Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 16 08:51:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uw4_20917/08_2023/6uw4_20917_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uw4_20917/08_2023/6uw4_20917.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uw4_20917/08_2023/6uw4_20917.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uw4_20917/08_2023/6uw4_20917.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uw4_20917/08_2023/6uw4_20917_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uw4_20917/08_2023/6uw4_20917_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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: 6 Type Number sf(0) Gaussians P 20 5.49 5 S 116 5.16 5 Na 1 4.78 5 C 13220 2.51 5 N 3280 2.21 5 O 3644 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 117": "NH1" <-> "NH2" Residue "A GLU 144": "OE1" <-> "OE2" Residue "A ARG 148": "NH1" <-> "NH2" Residue "A ASP 156": "OD1" <-> "OD2" Residue "A GLU 195": "OE1" <-> "OE2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A ARG 226": "NH1" <-> "NH2" Residue "A ASP 229": "OD1" <-> "OD2" Residue "A GLU 285": "OE1" <-> "OE2" Residue "A TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 327": "NH1" <-> "NH2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "A PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 618": "OD1" <-> "OD2" Residue "A TYR 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 687": "OE1" <-> "OE2" Residue "A ARG 690": "NH1" <-> "NH2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A ARG 714": "NH1" <-> "NH2" Residue "A PHE 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 752": "OD1" <-> "OD2" Residue "B ARG 117": "NH1" <-> "NH2" Residue "B GLU 144": "OE1" <-> "OE2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ASP 156": "OD1" <-> "OD2" Residue "B GLU 195": "OE1" <-> "OE2" Residue "B ASP 198": "OD1" <-> "OD2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B ARG 226": "NH1" <-> "NH2" Residue "B ASP 229": "OD1" <-> "OD2" Residue "B GLU 285": "OE1" <-> "OE2" Residue "B TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 327": "NH1" <-> "NH2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "B TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 423": "OE1" <-> "OE2" Residue "B PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 618": "OD1" <-> "OD2" Residue "B TYR 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 687": "OE1" <-> "OE2" Residue "B ARG 690": "NH1" <-> "NH2" Residue "B GLU 702": "OE1" <-> "OE2" Residue "B ARG 714": "NH1" <-> "NH2" Residue "B PHE 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 752": "OD1" <-> "OD2" Residue "C ARG 117": "NH1" <-> "NH2" Residue "C GLU 144": "OE1" <-> "OE2" Residue "C ARG 148": "NH1" <-> "NH2" Residue "C ASP 156": "OD1" <-> "OD2" Residue "C GLU 195": "OE1" <-> "OE2" Residue "C ASP 198": "OD1" <-> "OD2" Residue "C ARG 225": "NH1" <-> "NH2" Residue "C ARG 226": "NH1" <-> "NH2" Residue "C ASP 229": "OD1" <-> "OD2" Residue "C GLU 285": "OE1" <-> "OE2" Residue "C TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 327": "NH1" <-> "NH2" Residue "C ARG 369": "NH1" <-> "NH2" Residue "C TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 423": "OE1" <-> "OE2" Residue "C PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 618": "OD1" <-> "OD2" Residue "C TYR 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 687": "OE1" <-> "OE2" Residue "C ARG 690": "NH1" <-> "NH2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C ARG 714": "NH1" <-> "NH2" Residue "C PHE 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 752": "OD1" <-> "OD2" Residue "D ARG 117": "NH1" <-> "NH2" Residue "D GLU 144": "OE1" <-> "OE2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D ASP 156": "OD1" <-> "OD2" Residue "D GLU 195": "OE1" <-> "OE2" Residue "D ASP 198": "OD1" <-> "OD2" Residue "D ARG 225": "NH1" <-> "NH2" Residue "D ARG 226": "NH1" <-> "NH2" Residue "D ASP 229": "OD1" <-> "OD2" Residue "D GLU 285": "OE1" <-> "OE2" Residue "D TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 327": "NH1" <-> "NH2" Residue "D ARG 369": "NH1" <-> "NH2" Residue "D TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 423": "OE1" <-> "OE2" Residue "D PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 618": "OD1" <-> "OD2" Residue "D TYR 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 687": "OE1" <-> "OE2" Residue "D ARG 690": "NH1" <-> "NH2" Residue "D GLU 702": "OE1" <-> "OE2" Residue "D ARG 714": "NH1" <-> "NH2" Residue "D PHE 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 752": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 20281 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4923 Classifications: {'peptide': 603} Link IDs: {'PTRANS': 12, 'TRANS': 590} Chain breaks: 4 Chain: "B" Number of atoms: 4923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4923 Classifications: {'peptide': 603} Link IDs: {'PTRANS': 12, 'TRANS': 590} Chain breaks: 4 Chain: "C" Number of atoms: 4923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4923 Classifications: {'peptide': 603} Link IDs: {'PTRANS': 12, 'TRANS': 590} Chain breaks: 4 Chain: "D" Number of atoms: 4923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4923 Classifications: {'peptide': 603} Link IDs: {'PTRANS': 12, 'TRANS': 590} Chain breaks: 4 Chain: "A" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 148 Unusual residues: {' NA': 1, '6OU': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 98 Planarities with less than four sites: {'6OU:plan-1': 4} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 147 Unusual residues: {'6OU': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 98 Planarities with less than four sites: {'6OU:plan-1': 4} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 147 Unusual residues: {'6OU': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 98 Planarities with less than four sites: {'6OU:plan-1': 4} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 147 Unusual residues: {'6OU': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 98 Planarities with less than four sites: {'6OU:plan-1': 4} Unresolved non-hydrogen planarities: 14 Time building chain proxies: 10.37, per 1000 atoms: 0.51 Number of scatterers: 20281 At special positions: 0 Unit cell: (130.9, 130.9, 127.6, 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 116 16.00 P 20 15.00 Na 1 11.00 O 3644 8.00 N 3280 7.00 C 13220 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.48 Conformation dependent library (CDL) restraints added in 2.6 seconds 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4600 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 108 helices and 4 sheets defined 56.1% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.53 Creating SS restraints... Processing helix chain 'A' and resid 119 through 129 removed outlier: 3.732A pdb=" N SER A 128 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 145 removed outlier: 3.755A pdb=" N GLU A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 162 Processing helix chain 'A' and resid 171 through 176 Processing helix chain 'A' and resid 183 through 195 Processing helix chain 'A' and resid 200 through 203 No H-bonds generated for 'chain 'A' and resid 200 through 203' Processing helix chain 'A' and resid 218 through 224 Processing helix chain 'A' and resid 228 through 237 Processing helix chain 'A' and resid 265 through 270 Processing helix chain 'A' and resid 275 through 283 Processing helix chain 'A' and resid 299 through 306 Processing helix chain 'A' and resid 316 through 328 Processing helix chain 'A' and resid 344 through 351 Processing helix chain 'A' and resid 354 through 361 removed outlier: 3.746A pdb=" N TYR A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 408 Processing helix chain 'A' and resid 416 through 418 No H-bonds generated for 'chain 'A' and resid 416 through 418' Processing helix chain 'A' and resid 423 through 435 removed outlier: 4.376A pdb=" N THR A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 461 Processing helix chain 'A' and resid 482 through 507 removed outlier: 4.189A pdb=" N LEU A 485 " --> pdb=" O LEU A 482 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLY A 486 " --> pdb=" O GLN A 483 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG A 487 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE A 492 " --> pdb=" O PHE A 489 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TRP A 493 " --> pdb=" O VAL A 490 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLU A 501 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N PHE A 506 " --> pdb=" O ILE A 503 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 507 " --> pdb=" O ALA A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 541 removed outlier: 3.975A pdb=" N VAL A 533 " --> pdb=" O GLN A 529 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 566 removed outlier: 3.568A pdb=" N LEU A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET A 562 " --> pdb=" O GLY A 558 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N LEU A 563 " --> pdb=" O TRP A 559 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N TYR A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N TYR A 565 " --> pdb=" O ASN A 561 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N THR A 566 " --> pdb=" O MET A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 585 removed outlier: 3.927A pdb=" N TYR A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 607 removed outlier: 3.861A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 636 removed outlier: 3.703A pdb=" N THR A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 665 Processing helix chain 'A' and resid 669 through 686 removed outlier: 3.745A pdb=" N ILE A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA A 675 " --> pdb=" O ASN A 671 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR A 680 " --> pdb=" O LEU A 676 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LYS A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 705 removed outlier: 3.590A pdb=" N ARG A 693 " --> pdb=" O GLU A 689 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG A 698 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR A 699 " --> pdb=" O GLN A 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 129 removed outlier: 3.731A pdb=" N SER B 128 " --> pdb=" O PHE B 124 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 145 removed outlier: 3.755A pdb=" N GLU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B 140 " --> pdb=" O VAL B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 162 Processing helix chain 'B' and resid 171 through 176 Processing helix chain 'B' and resid 183 through 195 Processing helix chain 'B' and resid 200 through 203 No H-bonds generated for 'chain 'B' and resid 200 through 203' Processing helix chain 'B' and resid 218 through 224 Processing helix chain 'B' and resid 228 through 237 Processing helix chain 'B' and resid 265 through 270 Processing helix chain 'B' and resid 275 through 283 Processing helix chain 'B' and resid 299 through 306 Processing helix chain 'B' and resid 316 through 328 Processing helix chain 'B' and resid 344 through 351 Processing helix chain 'B' and resid 354 through 361 removed outlier: 3.746A pdb=" N TYR B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 408 Processing helix chain 'B' and resid 416 through 418 No H-bonds generated for 'chain 'B' and resid 416 through 418' Processing helix chain 'B' and resid 423 through 435 removed outlier: 4.376A pdb=" N THR B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS B 432 " --> pdb=" O LEU B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 461 Processing helix chain 'B' and resid 482 through 507 removed outlier: 4.190A pdb=" N LEU B 485 " --> pdb=" O LEU B 482 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLY B 486 " --> pdb=" O GLN B 483 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG B 487 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE B 492 " --> pdb=" O PHE B 489 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TRP B 493 " --> pdb=" O VAL B 490 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLU B 501 " --> pdb=" O SER B 498 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N PHE B 506 " --> pdb=" O ILE B 503 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B 507 " --> pdb=" O ALA B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 541 removed outlier: 3.975A pdb=" N VAL B 533 " --> pdb=" O GLN B 529 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 566 removed outlier: 3.569A pdb=" N LEU B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET B 562 " --> pdb=" O GLY B 558 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N LEU B 563 " --> pdb=" O TRP B 559 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N TYR B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N TYR B 565 " --> pdb=" O ASN B 561 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N THR B 566 " --> pdb=" O MET B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 585 removed outlier: 3.927A pdb=" N TYR B 575 " --> pdb=" O SER B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 607 removed outlier: 3.860A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL B 603 " --> pdb=" O LEU B 599 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 634 Processing helix chain 'B' and resid 651 through 665 Processing helix chain 'B' and resid 669 through 686 removed outlier: 3.745A pdb=" N ILE B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA B 675 " --> pdb=" O ASN B 671 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU B 679 " --> pdb=" O ALA B 675 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR B 680 " --> pdb=" O LEU B 676 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LYS B 686 " --> pdb=" O GLU B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 705 removed outlier: 3.590A pdb=" N ARG B 693 " --> pdb=" O GLU B 689 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG B 698 " --> pdb=" O LEU B 694 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N THR B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 129 removed outlier: 3.732A pdb=" N SER C 128 " --> pdb=" O PHE C 124 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 145 removed outlier: 3.755A pdb=" N GLU C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL C 140 " --> pdb=" O VAL C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 162 Processing helix chain 'C' and resid 171 through 176 Processing helix chain 'C' and resid 183 through 195 Processing helix chain 'C' and resid 200 through 203 No H-bonds generated for 'chain 'C' and resid 200 through 203' Processing helix chain 'C' and resid 218 through 224 Processing helix chain 'C' and resid 228 through 237 Processing helix chain 'C' and resid 265 through 270 Processing helix chain 'C' and resid 275 through 283 Processing helix chain 'C' and resid 299 through 306 Processing helix chain 'C' and resid 316 through 328 Processing helix chain 'C' and resid 344 through 351 Processing helix chain 'C' and resid 354 through 361 removed outlier: 3.746A pdb=" N TYR C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 408 Processing helix chain 'C' and resid 416 through 418 No H-bonds generated for 'chain 'C' and resid 416 through 418' Processing helix chain 'C' and resid 423 through 435 removed outlier: 4.375A pdb=" N THR C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS C 432 " --> pdb=" O LEU C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 461 Processing helix chain 'C' and resid 482 through 507 removed outlier: 4.190A pdb=" N LEU C 485 " --> pdb=" O LEU C 482 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLY C 486 " --> pdb=" O GLN C 483 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG C 487 " --> pdb=" O LEU C 484 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ILE C 492 " --> pdb=" O PHE C 489 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TRP C 493 " --> pdb=" O VAL C 490 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLU C 501 " --> pdb=" O SER C 498 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N PHE C 506 " --> pdb=" O ILE C 503 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU C 507 " --> pdb=" O ALA C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 541 removed outlier: 3.975A pdb=" N VAL C 533 " --> pdb=" O GLN C 529 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE C 534 " --> pdb=" O ALA C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 566 removed outlier: 3.568A pdb=" N LEU C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET C 562 " --> pdb=" O GLY C 558 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N LEU C 563 " --> pdb=" O TRP C 559 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N TYR C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N TYR C 565 " --> pdb=" O ASN C 561 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N THR C 566 " --> pdb=" O MET C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 585 removed outlier: 3.927A pdb=" N TYR C 575 " --> pdb=" O SER C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 607 removed outlier: 3.862A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL C 603 " --> pdb=" O LEU C 599 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 634 Processing helix chain 'C' and resid 651 through 665 Processing helix chain 'C' and resid 669 through 686 removed outlier: 3.745A pdb=" N ILE C 674 " --> pdb=" O LEU C 670 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA C 675 " --> pdb=" O ASN C 671 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU C 679 " --> pdb=" O ALA C 675 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR C 680 " --> pdb=" O LEU C 676 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LYS C 686 " --> pdb=" O GLU C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 705 removed outlier: 3.590A pdb=" N ARG C 693 " --> pdb=" O GLU C 689 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG C 698 " --> pdb=" O LEU C 694 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR C 699 " --> pdb=" O GLN C 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 129 removed outlier: 3.731A pdb=" N SER D 128 " --> pdb=" O PHE D 124 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU D 129 " --> pdb=" O ALA D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 145 removed outlier: 3.755A pdb=" N GLU D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL D 140 " --> pdb=" O VAL D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 162 Processing helix chain 'D' and resid 171 through 176 Processing helix chain 'D' and resid 183 through 195 Processing helix chain 'D' and resid 200 through 203 No H-bonds generated for 'chain 'D' and resid 200 through 203' Processing helix chain 'D' and resid 218 through 224 Processing helix chain 'D' and resid 228 through 237 Processing helix chain 'D' and resid 265 through 270 Processing helix chain 'D' and resid 275 through 283 Processing helix chain 'D' and resid 299 through 306 Processing helix chain 'D' and resid 316 through 328 Processing helix chain 'D' and resid 344 through 351 Processing helix chain 'D' and resid 354 through 361 removed outlier: 3.746A pdb=" N TYR D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 408 Processing helix chain 'D' and resid 416 through 418 No H-bonds generated for 'chain 'D' and resid 416 through 418' Processing helix chain 'D' and resid 423 through 435 removed outlier: 4.376A pdb=" N THR D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS D 432 " --> pdb=" O LEU D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 461 Processing helix chain 'D' and resid 482 through 507 removed outlier: 4.189A pdb=" N LEU D 485 " --> pdb=" O LEU D 482 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLY D 486 " --> pdb=" O GLN D 483 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG D 487 " --> pdb=" O LEU D 484 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE D 492 " --> pdb=" O PHE D 489 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TRP D 493 " --> pdb=" O VAL D 490 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLU D 501 " --> pdb=" O SER D 498 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N PHE D 506 " --> pdb=" O ILE D 503 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU D 507 " --> pdb=" O ALA D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 541 removed outlier: 3.974A pdb=" N VAL D 533 " --> pdb=" O GLN D 529 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE D 534 " --> pdb=" O ALA D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 566 removed outlier: 3.568A pdb=" N LEU D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET D 562 " --> pdb=" O GLY D 558 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU D 563 " --> pdb=" O TRP D 559 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N TYR D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N TYR D 565 " --> pdb=" O ASN D 561 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N THR D 566 " --> pdb=" O MET D 562 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 585 removed outlier: 3.927A pdb=" N TYR D 575 " --> pdb=" O SER D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 607 removed outlier: 3.861A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL D 603 " --> pdb=" O LEU D 599 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 636 removed outlier: 3.703A pdb=" N THR D 636 " --> pdb=" O LEU D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 651 through 665 Processing helix chain 'D' and resid 669 through 686 removed outlier: 3.745A pdb=" N ILE D 674 " --> pdb=" O LEU D 670 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA D 675 " --> pdb=" O ASN D 671 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU D 679 " --> pdb=" O ALA D 675 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR D 680 " --> pdb=" O LEU D 676 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LYS D 686 " --> pdb=" O GLU D 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 705 removed outlier: 3.591A pdb=" N ARG D 693 " --> pdb=" O GLU D 689 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG D 698 " --> pdb=" O LEU D 694 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N THR D 699 " --> pdb=" O GLN D 695 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 733 through 737 removed outlier: 3.686A pdb=" N TRP A 380 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU A 389 " --> pdb=" O THR A 378 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N THR A 378 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 733 through 737 removed outlier: 3.685A pdb=" N TRP B 380 " --> pdb=" O SER B 387 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU B 389 " --> pdb=" O THR B 378 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N THR B 378 " --> pdb=" O LEU B 389 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 733 through 737 removed outlier: 3.687A pdb=" N TRP C 380 " --> pdb=" O SER C 387 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU C 389 " --> pdb=" O THR C 378 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N THR C 378 " --> pdb=" O LEU C 389 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 733 through 737 removed outlier: 3.685A pdb=" N TRP D 380 " --> pdb=" O SER D 387 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU D 389 " --> pdb=" O THR D 378 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N THR D 378 " --> pdb=" O LEU D 389 " (cutoff:3.500A) 810 hydrogen bonds defined for protein. 2238 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: 5.35 Time building geometry restraints manager: 8.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6016 1.34 - 1.45: 3359 1.45 - 1.57: 10725 1.57 - 1.69: 344 1.69 - 1.81: 236 Bond restraints: 20680 Sorted by residual: bond pdb=" C16 6OU D 803 " pdb=" O18 6OU D 803 " ideal model delta sigma weight residual 1.327 1.468 -0.141 2.00e-02 2.50e+03 4.98e+01 bond pdb=" C16 6OU B 803 " pdb=" O18 6OU B 803 " ideal model delta sigma weight residual 1.327 1.468 -0.141 2.00e-02 2.50e+03 4.96e+01 bond pdb=" C16 6OU C 803 " pdb=" O18 6OU C 803 " ideal model delta sigma weight residual 1.327 1.468 -0.141 2.00e-02 2.50e+03 4.96e+01 bond pdb=" C16 6OU A 803 " pdb=" O18 6OU A 803 " ideal model delta sigma weight residual 1.327 1.468 -0.141 2.00e-02 2.50e+03 4.95e+01 bond pdb=" C16 6OU C 802 " pdb=" O18 6OU C 802 " ideal model delta sigma weight residual 1.327 1.467 -0.140 2.00e-02 2.50e+03 4.91e+01 ... (remaining 20675 not shown) Histogram of bond angle deviations from ideal: 96.92 - 104.36: 204 104.36 - 111.80: 9539 111.80 - 119.24: 7456 119.24 - 126.68: 10336 126.68 - 134.12: 309 Bond angle restraints: 27844 Sorted by residual: angle pdb=" C HIS A 150 " pdb=" N ASP A 151 " pdb=" CA ASP A 151 " ideal model delta sigma weight residual 121.54 132.17 -10.63 1.91e+00 2.74e-01 3.10e+01 angle pdb=" C HIS B 150 " pdb=" N ASP B 151 " pdb=" CA ASP B 151 " ideal model delta sigma weight residual 121.54 132.16 -10.62 1.91e+00 2.74e-01 3.09e+01 angle pdb=" C HIS C 150 " pdb=" N ASP C 151 " pdb=" CA ASP C 151 " ideal model delta sigma weight residual 121.54 132.13 -10.59 1.91e+00 2.74e-01 3.08e+01 angle pdb=" C HIS D 150 " pdb=" N ASP D 151 " pdb=" CA ASP D 151 " ideal model delta sigma weight residual 121.54 132.11 -10.57 1.91e+00 2.74e-01 3.06e+01 angle pdb=" O22 6OU D 804 " pdb=" P23 6OU D 804 " pdb=" O26 6OU D 804 " ideal model delta sigma weight residual 93.95 109.95 -16.00 3.00e+00 1.11e-01 2.85e+01 ... (remaining 27839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.32: 11692 29.32 - 58.65: 484 58.65 - 87.97: 40 87.97 - 117.29: 4 117.29 - 146.62: 20 Dihedral angle restraints: 12240 sinusoidal: 5156 harmonic: 7084 Sorted by residual: dihedral pdb=" CA GLY C 718 " pdb=" C GLY C 718 " pdb=" N GLU C 719 " pdb=" CA GLU C 719 " ideal model delta harmonic sigma weight residual -180.00 -156.48 -23.52 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA GLY A 718 " pdb=" C GLY A 718 " pdb=" N GLU A 719 " pdb=" CA GLU A 719 " ideal model delta harmonic sigma weight residual 180.00 -156.49 -23.51 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA GLY D 718 " pdb=" C GLY D 718 " pdb=" N GLU D 719 " pdb=" CA GLU D 719 " ideal model delta harmonic sigma weight residual -180.00 -156.50 -23.50 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 12237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 3020 0.123 - 0.246: 68 0.246 - 0.369: 4 0.369 - 0.491: 4 0.491 - 0.614: 16 Chirality restraints: 3112 Sorted by residual: chirality pdb=" C20 6OU C 801 " pdb=" C19 6OU C 801 " pdb=" C21 6OU C 801 " pdb=" O30 6OU C 801 " both_signs ideal model delta sigma weight residual False 2.35 2.96 -0.61 2.00e-01 2.50e+01 9.43e+00 chirality pdb=" C20 6OU B 801 " pdb=" C19 6OU B 801 " pdb=" C21 6OU B 801 " pdb=" O30 6OU B 801 " both_signs ideal model delta sigma weight residual False 2.35 2.96 -0.61 2.00e-01 2.50e+01 9.42e+00 chirality pdb=" C20 6OU D 801 " pdb=" C19 6OU D 801 " pdb=" C21 6OU D 801 " pdb=" O30 6OU D 801 " both_signs ideal model delta sigma weight residual False 2.35 2.96 -0.61 2.00e-01 2.50e+01 9.39e+00 ... (remaining 3109 not shown) Planarity restraints: 3416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 343 " 0.037 5.00e-02 4.00e+02 5.51e-02 4.85e+00 pdb=" N PRO D 344 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO D 344 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 344 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 343 " -0.037 5.00e-02 4.00e+02 5.50e-02 4.83e+00 pdb=" N PRO B 344 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 344 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 344 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 343 " -0.037 5.00e-02 4.00e+02 5.49e-02 4.82e+00 pdb=" N PRO A 344 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 344 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 344 " -0.031 5.00e-02 4.00e+02 ... (remaining 3413 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 5735 2.80 - 3.33: 17839 3.33 - 3.85: 32702 3.85 - 4.38: 38020 4.38 - 4.90: 66387 Nonbonded interactions: 160683 Sorted by model distance: nonbonded pdb=" OD1 ASN B 180 " pdb=" OG1 THR B 183 " model vdw 2.280 2.440 nonbonded pdb=" OD1 ASN D 180 " pdb=" OG1 THR D 183 " model vdw 2.280 2.440 nonbonded pdb=" OD1 ASN C 180 " pdb=" OG1 THR C 183 " model vdw 2.280 2.440 nonbonded pdb=" OD1 ASN A 180 " pdb=" OG1 THR A 183 " model vdw 2.280 2.440 nonbonded pdb=" OH TYR B 650 " pdb=" O LYS C 545 " model vdw 2.290 2.440 ... (remaining 160678 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 117 through 755 or resid 801 through 805)) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 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: 5.600 Check model and map are aligned: 0.300 Set scattering table: 0.190 Process input model: 48.430 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.010 Internal consistency checks: 0.000 Total: 59.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 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 : 0.015 0.141 20680 Z= 0.939 Angle : 1.184 16.004 27844 Z= 0.543 Chirality : 0.066 0.614 3112 Planarity : 0.006 0.055 3416 Dihedral : 17.291 146.618 7640 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer Outliers : 0.00 % 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: -4.45 (0.12), residues: 2372 helix: -2.70 (0.09), residues: 1504 sheet: -2.43 (0.49), residues: 64 loop : -3.18 (0.17), residues: 804 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 241 time to evaluate : 2.381 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.3577 time to fit residues: 128.6403 Evaluate side-chains 177 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 2.253 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 0.0980 chunk 181 optimal weight: 0.0980 chunk 100 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 188 optimal weight: 9.9990 chunk 72 optimal weight: 0.0470 chunk 114 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 217 optimal weight: 6.9990 overall best weight: 1.6482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 ASN A 646 GLN ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 ASN B 646 GLN C 143 GLN ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 561 ASN C 646 GLN D 143 GLN ** D 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 561 ASN D 646 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 20680 Z= 0.185 Angle : 0.530 8.070 27844 Z= 0.274 Chirality : 0.037 0.157 3112 Planarity : 0.004 0.033 3416 Dihedral : 13.879 112.743 2920 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer Outliers : 1.36 % 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: -2.18 (0.15), residues: 2372 helix: -0.67 (0.12), residues: 1468 sheet: -2.33 (0.51), residues: 64 loop : -2.69 (0.19), residues: 840 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 209 time to evaluate : 2.280 Fit side-chains outliers start: 29 outliers final: 19 residues processed: 227 average time/residue: 0.2944 time to fit residues: 106.1929 Evaluate side-chains 197 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 178 time to evaluate : 2.102 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1736 time to fit residues: 9.2127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 181 optimal weight: 0.7980 chunk 148 optimal weight: 0.6980 chunk 60 optimal weight: 10.0000 chunk 218 optimal weight: 8.9990 chunk 235 optimal weight: 0.8980 chunk 194 optimal weight: 8.9990 chunk 216 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 chunk 175 optimal weight: 2.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 20680 Z= 0.217 Angle : 0.541 8.268 27844 Z= 0.277 Chirality : 0.038 0.161 3112 Planarity : 0.003 0.035 3416 Dihedral : 12.689 112.229 2920 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer Outliers : 0.56 % 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: -1.51 (0.16), residues: 2372 helix: -0.12 (0.13), residues: 1512 sheet: -2.14 (0.54), residues: 64 loop : -2.56 (0.20), residues: 796 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 192 time to evaluate : 2.255 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 200 average time/residue: 0.3152 time to fit residues: 99.4847 Evaluate side-chains 186 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 180 time to evaluate : 2.271 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2079 time to fit residues: 5.3430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 0.9990 chunk 164 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 219 optimal weight: 6.9990 chunk 231 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 207 optimal weight: 0.0070 chunk 62 optimal weight: 5.9990 overall best weight: 1.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 20680 Z= 0.148 Angle : 0.501 8.200 27844 Z= 0.254 Chirality : 0.036 0.153 3112 Planarity : 0.003 0.025 3416 Dihedral : 11.605 109.235 2920 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer Outliers : 0.19 % 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: -0.92 (0.17), residues: 2372 helix: 0.47 (0.13), residues: 1488 sheet: -2.00 (0.56), residues: 64 loop : -2.53 (0.20), residues: 820 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 189 time to evaluate : 2.379 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 192 average time/residue: 0.3032 time to fit residues: 94.1134 Evaluate side-chains 181 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 178 time to evaluate : 2.503 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1861 time to fit residues: 4.4153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 3 optimal weight: 20.0000 chunk 172 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 chunk 197 optimal weight: 8.9990 chunk 160 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 0.9990 chunk 208 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 GLN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 GLN ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 313 GLN ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 GLN ** D 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 20680 Z= 0.340 Angle : 0.609 8.614 27844 Z= 0.308 Chirality : 0.041 0.172 3112 Planarity : 0.003 0.025 3416 Dihedral : 11.934 110.232 2920 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer Outliers : 1.31 % 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: -1.01 (0.17), residues: 2372 helix: 0.27 (0.13), residues: 1532 sheet: -1.93 (0.59), residues: 64 loop : -2.42 (0.21), residues: 776 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 180 time to evaluate : 2.346 Fit side-chains outliers start: 28 outliers final: 19 residues processed: 197 average time/residue: 0.3040 time to fit residues: 96.3554 Evaluate side-chains 192 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 173 time to evaluate : 2.342 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1816 time to fit residues: 9.7627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 232 optimal weight: 0.7980 chunk 192 optimal weight: 9.9990 chunk 107 optimal weight: 0.0870 chunk 19 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 20680 Z= 0.138 Angle : 0.512 8.071 27844 Z= 0.258 Chirality : 0.036 0.151 3112 Planarity : 0.003 0.024 3416 Dihedral : 10.886 106.205 2920 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer Outliers : 0.52 % 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: -0.51 (0.17), residues: 2372 helix: 0.79 (0.13), residues: 1476 sheet: -1.70 (0.62), residues: 64 loop : -2.34 (0.20), residues: 832 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 178 time to evaluate : 2.236 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 184 average time/residue: 0.3132 time to fit residues: 92.7569 Evaluate side-chains 184 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 177 time to evaluate : 2.349 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1844 time to fit residues: 5.6376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 132 optimal weight: 9.9990 chunk 169 optimal weight: 6.9990 chunk 131 optimal weight: 0.9990 chunk 195 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 231 optimal weight: 0.9990 chunk 144 optimal weight: 0.9980 chunk 141 optimal weight: 8.9990 chunk 106 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 20680 Z= 0.137 Angle : 0.506 8.325 27844 Z= 0.254 Chirality : 0.036 0.151 3112 Planarity : 0.003 0.023 3416 Dihedral : 10.623 108.186 2920 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer Outliers : 0.61 % 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: -0.28 (0.17), residues: 2372 helix: 0.99 (0.14), residues: 1476 sheet: -1.73 (0.65), residues: 64 loop : -2.28 (0.20), residues: 832 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 178 time to evaluate : 2.429 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 3 residues processed: 186 average time/residue: 0.2982 time to fit residues: 90.1969 Evaluate side-chains 177 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 174 time to evaluate : 2.305 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1735 time to fit residues: 4.0953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 138 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 chunk 157 optimal weight: 0.0020 chunk 114 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 181 optimal weight: 9.9990 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 20680 Z= 0.148 Angle : 0.515 8.581 27844 Z= 0.256 Chirality : 0.036 0.152 3112 Planarity : 0.003 0.024 3416 Dihedral : 10.368 104.800 2920 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer Outliers : 0.19 % 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: -0.16 (0.17), residues: 2372 helix: 1.08 (0.14), residues: 1476 sheet: -1.68 (0.65), residues: 64 loop : -2.21 (0.21), residues: 832 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 178 time to evaluate : 2.240 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 182 average time/residue: 0.2914 time to fit residues: 85.7195 Evaluate side-chains 167 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 2.151 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 4.9990 chunk 221 optimal weight: 2.9990 chunk 202 optimal weight: 0.8980 chunk 215 optimal weight: 7.9990 chunk 129 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 169 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 194 optimal weight: 0.0980 chunk 203 optimal weight: 5.9990 chunk 214 optimal weight: 0.9980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 20680 Z= 0.181 Angle : 0.532 9.019 27844 Z= 0.264 Chirality : 0.037 0.155 3112 Planarity : 0.003 0.023 3416 Dihedral : 10.229 99.952 2920 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer Outliers : 0.09 % 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: -0.16 (0.17), residues: 2372 helix: 1.08 (0.13), residues: 1476 sheet: -1.71 (0.66), residues: 64 loop : -2.20 (0.21), residues: 832 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 173 time to evaluate : 2.362 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 174 average time/residue: 0.2997 time to fit residues: 84.6559 Evaluate side-chains 171 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 170 time to evaluate : 2.379 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2129 time to fit residues: 3.5416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 8.9990 chunk 227 optimal weight: 10.0000 chunk 139 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 158 optimal weight: 0.9990 chunk 239 optimal weight: 9.9990 chunk 220 optimal weight: 6.9990 chunk 190 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 20680 Z= 0.228 Angle : 0.560 8.898 27844 Z= 0.278 Chirality : 0.038 0.159 3112 Planarity : 0.003 0.023 3416 Dihedral : 10.360 94.867 2920 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.17), residues: 2372 helix: 0.96 (0.13), residues: 1480 sheet: -1.80 (0.67), residues: 64 loop : -2.23 (0.21), residues: 828 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 168 time to evaluate : 2.376 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 173 average time/residue: 0.2966 time to fit residues: 83.2952 Evaluate side-chains 168 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 2.342 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 1.9990 chunk 202 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 175 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 52 optimal weight: 0.0030 chunk 190 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 195 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 313 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.112082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.087685 restraints weight = 38055.144| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.28 r_work: 0.3067 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 20680 Z= 0.130 Angle : 0.506 8.202 27844 Z= 0.252 Chirality : 0.036 0.151 3112 Planarity : 0.003 0.023 3416 Dihedral : 9.426 91.665 2920 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer Outliers : 0.14 % 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: -0.02 (0.18), residues: 2372 helix: 1.22 (0.14), residues: 1476 sheet: -1.76 (0.67), residues: 64 loop : -2.18 (0.21), residues: 832 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3361.86 seconds wall clock time: 62 minutes 24.99 seconds (3744.99 seconds total)