Starting phenix.real_space_refine (version: dev) on Thu Apr 7 23:21:07 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mke_23893/04_2022/7mke_23893_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mke_23893/04_2022/7mke_23893.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mke_23893/04_2022/7mke_23893_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mke_23893/04_2022/7mke_23893_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mke_23893/04_2022/7mke_23893_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mke_23893/04_2022/7mke_23893.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mke_23893/04_2022/7mke_23893.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mke_23893/04_2022/7mke_23893_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mke_23893/04_2022/7mke_23893_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/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: {'PTRANS': 8, 'CIS': 1, 'TRANS': 212, 'PCIS': 1} 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: {'PTRANS': 55, 'CIS': 2, 'TRANS': 1281, 'PCIS': 1} 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: {'PTRANS': 55, 'CIS': 1, '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: 18 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: {' ZN': 2, ' MG': 1} 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: 18 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: 16.46, per 1000 atoms: 0.54 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: 12.32 Conformation dependent library (CDL) restraints added in 4.3 seconds Dynamic metal coordination Zn2+ tetrahedral 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: 12.04 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: 13.32 Time building geometry restraints manager: 13.27 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=" C17 1N7 L 702 " pdb=" O3 1N7 L 702 " ideal model delta sigma weight residual 0.000 1.411 -1.411 2.00e-02 2.50e+03 4.97e+03 bond pdb=" C17 1N7 I1401 " pdb=" O3 1N7 I1401 " ideal model delta sigma weight residual 0.000 1.407 -1.407 2.00e-02 2.50e+03 4.95e+03 bond pdb=" C17 1N7 L 701 " pdb=" O3 1N7 L 701 " ideal model delta sigma weight residual 0.000 1.407 -1.407 2.00e-02 2.50e+03 4.95e+03 bond pdb=" C17 1N7 I1402 " pdb=" O3 1N7 I1402 " ideal model delta sigma weight residual 0.000 1.405 -1.405 2.00e-02 2.50e+03 4.93e+03 bond pdb=" C3 1N7 L 701 " pdb=" C4 1N7 L 701 " ideal model delta sigma weight residual 1.261 1.729 -0.468 2.00e-02 2.50e+03 5.47e+02 ... (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=" 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 angle pdb=" C GLN I 517 " pdb=" N ASN I 518 " pdb=" CA ASN I 518 " ideal model delta sigma weight residual 122.65 115.66 6.99 1.60e+00 3.91e-01 1.91e+01 angle pdb=" C4 1N7 L 701 " pdb=" C5 1N7 L 701 " pdb=" C9 1N7 L 701 " ideal model delta sigma weight residual 121.90 109.01 12.89 3.00e+00 1.11e-01 1.85e+01 ... (remaining 42578 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.44: 18069 34.44 - 68.88: 808 68.88 - 103.31: 34 103.31 - 137.75: 1 137.75 - 172.19: 3 Dihedral angle restraints: 18915 sinusoidal: 8338 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 18912 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.305: 4855 0.305 - 0.609: 12 0.609 - 0.914: 4 0.914 - 1.218: 0 1.218 - 1.523: 4 Chirality restraints: 4875 Sorted by residual: chirality pdb=" C18 1N7 I1402 " pdb=" C17 1N7 I1402 " pdb=" C19 1N7 I1402 " pdb=" C6 1N7 I1402 " both_signs ideal model delta sigma weight residual False 1.21 2.74 -1.52 2.00e-01 2.50e+01 5.80e+01 chirality pdb=" C18 1N7 I1401 " pdb=" C17 1N7 I1401 " pdb=" C19 1N7 I1401 " pdb=" C6 1N7 I1401 " both_signs ideal model delta sigma weight residual False 1.21 2.63 -1.42 2.00e-01 2.50e+01 5.04e+01 chirality pdb=" C18 1N7 L 702 " pdb=" C17 1N7 L 702 " pdb=" C19 1N7 L 702 " pdb=" C6 1N7 L 702 " both_signs ideal model delta sigma weight residual False 1.21 2.63 -1.42 2.00e-01 2.50e+01 5.04e+01 ... (remaining 4872 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 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. 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 6.840 Check model and map are aligned: 0.520 Convert atoms to be neutral: 0.250 Process input model: 88.200 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 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 : 0.022 1.411 31269 Z= 0.967 Angle : 0.874 18.306 42583 Z= 0.486 Chirality : 0.071 1.523 4875 Planarity : 0.006 0.076 5259 Dihedral : 17.324 172.190 12097 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 % 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 *********************** 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 : 4.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 233 outliers final: 110 residues processed: 370 average time/residue: 0.3815 time to fit residues: 242.2501 Evaluate side-chains 241 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 131 time to evaluate : 3.584 Switching outliers to nearest non-outliers outliers start: 110 outliers final: 0 residues processed: 110 average time/residue: 0.2723 time to fit residues: 62.1340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 96 optimal weight: 3.9990 chunk 190 optimal weight: 0.9990 chunk 150 optimal weight: 0.9990 chunk 291 optimal weight: 9.9990 chunk 112 optimal weight: 0.7980 chunk 177 optimal weight: 0.9990 chunk 217 optimal weight: 4.9990 chunk 337 optimal weight: 50.0000 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 194 GLN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 658 GLN I 808 ASN ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 300 GLN J 335 GLN J 465 GLN ** J1289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1326 GLN K 75 GLN ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.0591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.088 31269 Z= 0.216 Angle : 0.699 12.937 42583 Z= 0.356 Chirality : 0.045 0.325 4875 Planarity : 0.005 0.083 5259 Dihedral : 15.264 173.343 4835 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.70 % Favored : 92.22 % Rotamer Outliers : 1.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.11 % Twisted Proline : 0.70 % Twisted General : 0.14 % 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: -1.68 (0.13), residues: 3651 helix: 0.32 (0.14), residues: 1380 sheet: -1.56 (0.23), residues: 470 loop : -2.20 (0.13), residues: 1801 *********************** 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 200 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 144 time to evaluate : 3.391 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 21 residues processed: 193 average time/residue: 0.3809 time to fit residues: 125.8754 Evaluate side-chains 153 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 132 time to evaluate : 3.677 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2663 time to fit residues: 15.4598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 187 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 chunk 281 optimal weight: 50.0000 chunk 230 optimal weight: 0.9980 chunk 93 optimal weight: 0.0000 chunk 338 optimal weight: 6.9990 chunk 365 optimal weight: 50.0000 chunk 301 optimal weight: 8.9990 chunk 335 optimal weight: 0.0870 chunk 115 optimal weight: 6.9990 chunk 271 optimal weight: 30.0000 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 465 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.0622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.242 31269 Z= 0.328 Angle : 0.732 26.849 42583 Z= 0.371 Chirality : 0.045 0.280 4875 Planarity : 0.005 0.135 5259 Dihedral : 15.245 173.203 4835 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.89 % Favored : 92.00 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.11 % Twisted Proline : 0.70 % Twisted General : 0.11 % 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: -1.64 (0.13), residues: 3651 helix: 0.37 (0.14), residues: 1381 sheet: -1.56 (0.23), residues: 468 loop : -2.17 (0.13), residues: 1802 *********************** 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 161 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 132 time to evaluate : 3.590 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 8 residues processed: 158 average time/residue: 0.3912 time to fit residues: 106.3903 Evaluate side-chains 138 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 130 time to evaluate : 3.554 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3050 time to fit residues: 9.1573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 334 optimal weight: 0.2980 chunk 254 optimal weight: 0.7980 chunk 175 optimal weight: 1.9990 chunk 37 optimal weight: 20.0000 chunk 161 optimal weight: 2.9990 chunk 227 optimal weight: 0.9990 chunk 339 optimal weight: 30.0000 chunk 359 optimal weight: 20.0000 chunk 177 optimal weight: 0.9980 chunk 321 optimal weight: 8.9990 chunk 96 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 465 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.0641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.242 31269 Z= 0.328 Angle : 0.732 26.849 42583 Z= 0.371 Chirality : 0.045 0.280 4875 Planarity : 0.005 0.135 5259 Dihedral : 15.245 173.203 4835 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.89 % Favored : 92.00 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.11 % Twisted Proline : 0.70 % Twisted General : 0.11 % 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: -1.64 (0.13), residues: 3651 helix: 0.37 (0.14), residues: 1381 sheet: -1.56 (0.23), residues: 468 loop : -2.17 (0.13), residues: 1802 *********************** 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 132 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 3.646 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.4127 time to fit residues: 93.6393 Evaluate side-chains 130 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 3.885 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 299 optimal weight: 8.9990 chunk 204 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 267 optimal weight: 10.0000 chunk 148 optimal weight: 0.8980 chunk 306 optimal weight: 7.9990 chunk 248 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 183 optimal weight: 8.9990 chunk 322 optimal weight: 20.0000 chunk 90 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 465 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.0671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.105 31269 Z= 0.276 Angle : 0.681 12.792 42583 Z= 0.346 Chirality : 0.044 0.258 4875 Planarity : 0.005 0.106 5259 Dihedral : 15.204 172.929 4835 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.78 % Favored : 92.11 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.11 % Twisted Proline : 0.70 % Twisted General : 0.11 % 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: -1.54 (0.13), residues: 3651 helix: 0.48 (0.14), residues: 1381 sheet: -1.56 (0.23), residues: 471 loop : -2.13 (0.13), residues: 1799 *********************** 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 160 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 134 time to evaluate : 3.587 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 9 residues processed: 156 average time/residue: 0.3866 time to fit residues: 103.9622 Evaluate side-chains 139 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 130 time to evaluate : 3.553 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2671 time to fit residues: 9.4576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 120 optimal weight: 6.9990 chunk 323 optimal weight: 2.9990 chunk 71 optimal weight: 40.0000 chunk 211 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 359 optimal weight: 10.0000 chunk 298 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 119 optimal weight: 7.9990 chunk 188 optimal weight: 9.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 465 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.0690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.105 31269 Z= 0.276 Angle : 0.681 12.791 42583 Z= 0.346 Chirality : 0.044 0.258 4875 Planarity : 0.005 0.106 5259 Dihedral : 15.204 172.929 4835 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.78 % Favored : 92.11 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.11 % Twisted Proline : 0.70 % Twisted General : 0.11 % 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: -1.54 (0.13), residues: 3651 helix: 0.48 (0.14), residues: 1381 sheet: -1.56 (0.23), residues: 471 loop : -2.13 (0.13), residues: 1799 *********************** 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 130 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 3.532 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.3994 time to fit residues: 88.9294 Evaluate side-chains 130 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 3.478 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.8189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 347 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 205 optimal weight: 6.9990 chunk 262 optimal weight: 0.7980 chunk 203 optimal weight: 6.9990 chunk 302 optimal weight: 20.0000 chunk 200 optimal weight: 4.9990 chunk 358 optimal weight: 9.9990 chunk 224 optimal weight: 1.9990 chunk 218 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 465 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.0688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.105 31269 Z= 0.276 Angle : 0.681 12.777 42583 Z= 0.346 Chirality : 0.044 0.257 4875 Planarity : 0.005 0.106 5259 Dihedral : 15.203 172.929 4835 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.78 % Favored : 92.11 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.11 % Twisted Proline : 0.70 % Twisted General : 0.11 % 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: -1.54 (0.13), residues: 3651 helix: 0.48 (0.14), residues: 1381 sheet: -1.56 (0.23), residues: 471 loop : -2.13 (0.13), residues: 1799 *********************** 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 130 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 3.762 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.4217 time to fit residues: 94.1780 Evaluate side-chains 130 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 3.616 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.8766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 221 optimal weight: 0.9990 chunk 143 optimal weight: 7.9990 chunk 214 optimal weight: 2.9990 chunk 108 optimal weight: 0.2980 chunk 70 optimal weight: 20.0000 chunk 69 optimal weight: 20.0000 chunk 227 optimal weight: 0.8980 chunk 244 optimal weight: 10.0000 chunk 177 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 281 optimal weight: 50.0000 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 465 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.0691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.083 31269 Z= 0.273 Angle : 0.674 11.407 42583 Z= 0.344 Chirality : 0.044 0.275 4875 Planarity : 0.005 0.105 5259 Dihedral : 15.201 172.928 4835 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.75 % Favored : 92.14 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.11 % Twisted Proline : 0.70 % Twisted General : 0.11 % 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: -1.53 (0.13), residues: 3651 helix: 0.49 (0.14), residues: 1382 sheet: -1.56 (0.23), residues: 471 loop : -2.13 (0.13), residues: 1798 *********************** REFINEMENT MACRO_CYCLE 8 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 139 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 130 time to evaluate : 3.407 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 135 average time/residue: 0.4045 time to fit residues: 93.8575 Evaluate side-chains 136 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 130 time to evaluate : 3.392 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2854 time to fit residues: 7.7835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 326 optimal weight: 0.0000 chunk 343 optimal weight: 4.9990 chunk 313 optimal weight: 9.9990 chunk 334 optimal weight: 20.0000 chunk 201 optimal weight: 0.8980 chunk 145 optimal weight: 7.9990 chunk 262 optimal weight: 20.0000 chunk 102 optimal weight: 7.9990 chunk 301 optimal weight: 9.9990 chunk 316 optimal weight: 0.6980 chunk 332 optimal weight: 20.0000 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 465 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.0691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.084 31269 Z= 0.271 Angle : 0.678 17.254 42583 Z= 0.344 Chirality : 0.043 0.274 4875 Planarity : 0.005 0.104 5259 Dihedral : 15.201 172.928 4835 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.75 % Favored : 92.14 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.11 % Twisted Proline : 0.70 % Twisted General : 0.11 % 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: -1.53 (0.13), residues: 3651 helix: 0.49 (0.14), residues: 1382 sheet: -1.56 (0.23), residues: 471 loop : -2.13 (0.13), residues: 1798 *********************** REFINEMENT MACRO_CYCLE 9 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 132 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 130 time to evaluate : 3.898 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 131 average time/residue: 0.4146 time to fit residues: 93.7058 Evaluate side-chains 132 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 130 time to evaluate : 3.949 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3004 time to fit residues: 6.2822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 219 optimal weight: 6.9990 chunk 353 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 167 optimal weight: 6.9990 chunk 245 optimal weight: 10.0000 chunk 370 optimal weight: 30.0000 chunk 341 optimal weight: 20.0000 chunk 295 optimal weight: 20.0000 chunk 30 optimal weight: 8.9990 chunk 227 optimal weight: 0.5980 chunk 180 optimal weight: 2.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 465 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.0691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.084 31269 Z= 0.271 Angle : 0.678 17.254 42583 Z= 0.344 Chirality : 0.043 0.274 4875 Planarity : 0.005 0.104 5259 Dihedral : 15.201 172.928 4835 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.75 % Favored : 92.14 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.11 % Twisted Proline : 0.70 % Twisted General : 0.11 % 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: -1.53 (0.13), residues: 3651 helix: 0.49 (0.14), residues: 1382 sheet: -1.56 (0.23), residues: 471 loop : -2.13 (0.13), residues: 1798 ********************** REFINEMENT MACRO_CYCLE 10 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 130 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 3.691 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.4293 time to fit residues: 96.1054 Evaluate side-chains 130 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 3.713 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 234 optimal weight: 7.9990 chunk 314 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 272 optimal weight: 30.0000 chunk 43 optimal weight: 6.9990 chunk 82 optimal weight: 0.0170 chunk 295 optimal weight: 20.0000 chunk 123 optimal weight: 10.0000 chunk 303 optimal weight: 0.0370 chunk 37 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.1700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 465 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.078221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.048686 restraints weight = 154898.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.050478 restraints weight = 71039.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.051640 restraints weight = 44287.539| |-----------------------------------------------------------------------------| r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.0691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.084 31269 Z= 0.271 Angle : 0.677 16.368 42583 Z= 0.343 Chirality : 0.043 0.274 4875 Planarity : 0.005 0.104 5259 Dihedral : 15.201 172.928 4835 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.75 % Favored : 92.14 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.11 % Twisted Proline : 0.70 % Twisted General : 0.11 % 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: -1.53 (0.13), residues: 3651 helix: 0.49 (0.14), residues: 1382 sheet: -1.56 (0.23), residues: 471 loop : -2.13 (0.13), residues: 1798 =============================================================================== Job complete usr+sys time: 4167.32 seconds wall clock time: 78 minutes 36.06 seconds (4716.06 seconds total)