirality : 0.041 0.169 4879 Planarity : 0.004 0.064 5259 Dihedral : 15.050 171.172 5288 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.03 % Favored : 91.92 % Rotamer: Outliers : 4.93 % Allowed : 20.21 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.11 % Twisted Proline : 0.70 % Twisted General : 0.03 % 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: -0.72 (0.14), residues: 3651 helix: 1.29 (0.14), residues: 1388 sheet: -1.32 (0.24), residues: 462 loop : -1.73 (0.14), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 326 HIS 0.003 0.001 HIS J 545 PHE 0.012 0.001 PHE I1144 TYR 0.015 0.001 TYR I 215 ARG 0.006 0.000 ARG I 678 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 139 time to evaluate : 3.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 27 THR cc_start: 0.9298 (OUTLIER) cc_final: 0.9076 (p) REVERT: G 204 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7751 (tm-30) REVERT: I 369 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8055 (tmm) REVERT: I 492 MET cc_start: 0.8484 (pmm) cc_final: 0.7774 (pmm) REVERT: I 658 GLN cc_start: 0.9205 (OUTLIER) cc_final: 0.7225 (pp30) REVERT: I 800 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.7284 (mtm) REVERT: I 909 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.8041 (ptmm) REVERT: I 1244 HIS cc_start: 0.8995 (OUTLIER) cc_final: 0.8360 (p-80) REVERT: I 1287 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8734 (tp) REVERT: J 180 MET cc_start: 0.6988 (ttt) cc_final: 0.6574 (tpt) REVERT: J 898 CYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7652 (m) REVERT: J 1215 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7862 (mp0) REVERT: K 25 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.8173 (ttp80) REVERT: K 43 ASN cc_start: 0.8423 (t0) cc_final: 0.8158 (t0) REVERT: K 69 ARG cc_start: 0.9153 (tpp80) cc_final: 0.8638 (tpp80) REVERT: L 291 CYS cc_start: 0.1287 (OUTLIER) cc_final: 0.0753 (m) REVERT: L 365 MET cc_start: 0.8982 (mmt) cc_final: 0.8630 (mmm) REVERT: L 567 MET cc_start: 0.8349 (ppp) cc_final: 0.7877 (ppp) outliers start: 155 outliers final: 127 residues processed: 284 average time/residue: 0.3692 time to fit residues: 180.1662 Evaluate side-chains 275 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 136 time to evaluate : 3.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 8 PHE Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 32 GLU Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 222 THR Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 15 ASP Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 81 ILE Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 42 ASP Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 396 ASP Chi-restraints excluded: chain I residue 435 ILE Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 513 GLN Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 553 THR Chi-restraints excluded: chain I residue 602 GLU Chi-restraints excluded: chain I residue 606 LEU Chi-restraints excluded: chain I residue 658 GLN Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 781 ASP Chi-restraints excluded: chain I residue 782 VAL Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 830 THR Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 909 LYS Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 990 ASP Chi-restraints excluded: chain I residue 1036 ILE Chi-restraints excluded: chain I residue 1040 ASP Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1047 LEU Chi-restraints excluded: chain I residue 1203 ASP Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1287 LEU Chi-restraints excluded: chain I residue 1337 ILE Chi-restraints excluded: chain J residue 20 ILE Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 70 CYS Chi-restraints excluded: chain J residue 115 TRP Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 353 SER Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 516 ASP Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 536 LEU Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 554 GLU Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 684 ASP Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 703 THR Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 760 THR Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 767 LEU Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 806 ASP Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 886 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 898 CYS Chi-restraints excluded: chain J residue 962 ASN Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1046 ILE Chi-restraints excluded: chain J residue 1120 THR Chi-restraints excluded: chain J residue 1215 GLU Chi-restraints excluded: chain J residue 1250 ASP Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1273 ASP Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 25 ARG Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 291 CYS Chi-restraints excluded: chain L residue 331 HIS Chi-restraints excluded: chain L residue 344 LEU Chi-restraints excluded: chain L residue 354 THR Chi-restraints excluded: chain L residue 402 LEU Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 558 VAL Chi-restraints excluded: chain L residue 573 LEU Chi-restraints excluded: chain L residue 604 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.5581 > 50: distance: 1 - 19: 12.515 distance: 5 - 28: 16.657 distance: 10 - 37: 13.919 distance: 14 - 19: 12.350 distance: 15 - 48: 12.248 distance: 19 - 20: 16.499 distance: 20 - 21: 17.807 distance: 20 - 23: 13.771 distance: 21 - 22: 6.648 distance: 21 - 28: 10.405 distance: 23 - 24: 16.512 distance: 24 - 25: 8.782 distance: 25 - 26: 8.721 distance: 25 - 27: 12.863 distance: 28 - 29: 6.340 distance: 29 - 30: 20.355 distance: 29 - 32: 9.272 distance: 30 - 31: 8.593 distance: 30 - 37: 6.472 distance: 32 - 33: 6.182 distance: 33 - 34: 5.216 distance: 34 - 35: 6.364 distance: 34 - 36: 10.364 distance: 37 - 38: 7.644 distance: 38 - 41: 6.269 distance: 39 - 40: 17.671 distance: 39 - 48: 3.929 distance: 41 - 42: 7.260 distance: 42 - 43: 12.189 distance: 42 - 44: 9.357 distance: 43 - 45: 6.309 distance: 44 - 46: 5.190 distance: 45 - 47: 9.488 distance: 46 - 47: 12.307 distance: 48 - 49: 6.583 distance: 49 - 50: 12.487 distance: 49 - 52: 9.299 distance: 50 - 51: 11.127 distance: 50 - 57: 16.633 distance: 52 - 53: 7.685 distance: 53 - 54: 8.188 distance: 54 - 55: 12.624 distance: 54 - 56: 7.834 distance: 57 - 58: 31.435 distance: 58 - 59: 12.412 distance: 58 - 61: 24.763 distance: 59 - 60: 6.447 distance: 59 - 63: 27.253 distance: 61 - 62: 26.341 distance: 63 - 64: 30.540 distance: 64 - 65: 10.337 distance: 65 - 66: 16.358 distance: 65 - 67: 41.567 distance: 67 - 68: 21.044 distance: 68 - 69: 8.875 distance: 68 - 71: 30.217 distance: 69 - 70: 35.752 distance: 69 - 75: 14.484 distance: 72 - 73: 13.354 distance: 72 - 74: 11.887 distance: 75 - 76: 29.789 distance: 76 - 77: 20.780 distance: 76 - 79: 17.347 distance: 77 - 78: 9.527 distance: 77 - 82: 13.224 distance: 79 - 80: 16.081 distance: 79 - 81: 31.476 distance: 82 - 83: 15.968 distance: 83 - 84: 13.552 distance: 83 - 86: 10.699 distance: 84 - 85: 12.731 distance: 84 - 89: 13.634 distance: 86 - 87: 9.201 distance: 86 - 88: 17.632 distance: 89 - 90: 23.282 distance: 90 - 91: 4.904 distance: 90 - 93: 4.224 distance: 91 - 92: 10.928 distance: 91 - 94: 23.777 distance: 92 - 115: 31.725