Starting phenix.real_space_refine (version: dev) on Fri Feb 24 13:42:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mij_23853/02_2023/7mij_23853_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mij_23853/02_2023/7mij_23853.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mij_23853/02_2023/7mij_23853.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mij_23853/02_2023/7mij_23853.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mij_23853/02_2023/7mij_23853_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mij_23853/02_2023/7mij_23853_updated.pdb" } resolution = 1.98 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= 0.005 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 Process input model Symmetric amino acids flipped Residue "A ARG 118": "NH1" <-> "NH2" Residue "A ARG 147": "NH1" <-> "NH2" Residue "A ARG 149": "NH1" <-> "NH2" Residue "A ARG 188": "NH1" <-> "NH2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 327": "NH1" <-> "NH2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "A ARG 416": "NH1" <-> "NH2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A ARG 509": "NH1" <-> "NH2" Residue "A TYR 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 690": "NH1" <-> "NH2" Residue "A ARG 716": "NH1" <-> "NH2" Residue "A ARG 733": "NH1" <-> "NH2" Residue "A PHE 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 118": "NH1" <-> "NH2" Residue "B ARG 147": "NH1" <-> "NH2" Residue "B ARG 149": "NH1" <-> "NH2" Residue "B ARG 188": "NH1" <-> "NH2" Residue "B TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 327": "NH1" <-> "NH2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "B ARG 416": "NH1" <-> "NH2" Residue "B ARG 464": "NH1" <-> "NH2" Residue "B ARG 509": "NH1" <-> "NH2" Residue "B TYR 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 690": "NH1" <-> "NH2" Residue "B ARG 716": "NH1" <-> "NH2" Residue "B ARG 733": "NH1" <-> "NH2" Residue "B PHE 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 118": "NH1" <-> "NH2" Residue "C ARG 147": "NH1" <-> "NH2" Residue "C ARG 149": "NH1" <-> "NH2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "C ARG 225": "NH1" <-> "NH2" Residue "C PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 327": "NH1" <-> "NH2" Residue "C ARG 363": "NH1" <-> "NH2" Residue "C ARG 416": "NH1" <-> "NH2" Residue "C ARG 464": "NH1" <-> "NH2" Residue "C ARG 509": "NH1" <-> "NH2" Residue "C TYR 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 690": "NH1" <-> "NH2" Residue "C ARG 716": "NH1" <-> "NH2" Residue "C ARG 733": "NH1" <-> "NH2" Residue "C PHE 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 118": "NH1" <-> "NH2" Residue "D ARG 147": "NH1" <-> "NH2" Residue "D ARG 149": "NH1" <-> "NH2" Residue "D ARG 188": "NH1" <-> "NH2" Residue "D TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 225": "NH1" <-> "NH2" Residue "D PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 327": "NH1" <-> "NH2" Residue "D ARG 363": "NH1" <-> "NH2" Residue "D ARG 416": "NH1" <-> "NH2" Residue "D ARG 464": "NH1" <-> "NH2" Residue "D ARG 509": "NH1" <-> "NH2" Residue "D TYR 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 690": "NH1" <-> "NH2" Residue "D ARG 716": "NH1" <-> "NH2" Residue "D ARG 733": "NH1" <-> "NH2" Residue "D PHE 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 23010 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 5202 Classifications: {'peptide': 639} Link IDs: {'PTRANS': 17, 'TRANS': 621} Chain: "B" Number of atoms: 5202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 5202 Classifications: {'peptide': 639} Link IDs: {'PTRANS': 17, 'TRANS': 621} Chain: "C" Number of atoms: 5202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 5202 Classifications: {'peptide': 639} Link IDs: {'PTRANS': 17, 'TRANS': 621} Chain: "D" Number of atoms: 5202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 5202 Classifications: {'peptide': 639} Link IDs: {'PTRANS': 17, 'TRANS': 621} Chain: "A" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 626 Unusual residues: {' NA': 2, 'POV': 12} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "B" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 468 Unusual residues: {'POV': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 468 Unusual residues: {'POV': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "D" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 312 Unusual residues: {'POV': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "A" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "B" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} Chain: "C" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "D" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Time building chain proxies: 12.62, per 1000 atoms: 0.55 Number of scatterers: 23010 At special positions: 0 Unit cell: (126.42, 126.42, 133.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 124 16.00 P 36 15.00 Na 2 11.00 O 4348 8.00 N 3460 7.00 C 15040 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 619 " distance=2.03 Simple disulfide: pdb=" SG CYS B 612 " - pdb=" SG CYS B 619 " distance=2.03 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 619 " distance=2.03 Simple disulfide: pdb=" SG CYS D 612 " - pdb=" SG CYS D 619 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.63 Conformation dependent library (CDL) restraints added in 3.2 seconds 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4896 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 128 helices and 4 sheets defined 56.0% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.33 Creating SS restraints... Processing helix chain 'A' and resid 119 through 129 Processing helix chain 'A' and resid 132 through 147 removed outlier: 3.896A pdb=" N GLU A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 158 Processing helix chain 'A' and resid 171 through 176 Processing helix chain 'A' and resid 183 through 195 removed outlier: 3.911A pdb=" N ARG A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 218 through 224 Processing helix chain 'A' and resid 228 through 236 removed outlier: 3.930A pdb=" N ALA A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'A' and resid 265 through 271 Processing helix chain 'A' and resid 275 through 283 Processing helix chain 'A' and resid 299 through 305 Processing helix chain 'A' and resid 310 through 313 No H-bonds generated for 'chain 'A' and resid 310 through 313' Processing helix chain 'A' and resid 316 through 328 Processing helix chain 'A' and resid 344 through 350 Processing helix chain 'A' and resid 354 through 361 Processing helix chain 'A' and resid 371 through 373 No H-bonds generated for 'chain 'A' and resid 371 through 373' Processing helix chain 'A' and resid 403 through 408 Processing helix chain 'A' and resid 416 through 421 removed outlier: 4.665A pdb=" N THR A 421 " --> pdb=" O HIS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 435 removed outlier: 3.972A pdb=" N THR A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 460 removed outlier: 3.534A pdb=" N SER A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 507 removed outlier: 4.145A pdb=" N LEU A 491 " --> pdb=" O ARG A 487 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE A 506 " --> pdb=" O GLY A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 516 No H-bonds generated for 'chain 'A' and resid 513 through 516' Processing helix chain 'A' and resid 521 through 541 removed outlier: 3.502A pdb=" N VAL A 533 " --> pdb=" O GLN A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 568 removed outlier: 3.770A pdb=" N MET A 562 " --> pdb=" O GLY A 558 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N LEU A 563 " --> pdb=" O TRP A 559 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N TYR A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N TYR A 565 " --> pdb=" O ASN A 561 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N THR A 566 " --> pdb=" O MET A 562 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ARG A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N GLY A 568 " --> pdb=" O TYR A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 585 Processing helix chain 'A' and resid 587 through 608 removed outlier: 3.578A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 637 Processing helix chain 'A' and resid 651 through 665 Processing helix chain 'A' and resid 669 through 686 removed outlier: 3.663A pdb=" N ILE A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LYS A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 705 Processing helix chain 'A' and resid 709 through 712 No H-bonds generated for 'chain 'A' and resid 709 through 712' Processing helix chain 'B' and resid 119 through 129 Processing helix chain 'B' and resid 132 through 147 removed outlier: 3.896A pdb=" N GLU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 158 Processing helix chain 'B' and resid 171 through 176 Processing helix chain 'B' and resid 183 through 195 removed outlier: 3.911A pdb=" N ARG B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 Processing helix chain 'B' and resid 218 through 224 Processing helix chain 'B' and resid 228 through 236 removed outlier: 3.930A pdb=" N ALA B 232 " --> pdb=" O GLY B 228 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 233 " --> pdb=" O ASP B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 257 No H-bonds generated for 'chain 'B' and resid 255 through 257' Processing helix chain 'B' and resid 265 through 271 Processing helix chain 'B' and resid 275 through 283 Processing helix chain 'B' and resid 299 through 305 Processing helix chain 'B' and resid 310 through 313 No H-bonds generated for 'chain 'B' and resid 310 through 313' Processing helix chain 'B' and resid 316 through 328 Processing helix chain 'B' and resid 344 through 350 Processing helix chain 'B' and resid 354 through 361 Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 403 through 408 Processing helix chain 'B' and resid 416 through 421 removed outlier: 4.666A pdb=" N THR B 421 " --> pdb=" O HIS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 435 removed outlier: 3.972A pdb=" N THR B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 460 removed outlier: 3.533A pdb=" N SER B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 507 removed outlier: 4.145A pdb=" N LEU B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE B 506 " --> pdb=" O GLY B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 516 No H-bonds generated for 'chain 'B' and resid 513 through 516' Processing helix chain 'B' and resid 521 through 541 removed outlier: 3.501A pdb=" N VAL B 533 " --> pdb=" O GLN B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 568 removed outlier: 3.770A pdb=" N MET B 562 " --> pdb=" O GLY B 558 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N LEU B 563 " --> pdb=" O TRP B 559 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N TYR B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N TYR B 565 " --> pdb=" O ASN B 561 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR B 566 " --> pdb=" O MET B 562 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ARG B 567 " --> pdb=" O LEU B 563 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N GLY B 568 " --> pdb=" O TYR B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 585 Processing helix chain 'B' and resid 587 through 608 removed outlier: 3.577A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B 608 " --> pdb=" O ALA B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 637 Processing helix chain 'B' and resid 651 through 665 Processing helix chain 'B' and resid 669 through 686 removed outlier: 3.663A pdb=" N ILE B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU B 679 " --> pdb=" O ALA B 675 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LYS B 686 " --> pdb=" O GLU B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 705 Processing helix chain 'B' and resid 709 through 712 No H-bonds generated for 'chain 'B' and resid 709 through 712' Processing helix chain 'C' and resid 119 through 129 Processing helix chain 'C' and resid 132 through 147 removed outlier: 3.897A pdb=" N GLU C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 158 Processing helix chain 'C' and resid 171 through 176 Processing helix chain 'C' and resid 183 through 195 removed outlier: 3.911A pdb=" N ARG C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 204 Processing helix chain 'C' and resid 218 through 224 Processing helix chain 'C' and resid 228 through 236 removed outlier: 3.930A pdb=" N ALA C 232 " --> pdb=" O GLY C 228 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL C 233 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 257 No H-bonds generated for 'chain 'C' and resid 255 through 257' Processing helix chain 'C' and resid 265 through 271 Processing helix chain 'C' and resid 275 through 283 Processing helix chain 'C' and resid 299 through 305 Processing helix chain 'C' and resid 310 through 313 No H-bonds generated for 'chain 'C' and resid 310 through 313' Processing helix chain 'C' and resid 316 through 328 Processing helix chain 'C' and resid 344 through 350 Processing helix chain 'C' and resid 354 through 361 Processing helix chain 'C' and resid 371 through 373 No H-bonds generated for 'chain 'C' and resid 371 through 373' Processing helix chain 'C' and resid 403 through 408 Processing helix chain 'C' and resid 416 through 421 removed outlier: 4.665A pdb=" N THR C 421 " --> pdb=" O HIS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 435 removed outlier: 3.972A pdb=" N THR C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 460 removed outlier: 3.534A pdb=" N SER C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 507 removed outlier: 4.146A pdb=" N LEU C 491 " --> pdb=" O ARG C 487 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE C 506 " --> pdb=" O GLY C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 516 No H-bonds generated for 'chain 'C' and resid 513 through 516' Processing helix chain 'C' and resid 521 through 541 removed outlier: 3.501A pdb=" N VAL C 533 " --> pdb=" O GLN C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 568 removed outlier: 3.770A pdb=" N MET C 562 " --> pdb=" O GLY C 558 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N LEU C 563 " --> pdb=" O TRP C 559 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N TYR C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N TYR C 565 " --> pdb=" O ASN C 561 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR C 566 " --> pdb=" O MET C 562 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ARG C 567 " --> pdb=" O LEU C 563 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N GLY C 568 " --> pdb=" O TYR C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 585 Processing helix chain 'C' and resid 587 through 608 removed outlier: 3.578A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU C 608 " --> pdb=" O ALA C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 637 Processing helix chain 'C' and resid 651 through 665 Processing helix chain 'C' and resid 669 through 686 removed outlier: 3.662A pdb=" N ILE C 674 " --> pdb=" O LEU C 670 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU C 679 " --> pdb=" O ALA C 675 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LYS C 686 " --> pdb=" O GLU C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 705 Processing helix chain 'C' and resid 709 through 712 No H-bonds generated for 'chain 'C' and resid 709 through 712' Processing helix chain 'D' and resid 119 through 129 Processing helix chain 'D' and resid 132 through 147 removed outlier: 3.897A pdb=" N GLU D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 158 Processing helix chain 'D' and resid 171 through 176 Processing helix chain 'D' and resid 183 through 195 removed outlier: 3.911A pdb=" N ARG D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 204 Processing helix chain 'D' and resid 218 through 224 Processing helix chain 'D' and resid 228 through 236 removed outlier: 3.931A pdb=" N ALA D 232 " --> pdb=" O GLY D 228 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL D 233 " --> pdb=" O ASP D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 257 No H-bonds generated for 'chain 'D' and resid 255 through 257' Processing helix chain 'D' and resid 265 through 271 Processing helix chain 'D' and resid 275 through 283 Processing helix chain 'D' and resid 299 through 305 Processing helix chain 'D' and resid 310 through 313 No H-bonds generated for 'chain 'D' and resid 310 through 313' Processing helix chain 'D' and resid 316 through 328 Processing helix chain 'D' and resid 344 through 350 Processing helix chain 'D' and resid 354 through 361 Processing helix chain 'D' and resid 371 through 373 No H-bonds generated for 'chain 'D' and resid 371 through 373' Processing helix chain 'D' and resid 403 through 408 Processing helix chain 'D' and resid 416 through 421 removed outlier: 4.666A pdb=" N THR D 421 " --> pdb=" O HIS D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 435 removed outlier: 3.972A pdb=" N THR D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 460 removed outlier: 3.534A pdb=" N SER D 459 " --> pdb=" O LEU D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 507 removed outlier: 4.145A pdb=" N LEU D 491 " --> pdb=" O ARG D 487 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE D 506 " --> pdb=" O GLY D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 516 No H-bonds generated for 'chain 'D' and resid 513 through 516' Processing helix chain 'D' and resid 521 through 541 removed outlier: 3.501A pdb=" N VAL D 533 " --> pdb=" O GLN D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 568 removed outlier: 3.770A pdb=" N MET D 562 " --> pdb=" O GLY D 558 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N LEU D 563 " --> pdb=" O TRP D 559 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N TYR D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N TYR D 565 " --> pdb=" O ASN D 561 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR D 566 " --> pdb=" O MET D 562 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ARG D 567 " --> pdb=" O LEU D 563 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N GLY D 568 " --> pdb=" O TYR D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 585 Processing helix chain 'D' and resid 587 through 608 removed outlier: 3.578A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU D 608 " --> pdb=" O ALA D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 637 Processing helix chain 'D' and resid 651 through 665 Processing helix chain 'D' and resid 669 through 686 removed outlier: 3.663A pdb=" N ILE D 674 " --> pdb=" O LEU D 670 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU D 679 " --> pdb=" O ALA D 675 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LYS D 686 " --> pdb=" O GLU D 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 705 Processing helix chain 'D' and resid 709 through 712 No H-bonds generated for 'chain 'D' and resid 709 through 712' Processing sheet with id= A, first strand: chain 'A' and resid 376 through 382 removed outlier: 6.910A pdb=" N SER A 387 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ALA A 381 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA A 724 " --> pdb=" O ASP A 727 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ARG A 729 " --> pdb=" O LYS A 722 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N LYS A 722 " --> pdb=" O ARG A 729 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N CYS A 731 " --> pdb=" O LEU A 720 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LEU A 720 " --> pdb=" O CYS A 731 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 376 through 382 removed outlier: 6.909A pdb=" N SER B 387 " --> pdb=" O ASP B 379 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ALA B 381 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA B 724 " --> pdb=" O ASP B 727 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ARG B 729 " --> pdb=" O LYS B 722 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N LYS B 722 " --> pdb=" O ARG B 729 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N CYS B 731 " --> pdb=" O LEU B 720 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LEU B 720 " --> pdb=" O CYS B 731 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 376 through 382 removed outlier: 6.909A pdb=" N SER C 387 " --> pdb=" O ASP C 379 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ALA C 381 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA C 724 " --> pdb=" O ASP C 727 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ARG C 729 " --> pdb=" O LYS C 722 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N LYS C 722 " --> pdb=" O ARG C 729 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N CYS C 731 " --> pdb=" O LEU C 720 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LEU C 720 " --> pdb=" O CYS C 731 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 376 through 382 removed outlier: 6.909A pdb=" N SER D 387 " --> pdb=" O ASP D 379 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ALA D 381 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA D 724 " --> pdb=" O ASP D 727 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ARG D 729 " --> pdb=" O LYS D 722 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N LYS D 722 " --> pdb=" O ARG D 729 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N CYS D 731 " --> pdb=" O LEU D 720 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LEU D 720 " --> pdb=" O CYS D 731 " (cutoff:3.500A) 872 hydrogen bonds defined for protein. 2604 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: 6.42 Time building geometry restraints manager: 9.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3428 1.31 - 1.44: 5981 1.44 - 1.56: 13410 1.56 - 1.69: 77 1.69 - 1.82: 204 Bond restraints: 23100 Sorted by residual: bond pdb=" C21 POV B 909 " pdb=" O21 POV B 909 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C21 POV C 909 " pdb=" O21 POV C 909 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C21 POV A 911 " pdb=" O21 POV A 911 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" C21 POV B 901 " pdb=" O21 POV B 901 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" C21 POV A 905 " pdb=" O21 POV A 905 " ideal model delta sigma weight residual 1.330 1.419 -0.089 2.00e-02 2.50e+03 2.00e+01 ... (remaining 23095 not shown) Histogram of bond angle deviations from ideal: 100.16 - 106.94: 586 106.94 - 113.72: 13025 113.72 - 120.51: 9261 120.51 - 127.29: 7833 127.29 - 134.07: 207 Bond angle restraints: 30912 Sorted by residual: angle pdb=" C LYS D 614 " pdb=" N ASP D 615 " pdb=" CA ASP D 615 " ideal model delta sigma weight residual 120.82 129.64 -8.82 1.50e+00 4.44e-01 3.46e+01 angle pdb=" C LYS A 614 " pdb=" N ASP A 615 " pdb=" CA ASP A 615 " ideal model delta sigma weight residual 120.82 129.61 -8.79 1.50e+00 4.44e-01 3.44e+01 angle pdb=" C LYS C 614 " pdb=" N ASP C 615 " pdb=" CA ASP C 615 " ideal model delta sigma weight residual 120.82 129.59 -8.77 1.50e+00 4.44e-01 3.42e+01 angle pdb=" C LYS B 614 " pdb=" N ASP B 615 " pdb=" CA ASP B 615 " ideal model delta sigma weight residual 120.82 129.55 -8.73 1.50e+00 4.44e-01 3.39e+01 angle pdb=" N GLN A 313 " pdb=" CA GLN A 313 " pdb=" CB GLN A 313 " ideal model delta sigma weight residual 110.80 103.81 6.99 1.49e+00 4.50e-01 2.20e+01 ... (remaining 30907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.18: 13357 35.18 - 70.36: 555 70.36 - 105.53: 92 105.53 - 140.71: 36 140.71 - 175.89: 12 Dihedral angle restraints: 14052 sinusoidal: 6508 harmonic: 7544 Sorted by residual: dihedral pdb=" CB CYS B 612 " pdb=" SG CYS B 612 " pdb=" SG CYS B 619 " pdb=" CB CYS B 619 " ideal model delta sinusoidal sigma weight residual 93.00 173.79 -80.79 1 1.00e+01 1.00e-02 8.06e+01 dihedral pdb=" CB CYS C 612 " pdb=" SG CYS C 612 " pdb=" SG CYS C 619 " pdb=" CB CYS C 619 " ideal model delta sinusoidal sigma weight residual 93.00 173.78 -80.78 1 1.00e+01 1.00e-02 8.06e+01 dihedral pdb=" CB CYS D 612 " pdb=" SG CYS D 612 " pdb=" SG CYS D 619 " pdb=" CB CYS D 619 " ideal model delta sinusoidal sigma weight residual 93.00 173.78 -80.78 1 1.00e+01 1.00e-02 8.06e+01 ... (remaining 14049 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2604 0.054 - 0.109: 588 0.109 - 0.163: 94 0.163 - 0.217: 31 0.217 - 0.272: 7 Chirality restraints: 3324 Sorted by residual: chirality pdb=" CA ASN A 314 " pdb=" N ASN A 314 " pdb=" C ASN A 314 " pdb=" CB ASN A 314 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA ASN D 314 " pdb=" N ASN D 314 " pdb=" C ASN D 314 " pdb=" CB ASN D 314 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA ASN C 314 " pdb=" N ASN C 314 " pdb=" C ASN C 314 " pdb=" CB ASN C 314 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 3321 not shown) Planarity restraints: 3704 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 311 " 0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C LYS B 311 " -0.058 2.00e-02 2.50e+03 pdb=" O LYS B 311 " 0.022 2.00e-02 2.50e+03 pdb=" N THR B 312 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 509 " 0.052 5.00e-02 4.00e+02 7.87e-02 9.91e+00 pdb=" N PRO B 510 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO B 510 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 510 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 509 " -0.052 5.00e-02 4.00e+02 7.85e-02 9.87e+00 pdb=" N PRO D 510 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO D 510 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 510 " -0.043 5.00e-02 4.00e+02 ... (remaining 3701 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 6561 2.84 - 3.35: 19894 3.35 - 3.87: 35677 3.87 - 4.38: 44080 4.38 - 4.90: 72496 Nonbonded interactions: 178708 Sorted by model distance: nonbonded pdb=" O ALA A 206 " pdb=" O HOH A1001 " model vdw 2.320 2.440 nonbonded pdb=" O GLN A 255 " pdb=" O HOH A1002 " model vdw 2.327 2.440 nonbonded pdb=" O GLN C 255 " pdb=" O HOH C1001 " model vdw 2.339 2.440 nonbonded pdb=" O GLN D 255 " pdb=" O HOH D1001 " model vdw 2.342 2.440 nonbonded pdb=" O THR A 393 " pdb=" O HOH A1003 " model vdw 2.343 2.440 ... (remaining 178703 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 118 through 756 or resid 901 through 906)) selection = (chain 'B' and (resid 118 through 756 or resid 901 through 906)) selection = (chain 'C' and (resid 118 through 756 or resid 901 through 906)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 36 5.49 5 S 124 5.16 5 Na 2 4.78 5 C 15040 2.51 5 N 3460 2.21 5 O 4348 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.910 Check model and map are aligned: 0.370 Process input model: 55.670 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.220 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:12.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 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 : 0.010 0.090 23100 Z= 0.562 Angle : 1.379 14.011 30912 Z= 0.610 Chirality : 0.049 0.272 3324 Planarity : 0.006 0.079 3704 Dihedral : 19.919 175.890 9144 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.96 (0.12), residues: 2548 helix: -2.98 (0.09), residues: 1540 sheet: 0.69 (0.53), residues: 88 loop : -1.97 (0.16), residues: 920 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 428 time to evaluate : 2.720 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 431 average time/residue: 1.4512 time to fit residues: 707.6697 Evaluate side-chains 262 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 2.529 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 0.4980 chunk 191 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 197 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 chunk 147 optimal weight: 0.0020 chunk 228 optimal weight: 3.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 220 ASN A 227 GLN A 274 GLN A 426 HIS A 477 HIS A 643 ASN A 647 ASN A 750 ASN B 220 ASN B 274 GLN B 426 HIS B 477 HIS B 643 ASN B 647 ASN C 220 ASN C 274 GLN C 426 HIS C 477 HIS C 643 ASN C 647 ASN C 750 ASN D 220 ASN D 274 GLN D 426 HIS D 477 HIS D 643 ASN D 647 ASN D 750 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 23100 Z= 0.143 Angle : 0.539 7.897 30912 Z= 0.288 Chirality : 0.039 0.139 3324 Planarity : 0.005 0.053 3704 Dihedral : 23.639 150.288 4112 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 2.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.15), residues: 2548 helix: -0.16 (0.12), residues: 1608 sheet: 1.08 (0.52), residues: 88 loop : -2.02 (0.17), residues: 852 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 286 time to evaluate : 2.620 Fit side-chains outliers start: 48 outliers final: 4 residues processed: 317 average time/residue: 1.7480 time to fit residues: 619.4778 Evaluate side-chains 257 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 253 time to evaluate : 2.667 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 2.3081 time to fit residues: 13.4502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 190 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 63 optimal weight: 10.0000 chunk 229 optimal weight: 0.7980 chunk 247 optimal weight: 4.9990 chunk 204 optimal weight: 0.9980 chunk 227 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN A 580 GLN A 750 ASN C 178 ASN C 750 ASN D 523 HIS D 750 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 23100 Z= 0.171 Angle : 0.561 6.676 30912 Z= 0.298 Chirality : 0.040 0.145 3324 Planarity : 0.004 0.045 3704 Dihedral : 22.315 153.740 4112 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer Outliers : 2.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.00 (0.16), residues: 2548 helix: 0.83 (0.13), residues: 1588 sheet: 1.24 (0.52), residues: 88 loop : -1.66 (0.18), residues: 872 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 276 time to evaluate : 2.720 Fit side-chains outliers start: 46 outliers final: 7 residues processed: 303 average time/residue: 1.6950 time to fit residues: 574.8576 Evaluate side-chains 251 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 244 time to evaluate : 2.622 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 2.4230 time to fit residues: 6.1933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 153 optimal weight: 6.9990 chunk 230 optimal weight: 1.9990 chunk 243 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 218 optimal weight: 0.0030 chunk 65 optimal weight: 4.9990 overall best weight: 1.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 HIS A 580 GLN B 178 ASN B 227 GLN B 523 HIS B 580 GLN C 227 GLN C 523 HIS C 580 GLN D 227 GLN D 580 GLN ** D 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 23100 Z= 0.203 Angle : 0.606 7.687 30912 Z= 0.320 Chirality : 0.041 0.163 3324 Planarity : 0.005 0.048 3704 Dihedral : 21.789 156.911 4112 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer Outliers : 2.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.16), residues: 2548 helix: 1.06 (0.13), residues: 1584 sheet: 1.28 (0.52), residues: 88 loop : -1.61 (0.18), residues: 876 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 263 time to evaluate : 2.623 Fit side-chains outliers start: 50 outliers final: 13 residues processed: 287 average time/residue: 1.6262 time to fit residues: 525.6511 Evaluate side-chains 257 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 244 time to evaluate : 2.614 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 10 residues processed: 3 average time/residue: 1.2832 time to fit residues: 8.0622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 0.9980 chunk 138 optimal weight: 0.0060 chunk 3 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 207 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 124 optimal weight: 0.7980 chunk 218 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN B 580 GLN C 580 GLN D 580 GLN ** D 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 23100 Z= 0.168 Angle : 0.547 7.672 30912 Z= 0.291 Chirality : 0.039 0.154 3324 Planarity : 0.004 0.045 3704 Dihedral : 20.873 153.627 4112 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer Outliers : 1.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.16), residues: 2548 helix: 1.39 (0.13), residues: 1580 sheet: 1.32 (0.52), residues: 88 loop : -1.56 (0.18), residues: 880 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 261 time to evaluate : 2.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 12 residues processed: 280 average time/residue: 1.6262 time to fit residues: 511.7785 Evaluate side-chains 260 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 248 time to evaluate : 2.514 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 0 time to fit residues: 3.3713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 2.9990 chunk 219 optimal weight: 0.0980 chunk 48 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 243 optimal weight: 1.9990 chunk 202 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 128 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN B 580 GLN C 580 GLN C 647 ASN D 580 GLN D 647 ASN ** D 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 23100 Z= 0.168 Angle : 0.547 6.841 30912 Z= 0.290 Chirality : 0.039 0.158 3324 Planarity : 0.004 0.045 3704 Dihedral : 20.191 152.365 4112 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer Outliers : 2.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.16), residues: 2548 helix: 1.47 (0.13), residues: 1604 sheet: 1.31 (0.52), residues: 88 loop : -1.62 (0.18), residues: 856 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 266 time to evaluate : 2.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 14 residues processed: 294 average time/residue: 1.5635 time to fit residues: 520.7786 Evaluate side-chains 272 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 258 time to evaluate : 2.599 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 13 residues processed: 1 average time/residue: 2.5630 time to fit residues: 6.3328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 138 optimal weight: 4.9990 chunk 178 optimal weight: 0.0470 chunk 137 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 242 optimal weight: 6.9990 chunk 152 optimal weight: 4.9990 chunk 148 optimal weight: 0.3980 chunk 112 optimal weight: 8.9990 overall best weight: 1.0884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN A 647 ASN B 580 GLN B 647 ASN C 580 GLN C 647 ASN D 580 GLN D 647 ASN ** D 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 23100 Z= 0.163 Angle : 0.541 8.269 30912 Z= 0.287 Chirality : 0.039 0.155 3324 Planarity : 0.004 0.045 3704 Dihedral : 19.919 151.918 4112 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.16), residues: 2548 helix: 1.57 (0.13), residues: 1604 sheet: 1.28 (0.52), residues: 88 loop : -1.56 (0.19), residues: 856 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 263 time to evaluate : 2.813 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: 33 outliers final: 17 residues processed: 284 average time/residue: 1.6276 time to fit residues: 521.2408 Evaluate side-chains 270 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 253 time to evaluate : 2.770 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 15 residues processed: 2 average time/residue: 1.8237 time to fit residues: 7.3955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 145 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 154 optimal weight: 0.6980 chunk 165 optimal weight: 8.9990 chunk 120 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 190 optimal weight: 5.9990 chunk 220 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN A 647 ASN B 647 ASN C 580 GLN C 647 ASN D 227 GLN D 647 ASN ** D 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 23100 Z= 0.143 Angle : 0.511 8.607 30912 Z= 0.270 Chirality : 0.038 0.148 3324 Planarity : 0.003 0.042 3704 Dihedral : 19.463 150.688 4112 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.16), residues: 2548 helix: 1.71 (0.13), residues: 1604 sheet: 1.29 (0.52), residues: 88 loop : -1.53 (0.19), residues: 856 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 263 time to evaluate : 2.612 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: 32 outliers final: 15 residues processed: 285 average time/residue: 1.5643 time to fit residues: 503.1280 Evaluate side-chains 277 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 262 time to evaluate : 2.639 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 14 residues processed: 1 average time/residue: 2.0270 time to fit residues: 6.0508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 4.9990 chunk 212 optimal weight: 4.9990 chunk 226 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 chunk 177 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 204 optimal weight: 0.0030 chunk 214 optimal weight: 5.9990 chunk 225 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 overall best weight: 1.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 GLN B 580 GLN B 647 ASN C 227 GLN C 580 GLN C 647 ASN D 227 GLN D 580 GLN D 647 ASN ** D 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 23100 Z= 0.200 Angle : 0.593 8.965 30912 Z= 0.312 Chirality : 0.040 0.169 3324 Planarity : 0.004 0.046 3704 Dihedral : 19.853 152.927 4112 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 1.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.16), residues: 2548 helix: 1.49 (0.13), residues: 1592 sheet: 1.24 (0.52), residues: 88 loop : -1.53 (0.18), residues: 868 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 258 time to evaluate : 2.871 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 outliers start: 29 outliers final: 18 residues processed: 279 average time/residue: 1.6721 time to fit residues: 526.0926 Evaluate side-chains 265 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 247 time to evaluate : 2.518 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 16 residues processed: 2 average time/residue: 1.8461 time to fit residues: 7.4918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 7.9990 chunk 146 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 166 optimal weight: 0.5980 chunk 251 optimal weight: 3.9990 chunk 231 optimal weight: 2.9990 chunk 199 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 154 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 ASN C 580 GLN C 647 ASN D 647 ASN ** D 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 23100 Z= 0.137 Angle : 0.502 8.681 30912 Z= 0.264 Chirality : 0.038 0.146 3324 Planarity : 0.003 0.042 3704 Dihedral : 19.172 150.672 4112 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.16), residues: 2548 helix: 1.65 (0.13), residues: 1632 sheet: 1.30 (0.52), residues: 88 loop : -1.78 (0.18), residues: 828 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 263 time to evaluate : 2.824 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: 32 outliers final: 16 residues processed: 290 average time/residue: 1.5786 time to fit residues: 516.7384 Evaluate side-chains 277 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 261 time to evaluate : 2.584 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 16 residues processed: 0 time to fit residues: 3.6015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 184 optimal weight: 8.9990 chunk 29 optimal weight: 0.0000 chunk 55 optimal weight: 0.5980 chunk 200 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 205 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 36 optimal weight: 0.0980 chunk 175 optimal weight: 0.4980 overall best weight: 0.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 GLN B 580 GLN ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 227 GLN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 ASN D 580 GLN D 647 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.198878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.168576 restraints weight = 17120.012| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 0.73 r_work: 0.3748 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3699 rms_B_bonded: 1.88 restraints_weight: 0.2500 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4204 r_free = 0.4204 target_work(ls_wunit_k1) = 0.199 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4197 r_free = 0.4197 target_work(ls_wunit_k1) = 0.198 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.4197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 23100 Z= 0.110 Angle : 0.452 8.633 30912 Z= 0.236 Chirality : 0.036 0.132 3324 Planarity : 0.003 0.038 3704 Dihedral : 18.218 146.756 4112 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.17), residues: 2548 helix: 2.06 (0.13), residues: 1596 sheet: 1.23 (0.51), residues: 88 loop : -1.38 (0.19), residues: 864 =============================================================================== Job complete usr+sys time: 8894.58 seconds wall clock time: 158 minutes 12.13 seconds (9492.13 seconds total)