Starting phenix.real_space_refine (version: 1.21rc1) on Mon Jul 10 13:44:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j94_6204/07_2023/3j94_6204_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j94_6204/07_2023/3j94_6204.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j94_6204/07_2023/3j94_6204.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j94_6204/07_2023/3j94_6204.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j94_6204/07_2023/3j94_6204_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j94_6204/07_2023/3j94_6204_updated.pdb" } resolution = 4.2 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= -0.000 sd= 1.000 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: 5 Type Number sf(0) Gaussians P 33 5.49 5 S 93 5.16 5 C 13558 2.51 5 N 3719 2.21 5 O 4106 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 229": "OD1" <-> "OD2" Residue "A PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 246": "OE1" <-> "OE2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 310": "OE1" <-> "OE2" Residue "A ASP 377": "OD1" <-> "OD2" Residue "A GLU 381": "OE1" <-> "OE2" Residue "A TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 229": "OD1" <-> "OD2" Residue "B TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 571": "OD1" <-> "OD2" Residue "B TYR 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 617": "NH1" <-> "NH2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B PHE 661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 229": "OD1" <-> "OD2" Residue "C GLU 312": "OE1" <-> "OE2" Residue "C ARG 315": "NH1" <-> "NH2" Residue "C PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 377": "OD1" <-> "OD2" Residue "C ARG 385": "NH1" <-> "NH2" Residue "C TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 590": "OD1" <-> "OD2" Residue "C GLU 606": "OE1" <-> "OE2" Residue "C ARG 607": "NH1" <-> "NH2" Residue "D PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 299": "OE1" <-> "OE2" Residue "D GLU 311": "OE1" <-> "OE2" Residue "D GLU 312": "OE1" <-> "OE2" Residue "D ASP 571": "OD1" <-> "OD2" Residue "D ASP 591": "OD1" <-> "OD2" Residue "D ASP 603": "OD1" <-> "OD2" Residue "D TYR 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 674": "OE1" <-> "OE2" Residue "D GLU 715": "OE1" <-> "OE2" Residue "E PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 229": "OD1" <-> "OD2" Residue "E TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 532": "OD1" <-> "OD2" Residue "E ASP 590": "OD1" <-> "OD2" Residue "E ASP 603": "OD1" <-> "OD2" Residue "E PHE 661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 681": "OE1" <-> "OE2" Residue "E ASP 721": "OD1" <-> "OD2" Residue "E PHE 729": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 498": "OD1" <-> "OD2" Residue "F GLU 558": "OE1" <-> "OE2" Residue "F ASP 571": "OD1" <-> "OD2" Residue "F ASP 650": "OD1" <-> "OD2" Residue "F TYR 724": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 21509 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3559 Classifications: {'peptide': 490} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'CIS': 7, 'PCIS': 2, 'PTRANS': 20, 'TRANS': 460} Chain breaks: 2 Unresolved non-hydrogen bonds: 278 Unresolved non-hydrogen angles: 335 Unresolved non-hydrogen dihedrals: 229 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 12, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 166 Chain: "B" Number of atoms: 3563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3563 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'CIS': 5, 'PCIS': 3, 'PTRANS': 19, 'TRANS': 456} Chain breaks: 2 Unresolved non-hydrogen bonds: 227 Unresolved non-hydrogen angles: 276 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 133 Chain: "C" Number of atoms: 3573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3573 Classifications: {'peptide': 488} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'CIS': 4, 'PCIS': 3, 'PTRANS': 19, 'TRANS': 461} Chain breaks: 2 Unresolved non-hydrogen bonds: 244 Unresolved non-hydrogen angles: 296 Unresolved non-hydrogen dihedrals: 200 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 139 Chain: "D" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3526 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'CIS': 3, 'PCIS': 3, 'PTRANS': 19, 'TRANS': 459} Chain breaks: 2 Unresolved non-hydrogen bonds: 267 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 221 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 4, 'ASN:plan1': 6, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 160 Chain: "E" Number of atoms: 3529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3529 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'CIS': 5, 'PCIS': 3, 'PTRANS': 19, 'TRANS': 454} Chain breaks: 3 Unresolved non-hydrogen bonds: 244 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 202 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 4, 'ASN:plan1': 5, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 9, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 138 Chain: "F" Number of atoms: 3418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3418 Classifications: {'peptide': 466} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'CIS': 5, 'PCIS': 3, 'PTRANS': 18, 'TRANS': 439} Chain breaks: 2 Unresolved non-hydrogen bonds: 233 Unresolved non-hydrogen angles: 284 Unresolved non-hydrogen dihedrals: 191 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 122 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.13, per 1000 atoms: 0.56 Number of scatterers: 21509 At special positions: 0 Unit cell: (142.225, 137.363, 114.266, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 93 16.00 P 33 15.00 O 4106 8.00 N 3719 7.00 C 13558 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 Atom "HETATM21258 O5' ATP B 801 .*. O " rejected from bonding due to valence issues. Atom "HETATM21475 O5' ATP E 802 .*. O " rejected from bonding due to valence issues. Atom "HETATM21289 O5' ATP B 802 .*. O " rejected from bonding due to valence issues. Atom "HETATM21351 O5' ATP C 802 .*. O " rejected from bonding due to valence issues. Atom "HETATM21413 O5' ATP D 802 .*. O " rejected from bonding due to valence issues. Atom "HETATM21413 O5' ATP D 802 .*. O " rejected from bonding due to valence issues. Atom "HETATM21258 O5' ATP B 801 .*. O " rejected from bonding due to valence issues. Atom "HETATM21503 O3B ATP F 801 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=40, symmetry=0 Number of additional bonds: simple=40, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.47 Conformation dependent library (CDL) restraints added in 3.6 seconds 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5360 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 133 helices and 13 sheets defined 50.5% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.49 Creating SS restraints... Processing helix chain 'A' and resid 224 through 239 Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 266 through 277 Processing helix chain 'A' and resid 297 through 315 removed outlier: 4.352A pdb=" N LEU A 305 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHE A 306 " --> pdb=" O ILE A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 358 Processing helix chain 'A' and resid 381 through 384 No H-bonds generated for 'chain 'A' and resid 381 through 384' Processing helix chain 'A' and resid 400 through 416 Processing helix chain 'A' and resid 426 through 432 Processing helix chain 'A' and resid 438 through 456 Processing helix chain 'A' and resid 480 through 489 Processing helix chain 'A' and resid 497 through 503 Processing helix chain 'A' and resid 512 through 530 Processing helix chain 'A' and resid 549 through 560 removed outlier: 3.891A pdb=" N ALA A 554 " --> pdb=" O THR A 550 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS A 555 " --> pdb=" O ALA A 551 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU A 559 " --> pdb=" O LYS A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 573 No H-bonds generated for 'chain 'A' and resid 570 through 573' Processing helix chain 'A' and resid 578 through 594 Processing helix chain 'A' and resid 605 through 609 Processing helix chain 'A' and resid 620 through 631 Processing helix chain 'A' and resid 649 through 655 Processing helix chain 'A' and resid 657 through 660 No H-bonds generated for 'chain 'A' and resid 657 through 660' Processing helix chain 'A' and resid 673 through 683 Processing helix chain 'A' and resid 688 through 698 removed outlier: 3.622A pdb=" N GLN A 696 " --> pdb=" O THR A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 718 Processing helix chain 'A' and resid 722 through 735 removed outlier: 3.945A pdb=" N VAL A 726 " --> pdb=" O PRO A 722 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ARG A 727 " --> pdb=" O GLU A 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 239 removed outlier: 4.365A pdb=" N SER B 237 " --> pdb=" O ARG B 233 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG B 238 " --> pdb=" O ALA B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 248 Processing helix chain 'B' and resid 266 through 277 Processing helix chain 'B' and resid 298 through 316 removed outlier: 4.273A pdb=" N PHE B 306 " --> pdb=" O ILE B 302 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA B 309 " --> pdb=" O LEU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 358 Processing helix chain 'B' and resid 381 through 384 No H-bonds generated for 'chain 'B' and resid 381 through 384' Processing helix chain 'B' and resid 400 through 416 removed outlier: 3.718A pdb=" N HIS B 410 " --> pdb=" O ILE B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 432 Processing helix chain 'B' and resid 438 through 456 Processing helix chain 'B' and resid 480 through 487 Processing helix chain 'B' and resid 497 through 501 removed outlier: 4.094A pdb=" N SER B 501 " --> pdb=" O GLU B 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 497 through 501' Processing helix chain 'B' and resid 512 through 530 Processing helix chain 'B' and resid 549 through 560 Processing helix chain 'B' and resid 570 through 573 Processing helix chain 'B' and resid 578 through 594 Processing helix chain 'B' and resid 605 through 608 No H-bonds generated for 'chain 'B' and resid 605 through 608' Processing helix chain 'B' and resid 620 through 631 Processing helix chain 'B' and resid 649 through 655 Processing helix chain 'B' and resid 657 through 660 No H-bonds generated for 'chain 'B' and resid 657 through 660' Processing helix chain 'B' and resid 673 through 683 Processing helix chain 'B' and resid 688 through 697 Processing helix chain 'B' and resid 708 through 719 Processing helix chain 'B' and resid 725 through 735 removed outlier: 3.685A pdb=" N GLU B 735 " --> pdb=" O ALA B 731 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 239 removed outlier: 3.867A pdb=" N ALA C 234 " --> pdb=" O ILE C 230 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER C 237 " --> pdb=" O ARG C 233 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG C 238 " --> pdb=" O ALA C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 248 Processing helix chain 'C' and resid 266 through 277 Processing helix chain 'C' and resid 298 through 316 removed outlier: 3.575A pdb=" N ASP C 308 " --> pdb=" O LYS C 304 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ALA C 309 " --> pdb=" O LEU C 305 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU C 310 " --> pdb=" O PHE C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 333 No H-bonds generated for 'chain 'C' and resid 330 through 333' Processing helix chain 'C' and resid 348 through 358 removed outlier: 3.641A pdb=" N VAL C 351 " --> pdb=" O ASP C 348 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS C 357 " --> pdb=" O LEU C 354 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE C 358 " --> pdb=" O LEU C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 384 No H-bonds generated for 'chain 'C' and resid 381 through 384' Processing helix chain 'C' and resid 400 through 416 removed outlier: 3.756A pdb=" N HIS C 410 " --> pdb=" O ILE C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 432 Processing helix chain 'C' and resid 438 through 456 removed outlier: 3.615A pdb=" N VAL C 445 " --> pdb=" O LEU C 441 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER C 450 " --> pdb=" O ARG C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 488 Processing helix chain 'C' and resid 499 through 502 No H-bonds generated for 'chain 'C' and resid 499 through 502' Processing helix chain 'C' and resid 512 through 530 Processing helix chain 'C' and resid 549 through 560 Processing helix chain 'C' and resid 578 through 594 Processing helix chain 'C' and resid 605 through 609 Processing helix chain 'C' and resid 620 through 631 Processing helix chain 'C' and resid 649 through 655 Processing helix chain 'C' and resid 657 through 660 No H-bonds generated for 'chain 'C' and resid 657 through 660' Processing helix chain 'C' and resid 673 through 683 Processing helix chain 'C' and resid 688 through 698 Processing helix chain 'C' and resid 707 through 719 removed outlier: 3.522A pdb=" N GLN C 719 " --> pdb=" O GLU C 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 726 through 736 Processing helix chain 'D' and resid 224 through 239 removed outlier: 3.631A pdb=" N ALA D 236 " --> pdb=" O ARG D 232 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N SER D 237 " --> pdb=" O ARG D 233 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ARG D 238 " --> pdb=" O ALA D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 248 Processing helix chain 'D' and resid 266 through 277 Processing helix chain 'D' and resid 296 through 315 removed outlier: 3.935A pdb=" N PHE D 306 " --> pdb=" O ILE D 302 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA D 309 " --> pdb=" O LEU D 305 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN D 313 " --> pdb=" O ALA D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 356 Processing helix chain 'D' and resid 381 through 384 No H-bonds generated for 'chain 'D' and resid 381 through 384' Processing helix chain 'D' and resid 400 through 416 removed outlier: 3.692A pdb=" N ARG D 413 " --> pdb=" O ILE D 409 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N MET D 414 " --> pdb=" O HIS D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 432 Processing helix chain 'D' and resid 438 through 456 removed outlier: 3.595A pdb=" N GLN D 449 " --> pdb=" O VAL D 445 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER D 450 " --> pdb=" O ARG D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 481 through 487 Processing helix chain 'D' and resid 499 through 501 No H-bonds generated for 'chain 'D' and resid 499 through 501' Processing helix chain 'D' and resid 512 through 530 Processing helix chain 'D' and resid 549 through 560 Processing helix chain 'D' and resid 570 through 573 No H-bonds generated for 'chain 'D' and resid 570 through 573' Processing helix chain 'D' and resid 578 through 594 removed outlier: 3.700A pdb=" N CYS D 582 " --> pdb=" O GLU D 578 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LYS D 594 " --> pdb=" O ASP D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 609 Processing helix chain 'D' and resid 620 through 631 Processing helix chain 'D' and resid 649 through 655 Processing helix chain 'D' and resid 657 through 660 No H-bonds generated for 'chain 'D' and resid 657 through 660' Processing helix chain 'D' and resid 673 through 683 Processing helix chain 'D' and resid 688 through 698 Processing helix chain 'D' and resid 707 through 719 removed outlier: 3.638A pdb=" N GLN D 719 " --> pdb=" O GLU D 715 " (cutoff:3.500A) Processing helix chain 'D' and resid 726 through 735 Processing helix chain 'E' and resid 225 through 239 removed outlier: 4.320A pdb=" N SER E 237 " --> pdb=" O ARG E 233 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ARG E 238 " --> pdb=" O ALA E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 248 Processing helix chain 'E' and resid 266 through 277 Processing helix chain 'E' and resid 298 through 316 removed outlier: 4.178A pdb=" N PHE E 306 " --> pdb=" O ILE E 302 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA E 309 " --> pdb=" O LEU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 358 Processing helix chain 'E' and resid 381 through 384 No H-bonds generated for 'chain 'E' and resid 381 through 384' Processing helix chain 'E' and resid 400 through 416 removed outlier: 3.682A pdb=" N HIS E 410 " --> pdb=" O ILE E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 432 Processing helix chain 'E' and resid 438 through 456 removed outlier: 3.504A pdb=" N GLU E 442 " --> pdb=" O GLY E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 480 through 487 Processing helix chain 'E' and resid 512 through 529 Processing helix chain 'E' and resid 549 through 560 Processing helix chain 'E' and resid 570 through 573 No H-bonds generated for 'chain 'E' and resid 570 through 573' Processing helix chain 'E' and resid 578 through 594 removed outlier: 3.547A pdb=" N TYR E 593 " --> pdb=" O PHE E 589 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS E 594 " --> pdb=" O ASP E 590 " (cutoff:3.500A) Processing helix chain 'E' and resid 605 through 608 No H-bonds generated for 'chain 'E' and resid 605 through 608' Processing helix chain 'E' and resid 620 through 631 removed outlier: 3.816A pdb=" N LEU E 630 " --> pdb=" O LEU E 626 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS E 631 " --> pdb=" O LEU E 627 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 654 Processing helix chain 'E' and resid 657 through 660 No H-bonds generated for 'chain 'E' and resid 657 through 660' Processing helix chain 'E' and resid 673 through 683 Processing helix chain 'E' and resid 688 through 698 Processing helix chain 'E' and resid 707 through 718 Processing helix chain 'E' and resid 722 through 736 removed outlier: 4.292A pdb=" N VAL E 726 " --> pdb=" O PRO E 722 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ARG E 727 " --> pdb=" O GLU E 723 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 239 removed outlier: 4.212A pdb=" N SER F 237 " --> pdb=" O ARG F 233 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG F 238 " --> pdb=" O ALA F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 248 Processing helix chain 'F' and resid 266 through 277 Processing helix chain 'F' and resid 298 through 316 removed outlier: 4.025A pdb=" N PHE F 306 " --> pdb=" O ILE F 302 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA F 309 " --> pdb=" O LEU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 348 through 358 removed outlier: 3.553A pdb=" N ILE F 358 " --> pdb=" O LEU F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 416 removed outlier: 3.642A pdb=" N HIS F 410 " --> pdb=" O ILE F 406 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 432 Processing helix chain 'F' and resid 438 through 456 removed outlier: 3.794A pdb=" N GLU F 442 " --> pdb=" O GLY F 438 " (cutoff:3.500A) Processing helix chain 'F' and resid 499 through 502 No H-bonds generated for 'chain 'F' and resid 499 through 502' Processing helix chain 'F' and resid 512 through 530 removed outlier: 3.703A pdb=" N LEU F 518 " --> pdb=" O VAL F 514 " (cutoff:3.500A) Processing helix chain 'F' and resid 549 through 560 Processing helix chain 'F' and resid 578 through 594 Processing helix chain 'F' and resid 605 through 609 Processing helix chain 'F' and resid 620 through 631 Processing helix chain 'F' and resid 649 through 655 Processing helix chain 'F' and resid 673 through 683 Processing helix chain 'F' and resid 688 through 698 Processing helix chain 'F' and resid 707 through 718 removed outlier: 3.533A pdb=" N GLU F 715 " --> pdb=" O LEU F 711 " (cutoff:3.500A) Processing helix chain 'F' and resid 724 through 735 Processing sheet with id= A, first strand: chain 'A' and resid 391 through 395 removed outlier: 3.650A pdb=" N VAL A 391 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N ILE A 256 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL A 369 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N LEU A 258 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N GLY A 371 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N GLY A 260 " --> pdb=" O GLY A 371 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N HIS A 323 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ILE A 370 " --> pdb=" O HIS A 323 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE A 325 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N MET A 372 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N PHE A 327 " --> pdb=" O MET A 372 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 663 through 666 removed outlier: 3.528A pdb=" N LEU A 540 " --> pdb=" O THR A 663 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU A 542 " --> pdb=" O ILE A 665 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU A 640 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N VAL A 539 " --> pdb=" O LEU A 640 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ILE A 642 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N LEU A 541 " --> pdb=" O ILE A 642 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLY A 644 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N PHE A 564 " --> pdb=" O CYS A 599 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N VAL A 601 " --> pdb=" O PHE A 564 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LYS A 566 " --> pdb=" O VAL A 601 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 391 through 395 removed outlier: 4.129A pdb=" N VAL B 391 " --> pdb=" O GLY B 255 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ILE B 256 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N VAL B 369 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU B 258 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N GLY B 371 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N GLY B 260 " --> pdb=" O GLY B 371 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N THR B 373 " --> pdb=" O GLY B 260 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N HIS B 323 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ILE B 370 " --> pdb=" O HIS B 323 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ILE B 325 " --> pdb=" O ILE B 370 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N MET B 372 " --> pdb=" O ILE B 325 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N PHE B 327 " --> pdb=" O MET B 372 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL B 284 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ASP B 328 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ASN B 286 " --> pdb=" O ASP B 328 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 663 through 666 removed outlier: 7.535A pdb=" N LEU B 640 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N VAL B 539 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ILE B 642 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N LEU B 541 " --> pdb=" O ILE B 642 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N GLY B 644 " --> pdb=" O LEU B 541 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N PHE B 564 " --> pdb=" O CYS B 599 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N VAL B 601 " --> pdb=" O PHE B 564 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LYS B 566 " --> pdb=" O VAL B 601 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 391 through 395 removed outlier: 4.020A pdb=" N VAL C 391 " --> pdb=" O GLY C 255 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ILE C 256 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL C 369 " --> pdb=" O ILE C 256 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LEU C 258 " --> pdb=" O VAL C 369 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLY C 371 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N GLY C 260 " --> pdb=" O GLY C 371 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR C 373 " --> pdb=" O GLY C 260 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N HIS C 323 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ILE C 370 " --> pdb=" O HIS C 323 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE C 325 " --> pdb=" O ILE C 370 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N MET C 372 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N PHE C 327 " --> pdb=" O MET C 372 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL C 284 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ASP C 328 " --> pdb=" O VAL C 284 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ASN C 286 " --> pdb=" O ASP C 328 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 663 through 666 removed outlier: 6.760A pdb=" N LEU C 640 " --> pdb=" O VAL C 537 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N VAL C 539 " --> pdb=" O LEU C 640 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE C 642 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N LEU C 541 " --> pdb=" O ILE C 642 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLY C 644 " --> pdb=" O LEU C 541 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N PHE C 564 " --> pdb=" O CYS C 599 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N VAL C 601 " --> pdb=" O PHE C 564 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LYS C 566 " --> pdb=" O VAL C 601 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 391 through 395 removed outlier: 4.400A pdb=" N VAL D 391 " --> pdb=" O GLY D 255 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ILE D 256 " --> pdb=" O ILE D 367 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N VAL D 369 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N LEU D 258 " --> pdb=" O VAL D 369 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N GLY D 371 " --> pdb=" O LEU D 258 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N GLY D 260 " --> pdb=" O GLY D 371 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR D 373 " --> pdb=" O GLY D 260 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N HIS D 323 " --> pdb=" O LEU D 368 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N ILE D 370 " --> pdb=" O HIS D 323 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ILE D 325 " --> pdb=" O ILE D 370 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N MET D 372 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N PHE D 327 " --> pdb=" O MET D 372 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N VAL D 284 " --> pdb=" O ILE D 326 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 663 through 666 removed outlier: 3.506A pdb=" N THR D 663 " --> pdb=" O SER D 538 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LEU D 640 " --> pdb=" O VAL D 537 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N VAL D 539 " --> pdb=" O LEU D 640 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE D 642 " --> pdb=" O VAL D 539 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N LEU D 541 " --> pdb=" O ILE D 642 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLY D 644 " --> pdb=" O LEU D 541 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N PHE D 564 " --> pdb=" O CYS D 599 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N VAL D 601 " --> pdb=" O PHE D 564 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LYS D 566 " --> pdb=" O VAL D 601 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 391 through 395 removed outlier: 4.272A pdb=" N VAL E 391 " --> pdb=" O GLY E 255 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ILE E 256 " --> pdb=" O ILE E 367 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N VAL E 369 " --> pdb=" O ILE E 256 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N LEU E 258 " --> pdb=" O VAL E 369 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N GLY E 371 " --> pdb=" O LEU E 258 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N GLY E 260 " --> pdb=" O GLY E 371 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N THR E 373 " --> pdb=" O GLY E 260 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N HIS E 323 " --> pdb=" O LEU E 368 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ILE E 370 " --> pdb=" O HIS E 323 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ILE E 325 " --> pdb=" O ILE E 370 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N MET E 372 " --> pdb=" O ILE E 325 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N PHE E 327 " --> pdb=" O MET E 372 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 663 through 666 removed outlier: 6.651A pdb=" N LEU E 640 " --> pdb=" O VAL E 537 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N VAL E 539 " --> pdb=" O LEU E 640 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ILE E 642 " --> pdb=" O VAL E 539 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N LEU E 541 " --> pdb=" O ILE E 642 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLY E 644 " --> pdb=" O LEU E 541 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N PHE E 564 " --> pdb=" O CYS E 599 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N VAL E 601 " --> pdb=" O PHE E 564 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N LYS E 566 " --> pdb=" O VAL E 601 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 256 through 259 removed outlier: 6.549A pdb=" N VAL F 391 " --> pdb=" O LEU F 257 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N TYR F 259 " --> pdb=" O VAL F 391 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N MET F 393 " --> pdb=" O TYR F 259 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'F' and resid 284 through 286 removed outlier: 4.252A pdb=" N ASP F 328 " --> pdb=" O ASN F 286 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE F 370 " --> pdb=" O ILE F 325 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE F 327 " --> pdb=" O ILE F 370 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N MET F 372 " --> pdb=" O PHE F 327 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 536 through 542 removed outlier: 7.136A pdb=" N LEU F 640 " --> pdb=" O VAL F 537 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N VAL F 539 " --> pdb=" O LEU F 640 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE F 642 " --> pdb=" O VAL F 539 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N LEU F 541 " --> pdb=" O ILE F 642 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N GLY F 644 " --> pdb=" O LEU F 541 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N PHE F 564 " --> pdb=" O CYS F 599 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N VAL F 601 " --> pdb=" O PHE F 564 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LYS F 566 " --> pdb=" O VAL F 601 " (cutoff:3.500A) 952 hydrogen bonds defined for protein. 2790 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.54 Time building geometry restraints manager: 10.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3851 1.32 - 1.45: 4837 1.45 - 1.57: 12892 1.57 - 1.69: 103 1.69 - 1.82: 156 Bond restraints: 21839 Sorted by residual: bond pdb=" C5 ATP E 801 " pdb=" C6 ATP E 801 " ideal model delta sigma weight residual 1.409 1.517 -0.108 1.00e-02 1.00e+04 1.17e+02 bond pdb=" C4 ATP B 802 " pdb=" C5 ATP B 802 " ideal model delta sigma weight residual 1.388 1.482 -0.094 1.00e-02 1.00e+04 8.84e+01 bond pdb=" C4 ATP C 802 " pdb=" C5 ATP C 802 " ideal model delta sigma weight residual 1.388 1.482 -0.094 1.00e-02 1.00e+04 8.76e+01 bond pdb=" C5 ATP D 802 " pdb=" C6 ATP D 802 " ideal model delta sigma weight residual 1.409 1.501 -0.092 1.00e-02 1.00e+04 8.42e+01 bond pdb=" C5 ATP B 801 " pdb=" C6 ATP B 801 " ideal model delta sigma weight residual 1.409 1.496 -0.087 1.00e-02 1.00e+04 7.59e+01 ... (remaining 21834 not shown) Histogram of bond angle deviations from ideal: 96.64 - 105.79: 802 105.79 - 114.95: 13168 114.95 - 124.10: 15000 124.10 - 133.25: 684 133.25 - 142.40: 42 Bond angle restraints: 29696 Sorted by residual: angle pdb=" PB ATP E 801 " pdb=" O3B ATP E 801 " pdb=" PG ATP E 801 " ideal model delta sigma weight residual 139.87 117.35 22.52 1.00e+00 1.00e+00 5.07e+02 angle pdb=" PB ATP C 801 " pdb=" O3B ATP C 801 " pdb=" PG ATP C 801 " ideal model delta sigma weight residual 139.87 119.20 20.67 1.00e+00 1.00e+00 4.27e+02 angle pdb=" PB ATP F 801 " pdb=" O3B ATP F 801 " pdb=" PG ATP F 801 " ideal model delta sigma weight residual 139.87 119.45 20.42 1.00e+00 1.00e+00 4.17e+02 angle pdb=" PA ATP F 801 " pdb=" O3A ATP F 801 " pdb=" PB ATP F 801 " ideal model delta sigma weight residual 136.83 116.42 20.41 1.00e+00 1.00e+00 4.17e+02 angle pdb=" PB ATP A 801 " pdb=" O3B ATP A 801 " pdb=" PG ATP A 801 " ideal model delta sigma weight residual 139.87 119.52 20.35 1.00e+00 1.00e+00 4.14e+02 ... (remaining 29691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 11824 17.98 - 35.95: 952 35.95 - 53.93: 287 53.93 - 71.90: 80 71.90 - 89.88: 34 Dihedral angle restraints: 13177 sinusoidal: 4901 harmonic: 8276 Sorted by residual: dihedral pdb=" CA PRO A 261 " pdb=" C PRO A 261 " pdb=" N PRO A 262 " pdb=" CA PRO A 262 " ideal model delta harmonic sigma weight residual 180.00 135.63 44.37 0 5.00e+00 4.00e-02 7.87e+01 dihedral pdb=" CA GLY B 438 " pdb=" C GLY B 438 " pdb=" N ALA B 439 " pdb=" CA ALA B 439 " ideal model delta harmonic sigma weight residual 180.00 142.87 37.13 0 5.00e+00 4.00e-02 5.51e+01 dihedral pdb=" CA GLY F 438 " pdb=" C GLY F 438 " pdb=" N ALA F 439 " pdb=" CA ALA F 439 " ideal model delta harmonic sigma weight residual 180.00 143.61 36.39 0 5.00e+00 4.00e-02 5.30e+01 ... (remaining 13174 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 3020 0.101 - 0.203: 446 0.203 - 0.304: 55 0.304 - 0.405: 4 0.405 - 0.507: 5 Chirality restraints: 3530 Sorted by residual: chirality pdb=" CB VAL A 525 " pdb=" CA VAL A 525 " pdb=" CG1 VAL A 525 " pdb=" CG2 VAL A 525 " both_signs ideal model delta sigma weight residual False -2.63 -2.12 -0.51 2.00e-01 2.50e+01 6.42e+00 chirality pdb=" CB ILE E 670 " pdb=" CA ILE E 670 " pdb=" CG1 ILE E 670 " pdb=" CG2 ILE E 670 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.48 2.00e-01 2.50e+01 5.81e+00 chirality pdb=" CG LEU A 444 " pdb=" CB LEU A 444 " pdb=" CD1 LEU A 444 " pdb=" CD2 LEU A 444 " both_signs ideal model delta sigma weight residual False -2.59 -2.15 -0.44 2.00e-01 2.50e+01 4.82e+00 ... (remaining 3527 not shown) Planarity restraints: 3801 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 530 " -0.046 2.00e-02 2.50e+03 9.01e-02 8.11e+01 pdb=" CG ASN C 530 " 0.156 2.00e-02 2.50e+03 pdb=" OD1 ASN C 530 " -0.061 2.00e-02 2.50e+03 pdb=" ND2 ASN C 530 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN D 596 " -0.042 2.00e-02 2.50e+03 8.31e-02 6.90e+01 pdb=" CD GLN D 596 " 0.144 2.00e-02 2.50e+03 pdb=" OE1 GLN D 596 " -0.053 2.00e-02 2.50e+03 pdb=" NE2 GLN D 596 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 546 " 0.077 2.00e-02 2.50e+03 6.17e-02 5.70e+01 pdb=" CG HIS B 546 " -0.121 2.00e-02 2.50e+03 pdb=" ND1 HIS B 546 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 HIS B 546 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 HIS B 546 " 0.022 2.00e-02 2.50e+03 pdb=" NE2 HIS B 546 " 0.040 2.00e-02 2.50e+03 ... (remaining 3798 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.99: 16 1.99 - 2.72: 1533 2.72 - 3.44: 34754 3.44 - 4.17: 48944 4.17 - 4.90: 83692 Nonbonded interactions: 168939 Sorted by model distance: nonbonded pdb=" OE1 GLU E 442 " pdb=" O2' ATP E 802 " model vdw 1.261 2.440 nonbonded pdb=" O SER F 547 " pdb=" O2B ATP F 801 " model vdw 1.263 3.040 nonbonded pdb=" OG1 THR F 550 " pdb=" O1B ATP F 801 " model vdw 1.264 2.440 nonbonded pdb=" OE1 GLU B 442 " pdb=" O2' ATP B 802 " model vdw 1.264 2.440 nonbonded pdb=" OG1 THR D 267 " pdb=" O2B ATP D 802 " model vdw 1.264 2.440 ... (remaining 168934 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 217 through 222 or (resid 223 and (name N or name CA or na \ me C or name O or name CB )) or resid 224 or (resid 225 and (name N or name CA o \ r name C or name O or name CB )) or resid 226 through 230 or (resid 231 through \ 234 and (name N or name CA or name C or name O or name CB )) or resid 235 throug \ h 251 or (resid 252 and (name N or name CA or name C or name O or name CB )) or \ resid 253 through 267 or (resid 268 through 270 and (name N or name CA or name C \ or name O or name CB )) or resid 271 through 293 or (resid 294 through 295 and \ (name N or name CA or name C or name O or name CB )) or resid 296 through 302 or \ (resid 303 and (name N or name CA or name C or name O or name CB )) or resid 30 \ 4 through 305 or (resid 306 through 307 and (name N or name CA or name C or name \ O or name CB )) or resid 308 through 314 or (resid 315 and (name N or name CA o \ r name C or name O or name CB )) or resid 316 through 321 or (resid 322 and (nam \ e N or name CA or name C or name O or name CB )) or resid 323 through 324 or (re \ sid 325 and (name N or name CA or name C or name O or name CB )) or resid 326 th \ rough 329 or (resid 330 and (name N or name CA or name C or name O or name CB )) \ or resid 348 through 351 or (resid 352 through 353 and (name N or name CA or na \ me C or name O or name CB )) or resid 354 through 356 or (resid 357 through 359 \ and (name N or name CA or name C or name O or name CB )) or resid 360 through 38 \ 2 or (resid 383 and (name N or name CA or name C or name O or name CB )) or resi \ d 384 through 396 or (resid 397 and (name N or name CA or name C or name O or na \ me CB )) or resid 398 through 406 or (resid 407 and (name N or name CA or name C \ or name O or name CB )) or resid 408 through 413 or (resid 414 through 415 and \ (name N or name CA or name C or name O or name CB )) or resid 416 through 418 or \ (resid 419 and (name N or name CA or name C or name O or name CB )) or resid 42 \ 0 through 423 or (resid 424 and (name N or name CA or name C or name O or name C \ B )) or resid 425 through 435 or (resid 436 and (name N or name CA or name C or \ name O or name CB )) or resid 437 through 441 or (resid 442 and (name N or name \ CA or name C or name O or name CB )) or resid 443 or (resid 444 and (name N or n \ ame CA or name C or name O or name CB )) or resid 445 or (resid 446 through 448 \ and (name N or name CA or name C or name O or name CB )) or resid 449 through 45 \ 7 or (resid 497 and (name N or name CA or name C or name O or name CB )) or resi \ d 498 or (resid 499 through 500 and (name N or name CA or name C or name O or na \ me CB )) or resid 501 through 507 or (resid 508 and (name N or name CA or name C \ or name O or name CB )) or resid 509 through 523 or (resid 524 and (name N or n \ ame CA or name C or name O or name CB )) or resid 525 through 532 or (resid 533 \ and (name N or name CA or name C or name O or name CB )) or resid 534 through 54 \ 1 or (resid 542 and (name N or name CA or name C or name O or name CB )) or resi \ d 543 through 565 or (resid 566 and (name N or name CA or name C or name O or na \ me CB )) or resid 567 through 628 or (resid 629 and (name N or name CA or name C \ or name O or name CB )) or resid 630 through 635 or (resid 636 and (name N or n \ ame CA or name C or name O or name CB )) or resid 637 through 650 or (resid 651 \ and (name N or name CA or name C or name O or name CB )) or resid 652 through 65 \ 5 or (resid 656 and (name N or name CA or name C or name O or name CB )) or resi \ d 657 through 673 or (resid 674 and (name N or name CA or name C or name O or na \ me CB )) or resid 675 through 690 or (resid 691 and (name N or name CA or name C \ or name O or name CB )) or resid 692 through 701 or (resid 702 and (name N or n \ ame CA or name C or name O or name CB )) or resid 703 through 717 or (resid 718 \ and (name N or name CA or name C or name O or name CB )) or resid 719 through 73 \ 7 or resid 801)) selection = (chain 'B' and (resid 217 through 222 or (resid 223 and (name N or name CA or na \ me C or name O or name CB )) or resid 224 or (resid 225 and (name N or name CA o \ r name C or name O or name CB )) or resid 226 through 230 or (resid 231 through \ 234 and (name N or name CA or name C or name O or name CB )) or resid 235 throug \ h 251 or (resid 252 and (name N or name CA or name C or name O or name CB )) or \ resid 253 through 265 or (resid 266 and (name N or name CA or name C or name O o \ r name CB )) or resid 267 or (resid 268 through 270 and (name N or name CA or na \ me C or name O or name CB )) or resid 271 through 293 or (resid 294 through 295 \ and (name N or name CA or name C or name O or name CB )) or resid 296 through 30 \ 2 or (resid 303 and (name N or name CA or name C or name O or name CB )) or resi \ d 304 through 305 or (resid 306 through 307 and (name N or name CA or name C or \ name O or name CB )) or resid 308 through 311 or (resid 312 and (name N or name \ CA or name C or name O or name CB )) or resid 313 or (resid 314 through 315 and \ (name N or name CA or name C or name O or name CB )) or resid 316 through 321 or \ (resid 322 and (name N or name CA or name C or name O or name CB )) or resid 32 \ 3 through 324 or (resid 325 and (name N or name CA or name C or name O or name C \ B )) or resid 326 through 329 or (resid 330 and (name N or name CA or name C or \ name O or name CB )) or resid 348 through 351 or (resid 352 through 353 and (nam \ e N or name CA or name C or name O or name CB )) or resid 354 through 356 or (re \ sid 357 through 359 and (name N or name CA or name C or name O or name CB )) or \ resid 360 through 371 or (resid 372 through 373 and (name N or name CA or name C \ or name O or name CB )) or resid 374 through 382 or (resid 383 and (name N or n \ ame CA or name C or name O or name CB )) or resid 384 or (resid 385 and (name N \ or name CA or name C or name O or name CB )) or resid 386 through 387 or (resid \ 388 and (name N or name CA or name C or name O or name CB )) or resid 389 throug \ h 396 or (resid 397 and (name N or name CA or name C or name O or name CB )) or \ resid 398 through 406 or (resid 407 and (name N or name CA or name C or name O o \ r name CB )) or resid 408 through 412 or (resid 413 through 415 and (name N or n \ ame CA or name C or name O or name CB )) or resid 416 through 418 or (resid 419 \ and (name N or name CA or name C or name O or name CB )) or resid 420 through 42 \ 3 or (resid 424 and (name N or name CA or name C or name O or name CB )) or resi \ d 425 through 435 or (resid 436 and (name N or name CA or name C or name O or na \ me CB )) or resid 437 through 441 or (resid 442 and (name N or name CA or name C \ or name O or name CB )) or resid 443 or (resid 444 and (name N or name CA or na \ me C or name O or name CB )) or resid 445 through 454 or (resid 455 and (name N \ or name CA or name C or name O or name CB )) or resid 456 through 457 or (resid \ 497 and (name N or name CA or name C or name O or name CB )) or resid 498 throug \ h 523 or (resid 524 and (name N or name CA or name C or name O or name CB )) or \ resid 525 through 541 or (resid 542 and (name N or name CA or name C or name O o \ r name CB )) or resid 543 through 557 or (resid 558 and (name N or name CA or na \ me C or name O or name CB )) or resid 559 through 565 or (resid 566 and (name N \ or name CA or name C or name O or name CB )) or resid 567 through 596 or (resid \ 597 and (name N or name CA or name C or name O or name CB )) or resid 598 throug \ h 628 or (resid 629 and (name N or name CA or name C or name O or name CB )) or \ resid 630 through 635 or (resid 636 and (name N or name CA or name C or name O o \ r name CB )) or resid 637 through 648 or (resid 649 and (name N or name CA or na \ me C or name O or name CB )) or resid 650 through 655 or (resid 656 and (name N \ or name CA or name C or name O or name CB )) or resid 657 through 673 or (resid \ 674 and (name N or name CA or name C or name O or name CB )) or resid 675 throug \ h 690 or (resid 691 and (name N or name CA or name C or name O or name CB )) or \ resid 692 through 701 or (resid 702 and (name N or name CA or name C or name O o \ r name CB )) or resid 703 through 714 or (resid 715 and (name N or name CA or na \ me C or name O or name CB )) or resid 716 through 717 or (resid 718 and (name N \ or name CA or name C or name O or name CB )) or resid 719 through 737 or resid 8 \ 01)) selection = (chain 'C' and (resid 217 through 222 or (resid 223 and (name N or name CA or na \ me C or name O or name CB )) or resid 224 or (resid 225 and (name N or name CA o \ r name C or name O or name CB )) or resid 226 through 230 or (resid 231 through \ 234 and (name N or name CA or name C or name O or name CB )) or resid 235 throug \ h 251 or (resid 252 and (name N or name CA or name C or name O or name CB )) or \ resid 253 through 265 or (resid 266 and (name N or name CA or name C or name O o \ r name CB )) or resid 267 through 268 or (resid 269 through 270 and (name N or n \ ame CA or name C or name O or name CB )) or resid 271 through 293 or (resid 294 \ through 295 and (name N or name CA or name C or name O or name CB )) or resid 29 \ 6 through 311 or (resid 312 and (name N or name CA or name C or name O or name C \ B )) or resid 313 or (resid 314 through 315 and (name N or name CA or name C or \ name O or name CB )) or resid 316 through 321 or (resid 322 and (name N or name \ CA or name C or name O or name CB )) or resid 323 through 324 or (resid 325 and \ (name N or name CA or name C or name O or name CB )) or resid 326 through 330 or \ resid 348 through 351 or (resid 352 through 353 and (name N or name CA or name \ C or name O or name CB )) or resid 354 through 356 or (resid 357 through 359 and \ (name N or name CA or name C or name O or name CB )) or resid 360 through 372 o \ r (resid 373 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 74 through 382 or (resid 383 and (name N or name CA or name C or name O or name \ CB )) or resid 384 or (resid 385 and (name N or name CA or name C or name O or n \ ame CB )) or resid 386 through 387 or (resid 388 and (name N or name CA or name \ C or name O or name CB )) or resid 389 through 396 or (resid 397 and (name N or \ name CA or name C or name O or name CB )) or resid 398 through 406 or (resid 407 \ and (name N or name CA or name C or name O or name CB )) or resid 408 through 4 \ 12 or (resid 413 through 415 and (name N or name CA or name C or name O or name \ CB )) or resid 416 through 418 or (resid 419 and (name N or name CA or name C or \ name O or name CB )) or resid 420 through 423 or (resid 424 and (name N or name \ CA or name C or name O or name CB )) or resid 425 through 435 or (resid 436 and \ (name N or name CA or name C or name O or name CB )) or resid 437 through 441 o \ r (resid 442 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 43 or (resid 444 and (name N or name CA or name C or name O or name CB )) or res \ id 445 through 454 or (resid 455 and (name N or name CA or name C or name O or n \ ame CB )) or resid 456 through 457 or (resid 497 and (name N or name CA or name \ C or name O or name CB )) or resid 498 or (resid 499 through 500 and (name N or \ name CA or name C or name O or name CB )) or resid 501 through 507 or (resid 508 \ and (name N or name CA or name C or name O or name CB )) or resid 509 through 5 \ 23 or (resid 524 and (name N or name CA or name C or name O or name CB )) or res \ id 525 through 532 or (resid 533 and (name N or name CA or name C or name O or n \ ame CB )) or resid 534 through 541 or (resid 542 and (name N or name CA or name \ C or name O or name CB )) or resid 543 through 557 or (resid 558 and (name N or \ name CA or name C or name O or name CB )) or resid 559 through 565 or (resid 566 \ and (name N or name CA or name C or name O or name CB )) or resid 567 through 5 \ 96 or (resid 597 and (name N or name CA or name C or name O or name CB )) or res \ id 598 through 628 or (resid 629 and (name N or name CA or name C or name O or n \ ame CB )) or resid 630 through 635 or (resid 636 and (name N or name CA or name \ C or name O or name CB )) or resid 637 through 648 or (resid 649 and (name N or \ name CA or name C or name O or name CB )) or resid 650 or (resid 651 and (name N \ or name CA or name C or name O or name CB )) or resid 652 through 655 or (resid \ 656 and (name N or name CA or name C or name O or name CB )) or resid 657 throu \ gh 673 or (resid 674 and (name N or name CA or name C or name O or name CB )) or \ resid 675 through 690 or (resid 691 and (name N or name CA or name C or name O \ or name CB )) or resid 692 through 701 or (resid 702 and (name N or name CA or n \ ame C or name O or name CB )) or resid 703 through 714 or (resid 715 and (name N \ or name CA or name C or name O or name CB )) or resid 716 through 717 or (resid \ 718 and (name N or name CA or name C or name O or name CB )) or resid 719 throu \ gh 737 or resid 801)) selection = (chain 'D' and (resid 217 through 222 or (resid 223 and (name N or name CA or na \ me C or name O or name CB )) or resid 224 through 230 or (resid 231 through 234 \ and (name N or name CA or name C or name O or name CB )) or resid 235 through 26 \ 5 or (resid 266 and (name N or name CA or name C or name O or name CB )) or resi \ d 267 or (resid 268 through 270 and (name N or name CA or name C or name O or na \ me CB )) or resid 271 through 275 or (resid 276 through 281 and (name N or name \ CA or name C or name O or name CB )) or resid 282 through 293 or (resid 294 thro \ ugh 295 and (name N or name CA or name C or name O or name CB )) or resid 296 th \ rough 302 or (resid 303 and (name N or name CA or name C or name O or name CB )) \ or resid 304 through 311 or (resid 312 and (name N or name CA or name C or name \ O or name CB )) or resid 313 through 321 or (resid 322 and (name N or name CA o \ r name C or name O or name CB )) or resid 323 through 324 or (resid 325 and (nam \ e N or name CA or name C or name O or name CB )) or resid 326 through 329 or (re \ sid 330 and (name N or name CA or name C or name O or name CB )) or resid 348 th \ rough 351 or (resid 352 through 353 and (name N or name CA or name C or name O o \ r name CB )) or resid 354 through 357 or (resid 358 through 359 and (name N or n \ ame CA or name C or name O or name CB )) or resid 360 through 371 or (resid 372 \ through 373 and (name N or name CA or name C or name O or name CB )) or resid 37 \ 4 through 382 or (resid 383 and (name N or name CA or name C or name O or name C \ B )) or resid 384 through 387 or (resid 388 and (name N or name CA or name C or \ name O or name CB )) or resid 389 through 406 or (resid 407 and (name N or name \ CA or name C or name O or name CB )) or resid 408 through 412 or (resid 413 thro \ ugh 415 and (name N or name CA or name C or name O or name CB )) or resid 416 th \ rough 418 or (resid 419 and (name N or name CA or name C or name O or name CB )) \ or resid 420 through 423 or (resid 424 and (name N or name CA or name C or name \ O or name CB )) or resid 425 through 435 or (resid 436 and (name N or name CA o \ r name C or name O or name CB )) or resid 437 through 443 or (resid 444 and (nam \ e N or name CA or name C or name O or name CB )) or resid 445 through 457 or res \ id 497 through 498 or (resid 499 through 500 and (name N or name CA or name C or \ name O or name CB )) or resid 501 through 507 or (resid 508 and (name N or name \ CA or name C or name O or name CB )) or resid 509 through 523 or (resid 524 and \ (name N or name CA or name C or name O or name CB )) or resid 525 through 532 o \ r (resid 533 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 34 through 541 or (resid 542 and (name N or name CA or name C or name O or name \ CB )) or resid 543 through 557 or (resid 558 and (name N or name CA or name C or \ name O or name CB )) or resid 559 through 565 or (resid 566 and (name N or name \ CA or name C or name O or name CB )) or resid 567 through 596 or (resid 597 and \ (name N or name CA or name C or name O or name CB )) or resid 598 through 628 o \ r (resid 629 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 30 through 635 or (resid 636 and (name N or name CA or name C or name O or name \ CB )) or resid 637 through 648 or (resid 649 and (name N or name CA or name C or \ name O or name CB )) or resid 650 or (resid 651 and (name N or name CA or name \ C or name O or name CB )) or resid 652 through 655 or (resid 656 and (name N or \ name CA or name C or name O or name CB )) or resid 657 through 673 or (resid 674 \ and (name N or name CA or name C or name O or name CB )) or resid 675 through 6 \ 90 or (resid 691 and (name N or name CA or name C or name O or name CB )) or res \ id 692 through 701 or (resid 702 and (name N or name CA or name C or name O or n \ ame CB )) or resid 703 through 714 or (resid 715 and (name N or name CA or name \ C or name O or name CB )) or resid 716 through 717 or (resid 718 and (name N or \ name CA or name C or name O or name CB )) or resid 719 through 737 or resid 801) \ ) selection = (chain 'E' and (resid 217 through 222 or (resid 223 and (name N or name CA or na \ me C or name O or name CB )) or resid 224 or (resid 225 and (name N or name CA o \ r name C or name O or name CB )) or resid 226 through 231 or (resid 232 through \ 234 and (name N or name CA or name C or name O or name CB )) or resid 235 throug \ h 251 or (resid 252 and (name N or name CA or name C or name O or name CB )) or \ resid 253 through 265 or (resid 266 and (name N or name CA or name C or name O o \ r name CB )) or resid 267 or (resid 268 through 270 and (name N or name CA or na \ me C or name O or name CB )) or resid 271 through 293 or (resid 294 through 295 \ and (name N or name CA or name C or name O or name CB )) or resid 296 through 30 \ 2 or (resid 303 and (name N or name CA or name C or name O or name CB )) or resi \ d 304 through 305 or (resid 306 through 307 and (name N or name CA or name C or \ name O or name CB )) or resid 308 through 311 or (resid 312 and (name N or name \ CA or name C or name O or name CB )) or resid 313 or (resid 314 through 315 and \ (name N or name CA or name C or name O or name CB )) or resid 316 through 324 or \ (resid 325 and (name N or name CA or name C or name O or name CB )) or resid 32 \ 6 through 329 or (resid 330 and (name N or name CA or name C or name O or name C \ B )) or resid 348 through 351 or (resid 352 through 353 and (name N or name CA o \ r name C or name O or name CB )) or resid 354 through 356 or (resid 357 through \ 359 and (name N or name CA or name C or name O or name CB )) or resid 360 throug \ h 371 or (resid 372 through 373 and (name N or name CA or name C or name O or na \ me CB )) or resid 374 through 382 or (resid 383 and (name N or name CA or name C \ or name O or name CB )) or resid 384 through 387 or (resid 388 and (name N or n \ ame CA or name C or name O or name CB )) or resid 389 through 396 or (resid 397 \ and (name N or name CA or name C or name O or name CB )) or resid 398 through 41 \ 8 or (resid 419 and (name N or name CA or name C or name O or name CB )) or resi \ d 420 through 423 or (resid 424 and (name N or name CA or name C or name O or na \ me CB )) or resid 425 through 435 or (resid 436 and (name N or name CA or name C \ or name O or name CB )) or resid 437 through 441 or (resid 442 and (name N or n \ ame CA or name C or name O or name CB )) or resid 443 or (resid 444 and (name N \ or name CA or name C or name O or name CB )) or resid 445 through 454 or (resid \ 455 and (name N or name CA or name C or name O or name CB )) or resid 456 throug \ h 457 or (resid 497 and (name N or name CA or name C or name O or name CB )) or \ resid 498 or (resid 499 through 500 and (name N or name CA or name C or name O o \ r name CB )) or resid 501 through 507 or (resid 508 and (name N or name CA or na \ me C or name O or name CB )) or resid 509 through 523 or (resid 524 and (name N \ or name CA or name C or name O or name CB )) or resid 525 through 532 or (resid \ 533 and (name N or name CA or name C or name O or name CB )) or resid 534 throug \ h 557 or (resid 558 and (name N or name CA or name C or name O or name CB )) or \ resid 559 through 596 or (resid 597 and (name N or name CA or name C or name O o \ r name CB )) or resid 598 through 648 or (resid 649 and (name N or name CA or na \ me C or name O or name CB )) or resid 650 or (resid 651 and (name N or name CA o \ r name C or name O or name CB )) or resid 652 through 655 or (resid 656 and (nam \ e N or name CA or name C or name O or name CB )) or resid 657 through 673 or (re \ sid 674 and (name N or name CA or name C or name O or name CB )) or resid 675 th \ rough 701 or (resid 702 and (name N or name CA or name C or name O or name CB )) \ or resid 703 through 714 or (resid 715 and (name N or name CA or name C or name \ O or name CB )) or resid 716 through 717 or (resid 718 and (name N or name CA o \ r name C or name O or name CB )) or resid 719 through 737 or resid 801)) selection = (chain 'F' and (resid 217 through 224 or (resid 225 and (name N or name CA or na \ me C or name O or name CB )) or resid 226 through 230 or (resid 231 through 234 \ and (name N or name CA or name C or name O or name CB )) or resid 235 through 26 \ 7 or (resid 268 through 270 and (name N or name CA or name C or name O or name C \ B )) or resid 271 through 302 or (resid 303 and (name N or name CA or name C or \ name O or name CB )) or resid 304 through 305 or (resid 306 through 307 and (nam \ e N or name CA or name C or name O or name CB )) or resid 308 through 311 or (re \ sid 312 and (name N or name CA or name C or name O or name CB )) or resid 313 or \ (resid 314 through 315 and (name N or name CA or name C or name O or name CB )) \ or resid 316 through 321 or (resid 322 and (name N or name CA or name C or name \ O or name CB )) or resid 323 through 329 or (resid 330 and (name N or name CA o \ r name C or name O or name CB )) or resid 348 through 352 or (resid 353 and (nam \ e N or name CA or name C or name O or name CB )) or resid 354 through 356 or (re \ sid 357 through 359 and (name N or name CA or name C or name O or name CB )) or \ resid 360 through 371 or (resid 372 through 373 and (name N or name CA or name C \ or name O or name CB )) or resid 374 through 384 or (resid 385 and (name N or n \ ame CA or name C or name O or name CB )) or resid 386 through 387 or (resid 388 \ and (name N or name CA or name C or name O or name CB )) or resid 389 through 39 \ 6 or (resid 397 and (name N or name CA or name C or name O or name CB )) or resi \ d 398 through 412 or (resid 413 through 415 and (name N or name CA or name C or \ name O or name CB )) or resid 416 through 445 or (resid 446 through 448 and (nam \ e N or name CA or name C or name O or name CB )) or resid 449 through 457 or (re \ sid 497 and (name N or name CA or name C or name O or name CB )) or resid 498 or \ (resid 499 through 500 and (name N or name CA or name C or name O or name CB )) \ or resid 501 through 507 or (resid 508 and (name N or name CA or name C or name \ O or name CB )) or resid 509 through 541 or (resid 542 and (name N or name CA o \ r name C or name O or name CB )) or resid 543 through 557 or (resid 558 and (nam \ e N or name CA or name C or name O or name CB )) or resid 559 through 565 or (re \ sid 566 and (name N or name CA or name C or name O or name CB )) or resid 567 th \ rough 596 or (resid 597 and (name N or name CA or name C or name O or name CB )) \ or resid 598 through 628 or (resid 629 and (name N or name CA or name C or name \ O or name CB )) or resid 630 through 635 or (resid 636 and (name N or name CA o \ r name C or name O or name CB )) or resid 637 through 648 or (resid 649 and (nam \ e N or name CA or name C or name O or name CB )) or resid 650 or (resid 651 and \ (name N or name CA or name C or name O or name CB )) or resid 652 through 690 or \ (resid 691 and (name N or name CA or name C or name O or name CB )) or resid 69 \ 2 through 714 or (resid 715 and (name N or name CA or name C or name O or name C \ B )) or resid 716 through 737 or resid 801)) } 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.630 Check model and map are aligned: 0.310 Set scattering table: 0.180 Process input model: 56.070 Find NCS groups from input model: 1.910 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 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 0.117 21839 Z= 0.628 Angle : 1.965 22.523 29696 Z= 1.392 Chirality : 0.074 0.507 3530 Planarity : 0.006 0.090 3801 Dihedral : 15.844 89.875 7817 Min Nonbonded Distance : 1.261 Molprobity Statistics. All-atom Clashscore : 31.36 Ramachandran Plot: Outliers : 2.00 % Allowed : 4.97 % Favored : 93.03 % Rotamer Outliers : 5.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.21 % Cis-general : 1.06 % Twisted Proline : 1.53 % 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: 2.31 (0.16), residues: 2857 helix: 2.50 (0.13), residues: 1485 sheet: 3.34 (0.25), residues: 357 loop : -0.73 (0.20), residues: 1015 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 376 time to evaluate : 2.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 123 outliers final: 26 residues processed: 479 average time/residue: 0.3706 time to fit residues: 261.2010 Evaluate side-chains 233 residues out of total 2481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 207 time to evaluate : 2.473 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2498 time to fit residues: 13.9826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 242 optimal weight: 20.0000 chunk 217 optimal weight: 8.9990 chunk 120 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 chunk 224 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 chunk 136 optimal weight: 20.0000 chunk 167 optimal weight: 20.0000 chunk 260 optimal weight: 20.0000 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 HIS ** A 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 ASN ** B 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 546 HIS C 252 HIS C 526 GLN C 530 ASN ** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 546 HIS ** E 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 417 HIS ** F 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 620 ASN ** F 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 697 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.098 21839 Z= 0.445 Angle : 0.974 12.100 29696 Z= 0.502 Chirality : 0.048 0.447 3530 Planarity : 0.007 0.092 3801 Dihedral : 7.922 87.190 3056 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 27.10 Ramachandran Plot: Outliers : 0.88 % Allowed : 4.03 % Favored : 95.10 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.21 % Cis-general : 1.06 % Twisted Proline : 0.76 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.15), residues: 2857 helix: 0.87 (0.13), residues: 1495 sheet: 2.23 (0.25), residues: 377 loop : -0.98 (0.20), residues: 985 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 237 time to evaluate : 2.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 241 average time/residue: 0.3469 time to fit residues: 128.4494 Evaluate side-chains 168 residues out of total 2481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 167 time to evaluate : 2.742 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1944 time to fit residues: 4.0420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 144 optimal weight: 8.9990 chunk 80 optimal weight: 10.0000 chunk 216 optimal weight: 10.0000 chunk 177 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 261 optimal weight: 0.0070 chunk 282 optimal weight: 3.9990 chunk 232 optimal weight: 7.9990 chunk 258 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 209 optimal weight: 7.9990 overall best weight: 4.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 HIS B 286 ASN B 454 ASN ** B 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 319 ASN D 352 ASN D 530 ASN ** D 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 697 GLN F 286 ASN ** F 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 21839 Z= 0.284 Angle : 0.767 9.734 29696 Z= 0.397 Chirality : 0.043 0.444 3530 Planarity : 0.005 0.086 3801 Dihedral : 7.254 86.397 3056 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 20.61 Ramachandran Plot: Outliers : 0.67 % Allowed : 5.04 % Favored : 94.29 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.21 % Cis-general : 1.06 % Twisted Proline : 0.76 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.15), residues: 2857 helix: 0.88 (0.13), residues: 1483 sheet: 1.96 (0.26), residues: 366 loop : -1.00 (0.20), residues: 1008 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 2.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.3129 time to fit residues: 102.7369 Evaluate side-chains 158 residues out of total 2481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 2.359 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 257 optimal weight: 10.0000 chunk 196 optimal weight: 5.9990 chunk 135 optimal weight: 0.4980 chunk 28 optimal weight: 0.6980 chunk 124 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 262 optimal weight: 10.0000 chunk 277 optimal weight: 20.0000 chunk 136 optimal weight: 8.9990 chunk 248 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 ASN ** B 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 546 HIS ** D 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 313 GLN ** E 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 526 GLN ** F 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 21839 Z= 0.221 Angle : 0.709 11.006 29696 Z= 0.361 Chirality : 0.042 0.403 3530 Planarity : 0.005 0.078 3801 Dihedral : 6.967 86.660 3056 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.53 % Allowed : 4.94 % Favored : 94.54 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.21 % Cis-general : 1.06 % Twisted Proline : 0.76 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.15), residues: 2857 helix: 1.02 (0.13), residues: 1475 sheet: 1.73 (0.26), residues: 365 loop : -0.92 (0.19), residues: 1017 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 2.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.3124 time to fit residues: 101.2663 Evaluate side-chains 150 residues out of total 2481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 2.709 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 231 optimal weight: 5.9990 chunk 157 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 206 optimal weight: 0.0570 chunk 114 optimal weight: 0.0870 chunk 236 optimal weight: 10.0000 chunk 191 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 141 optimal weight: 1.9990 chunk 249 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 ASN ** B 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 ASN ** D 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.5045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 21839 Z= 0.188 Angle : 0.681 9.777 29696 Z= 0.343 Chirality : 0.041 0.398 3530 Planarity : 0.005 0.073 3801 Dihedral : 6.755 87.704 3056 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.60 % Allowed : 4.83 % Favored : 94.57 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.21 % Cis-general : 1.06 % Twisted Proline : 0.76 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.15), residues: 2857 helix: 1.09 (0.13), residues: 1474 sheet: 1.62 (0.26), residues: 369 loop : -0.86 (0.20), residues: 1014 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 202 time to evaluate : 2.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 203 average time/residue: 0.3063 time to fit residues: 100.4389 Evaluate side-chains 154 residues out of total 2481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 2.356 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 93 optimal weight: 9.9990 chunk 249 optimal weight: 30.0000 chunk 54 optimal weight: 20.0000 chunk 162 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 277 optimal weight: 0.0070 chunk 230 optimal weight: 0.0970 chunk 128 optimal weight: 0.9990 chunk 23 optimal weight: 20.0000 chunk 91 optimal weight: 1.9990 chunk 145 optimal weight: 10.0000 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 HIS ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 ASN B 526 GLN ** C 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 583 GLN ** D 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.5269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.088 21839 Z= 0.187 Angle : 0.672 11.205 29696 Z= 0.338 Chirality : 0.041 0.407 3530 Planarity : 0.005 0.069 3801 Dihedral : 6.589 88.954 3056 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.56 % Allowed : 4.66 % Favored : 94.78 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.98 % Cis-general : 1.06 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.16), residues: 2857 helix: 1.12 (0.13), residues: 1479 sheet: 1.55 (0.26), residues: 372 loop : -0.78 (0.20), residues: 1006 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 2.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.3100 time to fit residues: 101.6157 Evaluate side-chains 151 residues out of total 2481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 2.529 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 267 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 158 optimal weight: 9.9990 chunk 202 optimal weight: 4.9990 chunk 157 optimal weight: 5.9990 chunk 233 optimal weight: 7.9990 chunk 155 optimal weight: 0.1980 chunk 276 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 127 optimal weight: 7.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 252 HIS B 454 ASN ** C 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 583 GLN ** D 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 GLN ** E 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.5516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.091 21839 Z= 0.230 Angle : 0.689 12.181 29696 Z= 0.350 Chirality : 0.042 0.379 3530 Planarity : 0.005 0.077 3801 Dihedral : 6.577 89.920 3056 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.56 % Allowed : 4.87 % Favored : 94.57 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.98 % Cis-general : 1.06 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.16), residues: 2857 helix: 1.17 (0.13), residues: 1481 sheet: 1.31 (0.25), residues: 379 loop : -0.75 (0.20), residues: 997 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 2.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.3068 time to fit residues: 93.7640 Evaluate side-chains 150 residues out of total 2481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 2.492 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 171 optimal weight: 3.9990 chunk 110 optimal weight: 20.0000 chunk 165 optimal weight: 20.0000 chunk 83 optimal weight: 20.0000 chunk 54 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 chunk 175 optimal weight: 9.9990 chunk 188 optimal weight: 6.9990 chunk 136 optimal weight: 20.0000 chunk 25 optimal weight: 9.9990 chunk 217 optimal weight: 3.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 ASN B 454 ASN B 526 GLN ** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 HIS ** C 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 561 ASN ** D 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 301 ASN ** E 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.6102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.055 21839 Z= 0.373 Angle : 0.813 9.643 29696 Z= 0.420 Chirality : 0.045 0.401 3530 Planarity : 0.006 0.076 3801 Dihedral : 7.172 88.026 3056 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 24.23 Ramachandran Plot: Outliers : 0.60 % Allowed : 6.02 % Favored : 93.38 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.98 % Cis-general : 1.06 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.15), residues: 2857 helix: 0.54 (0.13), residues: 1482 sheet: 0.69 (0.25), residues: 375 loop : -1.03 (0.19), residues: 1000 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 2.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.3053 time to fit residues: 83.1167 Evaluate side-chains 145 residues out of total 2481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 2.887 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 251 optimal weight: 10.0000 chunk 265 optimal weight: 4.9990 chunk 241 optimal weight: 0.0170 chunk 257 optimal weight: 20.0000 chunk 264 optimal weight: 3.9990 chunk 155 optimal weight: 20.0000 chunk 112 optimal weight: 6.9990 chunk 202 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 232 optimal weight: 5.9990 chunk 243 optimal weight: 8.9990 overall best weight: 3.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 ASN B 526 GLN B 546 HIS ** C 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.6213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.094 21839 Z= 0.249 Angle : 0.707 15.168 29696 Z= 0.360 Chirality : 0.042 0.390 3530 Planarity : 0.005 0.074 3801 Dihedral : 6.966 86.314 3056 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 18.96 Ramachandran Plot: Outliers : 0.63 % Allowed : 5.57 % Favored : 93.80 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.98 % Cis-general : 1.06 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.15), residues: 2857 helix: 0.77 (0.13), residues: 1476 sheet: 0.68 (0.26), residues: 369 loop : -0.99 (0.19), residues: 1012 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 2.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.3185 time to fit residues: 90.5968 Evaluate side-chains 143 residues out of total 2481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 2.605 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 256 optimal weight: 10.0000 chunk 169 optimal weight: 20.0000 chunk 272 optimal weight: 0.9990 chunk 166 optimal weight: 0.9980 chunk 129 optimal weight: 0.6980 chunk 189 optimal weight: 7.9990 chunk 285 optimal weight: 4.9990 chunk 263 optimal weight: 9.9990 chunk 227 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 175 optimal weight: 0.8980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 ASN ** C 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.6318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.095 21839 Z= 0.205 Angle : 0.700 11.597 29696 Z= 0.350 Chirality : 0.042 0.353 3530 Planarity : 0.005 0.069 3801 Dihedral : 6.826 89.423 3056 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.32 % Favored : 94.12 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.98 % Cis-general : 1.06 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.16), residues: 2857 helix: 0.87 (0.13), residues: 1475 sheet: 0.78 (0.26), residues: 369 loop : -0.93 (0.20), residues: 1013 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 2.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.3172 time to fit residues: 91.7724 Evaluate side-chains 146 residues out of total 2481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 2.571 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 139 optimal weight: 0.8980 chunk 180 optimal weight: 3.9990 chunk 242 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 209 optimal weight: 0.0170 chunk 33 optimal weight: 8.9990 chunk 63 optimal weight: 0.0470 chunk 228 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 234 optimal weight: 20.0000 chunk 28 optimal weight: 4.9990 overall best weight: 0.5916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 GLN B 454 ASN ** C 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 675 GLN ** E 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.042977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.031720 restraints weight = 196222.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.032315 restraints weight = 148559.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.032965 restraints weight = 116519.401| |-----------------------------------------------------------------------------| r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.6418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.091 21839 Z= 0.190 Angle : 0.688 11.356 29696 Z= 0.343 Chirality : 0.042 0.335 3530 Planarity : 0.005 0.067 3801 Dihedral : 6.714 87.114 3056 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.53 % Allowed : 4.83 % Favored : 94.64 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.98 % Cis-general : 1.02 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.16), residues: 2857 helix: 0.93 (0.13), residues: 1479 sheet: 0.87 (0.26), residues: 366 loop : -0.91 (0.20), residues: 1012 =============================================================================== Job complete usr+sys time: 3507.97 seconds wall clock time: 65 minutes 20.25 seconds (3920.25 seconds total)