Starting phenix.real_space_refine on Sun Jun 30 20:23:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v6n_42997/06_2024/8v6n_42997_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v6n_42997/06_2024/8v6n_42997.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v6n_42997/06_2024/8v6n_42997.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v6n_42997/06_2024/8v6n_42997.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v6n_42997/06_2024/8v6n_42997_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v6n_42997/06_2024/8v6n_42997_updated.pdb" } resolution = 2.59 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= 0.003 sd= 0.074 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 20 5.49 5 S 132 5.16 5 Na 1 4.78 5 B 8 2.79 5 C 14500 2.51 5 N 3460 2.21 5 O 4064 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 73": "NH1" <-> "NH2" Residue "A ARG 122": "NH1" <-> "NH2" Residue "A ARG 148": "NH1" <-> "NH2" Residue "A ARG 188": "NH1" <-> "NH2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A ARG 226": "NH1" <-> "NH2" Residue "A PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 292": "NH1" <-> "NH2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 327": "NH1" <-> "NH2" Residue "A ARG 337": "NH1" <-> "NH2" Residue "A ARG 416": "NH1" <-> "NH2" Residue "A ARG 462": "NH1" <-> "NH2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ARG 690": "NH1" <-> "NH2" Residue "A ARG 716": "NH1" <-> "NH2" Residue "A ARG 729": "NH1" <-> "NH2" Residue "A ARG 733": "NH1" <-> "NH2" Residue "B ARG 73": "NH1" <-> "NH2" Residue "B ARG 122": "NH1" <-> "NH2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 188": "NH1" <-> "NH2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B ARG 226": "NH1" <-> "NH2" Residue "B PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 292": "NH1" <-> "NH2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B ARG 327": "NH1" <-> "NH2" Residue "B ARG 337": "NH1" <-> "NH2" Residue "B ARG 416": "NH1" <-> "NH2" Residue "B ARG 462": "NH1" <-> "NH2" Residue "B ARG 464": "NH1" <-> "NH2" Residue "B ARG 567": "NH1" <-> "NH2" Residue "B ARG 690": "NH1" <-> "NH2" Residue "B ARG 716": "NH1" <-> "NH2" Residue "B ARG 729": "NH1" <-> "NH2" Residue "B ARG 733": "NH1" <-> "NH2" Residue "C ARG 73": "NH1" <-> "NH2" Residue "C ARG 122": "NH1" <-> "NH2" Residue "C ARG 148": "NH1" <-> "NH2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "C ARG 225": "NH1" <-> "NH2" Residue "C ARG 226": "NH1" <-> "NH2" Residue "C PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 292": "NH1" <-> "NH2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C ARG 327": "NH1" <-> "NH2" Residue "C ARG 337": "NH1" <-> "NH2" Residue "C ARG 416": "NH1" <-> "NH2" Residue "C ARG 462": "NH1" <-> "NH2" Residue "C ARG 464": "NH1" <-> "NH2" Residue "C ARG 567": "NH1" <-> "NH2" Residue "C ARG 690": "NH1" <-> "NH2" Residue "C ARG 716": "NH1" <-> "NH2" Residue "C ARG 729": "NH1" <-> "NH2" Residue "C ARG 733": "NH1" <-> "NH2" Residue "D ARG 73": "NH1" <-> "NH2" Residue "D ARG 122": "NH1" <-> "NH2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D ARG 188": "NH1" <-> "NH2" Residue "D ARG 225": "NH1" <-> "NH2" Residue "D ARG 226": "NH1" <-> "NH2" Residue "D PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 292": "NH1" <-> "NH2" Residue "D ARG 319": "NH1" <-> "NH2" Residue "D ARG 327": "NH1" <-> "NH2" Residue "D ARG 337": "NH1" <-> "NH2" Residue "D ARG 416": "NH1" <-> "NH2" Residue "D ARG 462": "NH1" <-> "NH2" Residue "D ARG 464": "NH1" <-> "NH2" Residue "D ARG 567": "NH1" <-> "NH2" Residue "D ARG 690": "NH1" <-> "NH2" Residue "D ARG 716": "NH1" <-> "NH2" Residue "D ARG 729": "NH1" <-> "NH2" Residue "D ARG 733": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 22185 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5184 Classifications: {'peptide': 636} Link IDs: {'PTRANS': 14, 'TRANS': 621} Chain breaks: 2 Chain: "B" Number of atoms: 5184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5184 Classifications: {'peptide': 636} Link IDs: {'PTRANS': 14, 'TRANS': 621} Chain breaks: 2 Chain: "C" Number of atoms: 5184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5184 Classifications: {'peptide': 636} Link IDs: {'PTRANS': 14, 'TRANS': 621} Chain breaks: 2 Chain: "D" Number of atoms: 5184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5184 Classifications: {'peptide': 636} Link IDs: {'PTRANS': 14, 'TRANS': 621} Chain breaks: 2 Chain: "A" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 369 Unusual residues: {' NA': 1, 'ACD': 1, 'FZ4': 2, 'POV': 6} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 316 Unusual residues: {'ACD': 1, 'FZ4': 2, 'POV': 5} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 316 Unusual residues: {'ACD': 1, 'FZ4': 2, 'POV': 5} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 264 Unusual residues: {'ACD': 1, 'FZ4': 2, 'POV': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Time building chain proxies: 11.89, per 1000 atoms: 0.54 Number of scatterers: 22185 At special positions: 0 Unit cell: (152.8, 152.8, 125.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 132 16.00 P 20 15.00 Na 1 11.00 O 4064 8.00 N 3460 7.00 C 14500 6.00 B 8 5.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 619 " distance=2.03 Simple disulfide: pdb=" SG CYS A 721 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B 612 " - pdb=" SG CYS B 619 " distance=2.03 Simple disulfide: pdb=" SG CYS B 721 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 619 " distance=2.03 Simple disulfide: pdb=" SG CYS C 721 " - pdb=" SG CYS C 731 " distance=2.03 Simple disulfide: pdb=" SG CYS D 612 " - pdb=" SG CYS D 619 " distance=2.03 Simple disulfide: pdb=" SG CYS D 721 " - pdb=" SG CYS D 731 " 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: 7.59 Conformation dependent library (CDL) restraints added in 3.6 seconds 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4872 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 120 helices and 4 sheets defined 53.7% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.07 Creating SS restraints... Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.802A pdb=" N ILE A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 143 removed outlier: 3.639A pdb=" N GLU A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU A 141 " --> pdb=" O GLU A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 160 removed outlier: 4.048A pdb=" N MET A 159 " --> pdb=" O PRO A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 177 Processing helix chain 'A' and resid 184 through 196 removed outlier: 3.621A pdb=" N ILE A 189 " --> pdb=" O GLU A 185 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) 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 removed outlier: 3.640A pdb=" N GLU A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 235 Processing helix chain 'A' and resid 265 through 271 Processing helix chain 'A' and resid 275 through 282 Processing helix chain 'A' and resid 299 through 305 removed outlier: 3.726A pdb=" N LEU A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 328 Processing helix chain 'A' and resid 344 through 351 removed outlier: 3.537A pdb=" N ALA A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) 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 removed outlier: 3.503A pdb=" N VAL A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 419 No H-bonds generated for 'chain 'A' and resid 416 through 419' Processing helix chain 'A' and resid 425 through 433 removed outlier: 3.733A pdb=" N TRP A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 459 removed outlier: 3.560A pdb=" N TYR A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 506 removed outlier: 3.829A pdb=" N MET A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A 504 " --> pdb=" O LYS A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 541 removed outlier: 3.894A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE A 538 " --> pdb=" O ILE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 566 removed outlier: 4.041A pdb=" N LEU A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N MET A 562 " --> pdb=" O GLY A 558 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N LEU A 563 " --> pdb=" O TRP A 559 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N TYR A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N TYR A 565 " --> pdb=" O ASN A 561 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N THR A 566 " --> pdb=" O MET A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 585 Processing helix chain 'A' and resid 588 through 608 removed outlier: 4.371A pdb=" N PHE A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE A 597 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 637 removed outlier: 3.822A pdb=" N LEU A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 665 Processing helix chain 'A' and resid 669 through 686 removed outlier: 3.547A pdb=" N THR A 680 " --> pdb=" O LEU A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 705 removed outlier: 3.899A pdb=" N TRP A 692 " --> pdb=" O SER A 688 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ARG A 693 " --> pdb=" O GLU A 689 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 694 " --> pdb=" O ARG A 690 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA A 697 " --> pdb=" O ARG A 693 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG A 698 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 714 removed outlier: 3.806A pdb=" N ARG A 714 " --> pdb=" O TRP A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 749 removed outlier: 3.554A pdb=" N HIS A 745 " --> pdb=" O GLU A 741 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER A 747 " --> pdb=" O LYS A 743 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE A 748 " --> pdb=" O THR A 744 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU A 749 " --> pdb=" O HIS A 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.801A pdb=" N ILE B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 143 removed outlier: 3.639A pdb=" N GLU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU B 141 " --> pdb=" O GLU B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 160 removed outlier: 4.048A pdb=" N MET B 159 " --> pdb=" O PRO B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 177 Processing helix chain 'B' and resid 184 through 196 removed outlier: 3.621A pdb=" N ILE B 189 " --> pdb=" O GLU B 185 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU B 195 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) 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 removed outlier: 3.638A pdb=" N GLU B 224 " --> pdb=" O ASN B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 235 Processing helix chain 'B' and resid 265 through 271 Processing helix chain 'B' and resid 275 through 282 Processing helix chain 'B' and resid 299 through 305 removed outlier: 3.726A pdb=" N LEU B 303 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 328 Processing helix chain 'B' and resid 344 through 351 removed outlier: 3.537A pdb=" N ALA B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) 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 removed outlier: 3.503A pdb=" N VAL B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 419 No H-bonds generated for 'chain 'B' and resid 416 through 419' Processing helix chain 'B' and resid 425 through 433 removed outlier: 3.733A pdb=" N TRP B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 459 removed outlier: 3.558A pdb=" N TYR B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 506 removed outlier: 3.829A pdb=" N MET B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA B 504 " --> pdb=" O LYS B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 541 removed outlier: 3.894A pdb=" N PHE B 527 " --> pdb=" O HIS B 523 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE B 538 " --> pdb=" O ILE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 566 removed outlier: 4.041A pdb=" N LEU B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N MET B 562 " --> pdb=" O GLY B 558 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N LEU B 563 " --> pdb=" O TRP B 559 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N TYR B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N TYR B 565 " --> pdb=" O ASN B 561 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N THR B 566 " --> pdb=" O MET B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 585 Processing helix chain 'B' and resid 588 through 608 removed outlier: 4.371A pdb=" N PHE B 592 " --> pdb=" O LEU B 588 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE B 597 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B 603 " --> pdb=" O LEU B 599 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU B 608 " --> pdb=" O ALA B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 637 removed outlier: 3.822A pdb=" N LEU B 630 " --> pdb=" O SER B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 665 Processing helix chain 'B' and resid 669 through 686 removed outlier: 3.547A pdb=" N THR B 680 " --> pdb=" O LEU B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 705 removed outlier: 3.899A pdb=" N TRP B 692 " --> pdb=" O SER B 688 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG B 693 " --> pdb=" O GLU B 689 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU B 694 " --> pdb=" O ARG B 690 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA B 697 " --> pdb=" O ARG B 693 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG B 698 " --> pdb=" O LEU B 694 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU B 701 " --> pdb=" O ALA B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 714 removed outlier: 3.805A pdb=" N ARG B 714 " --> pdb=" O TRP B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 747 removed outlier: 3.554A pdb=" N HIS B 745 " --> pdb=" O GLU B 741 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER B 747 " --> pdb=" O LYS B 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.801A pdb=" N ILE C 123 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE C 124 " --> pdb=" O LYS C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 143 removed outlier: 3.639A pdb=" N GLU C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU C 141 " --> pdb=" O GLU C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 160 removed outlier: 4.048A pdb=" N MET C 159 " --> pdb=" O PRO C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 177 Processing helix chain 'C' and resid 184 through 196 removed outlier: 3.621A pdb=" N ILE C 189 " --> pdb=" O GLU C 185 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU C 195 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) 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 removed outlier: 3.639A pdb=" N GLU C 224 " --> pdb=" O ASN C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 235 Processing helix chain 'C' and resid 265 through 271 Processing helix chain 'C' and resid 275 through 282 Processing helix chain 'C' and resid 299 through 305 removed outlier: 3.725A pdb=" N LEU C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 328 Processing helix chain 'C' and resid 344 through 351 removed outlier: 3.537A pdb=" N ALA C 349 " --> pdb=" O LEU C 345 " (cutoff:3.500A) 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 removed outlier: 3.503A pdb=" N VAL C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 419 No H-bonds generated for 'chain 'C' and resid 416 through 419' Processing helix chain 'C' and resid 425 through 433 removed outlier: 3.733A pdb=" N TRP C 433 " --> pdb=" O LEU C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 459 removed outlier: 3.559A pdb=" N TYR C 448 " --> pdb=" O SER C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 506 removed outlier: 3.828A pdb=" N MET C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA C 504 " --> pdb=" O LYS C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 541 removed outlier: 3.894A pdb=" N PHE C 527 " --> pdb=" O HIS C 523 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE C 538 " --> pdb=" O ILE C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 566 removed outlier: 4.041A pdb=" N LEU C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N MET C 562 " --> pdb=" O GLY C 558 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N LEU C 563 " --> pdb=" O TRP C 559 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N TYR C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N TYR C 565 " --> pdb=" O ASN C 561 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N THR C 566 " --> pdb=" O MET C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 585 Processing helix chain 'C' and resid 588 through 608 removed outlier: 4.371A pdb=" N PHE C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE C 597 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL C 603 " --> pdb=" O LEU C 599 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU C 608 " --> pdb=" O ALA C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 637 removed outlier: 3.823A pdb=" N LEU C 630 " --> pdb=" O SER C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 665 Processing helix chain 'C' and resid 669 through 686 removed outlier: 3.547A pdb=" N THR C 680 " --> pdb=" O LEU C 676 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 705 removed outlier: 3.899A pdb=" N TRP C 692 " --> pdb=" O SER C 688 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG C 693 " --> pdb=" O GLU C 689 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU C 694 " --> pdb=" O ARG C 690 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA C 697 " --> pdb=" O ARG C 693 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG C 698 " --> pdb=" O LEU C 694 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU C 701 " --> pdb=" O ALA C 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 714 removed outlier: 3.805A pdb=" N ARG C 714 " --> pdb=" O TRP C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 749 removed outlier: 3.554A pdb=" N HIS C 745 " --> pdb=" O GLU C 741 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER C 747 " --> pdb=" O LYS C 743 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE C 748 " --> pdb=" O THR C 744 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU C 749 " --> pdb=" O HIS C 745 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.801A pdb=" N ILE D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 143 removed outlier: 3.639A pdb=" N GLU D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU D 141 " --> pdb=" O GLU D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 160 removed outlier: 4.048A pdb=" N MET D 159 " --> pdb=" O PRO D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 177 Processing helix chain 'D' and resid 184 through 196 removed outlier: 3.621A pdb=" N ILE D 189 " --> pdb=" O GLU D 185 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU D 195 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU D 196 " --> pdb=" O ALA D 192 " (cutoff:3.500A) 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 removed outlier: 3.638A pdb=" N GLU D 224 " --> pdb=" O ASN D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 235 Processing helix chain 'D' and resid 265 through 271 Processing helix chain 'D' and resid 275 through 282 Processing helix chain 'D' and resid 299 through 305 removed outlier: 3.726A pdb=" N LEU D 303 " --> pdb=" O ILE D 299 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 328 Processing helix chain 'D' and resid 344 through 351 removed outlier: 3.537A pdb=" N ALA D 349 " --> pdb=" O LEU D 345 " (cutoff:3.500A) 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 removed outlier: 3.504A pdb=" N VAL D 408 " --> pdb=" O LEU D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 419 No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 425 through 433 removed outlier: 3.732A pdb=" N TRP D 433 " --> pdb=" O LEU D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 459 removed outlier: 3.559A pdb=" N TYR D 448 " --> pdb=" O SER D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 481 through 506 removed outlier: 3.828A pdb=" N MET D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA D 504 " --> pdb=" O LYS D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 541 removed outlier: 3.894A pdb=" N PHE D 527 " --> pdb=" O HIS D 523 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE D 538 " --> pdb=" O ILE D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 566 removed outlier: 4.041A pdb=" N LEU D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N MET D 562 " --> pdb=" O GLY D 558 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N LEU D 563 " --> pdb=" O TRP D 559 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N TYR D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N TYR D 565 " --> pdb=" O ASN D 561 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N THR D 566 " --> pdb=" O MET D 562 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 585 Processing helix chain 'D' and resid 588 through 608 removed outlier: 4.371A pdb=" N PHE D 592 " --> pdb=" O LEU D 588 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE D 597 " --> pdb=" O VAL D 593 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL D 603 " --> pdb=" O LEU D 599 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU D 608 " --> pdb=" O ALA D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 637 removed outlier: 3.822A pdb=" N LEU D 630 " --> pdb=" O SER D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 651 through 665 Processing helix chain 'D' and resid 669 through 686 removed outlier: 3.546A pdb=" N THR D 680 " --> pdb=" O LEU D 676 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 705 removed outlier: 3.899A pdb=" N TRP D 692 " --> pdb=" O SER D 688 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG D 693 " --> pdb=" O GLU D 689 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU D 694 " --> pdb=" O ARG D 690 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA D 697 " --> pdb=" O ARG D 693 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG D 698 " --> pdb=" O LEU D 694 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU D 701 " --> pdb=" O ALA D 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 709 through 714 removed outlier: 3.806A pdb=" N ARG D 714 " --> pdb=" O TRP D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 749 removed outlier: 3.554A pdb=" N HIS D 745 " --> pdb=" O GLU D 741 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER D 747 " --> pdb=" O LYS D 743 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N PHE D 748 " --> pdb=" O THR D 744 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU D 749 " --> pdb=" O HIS D 745 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 733 through 737 removed outlier: 6.284A pdb=" N LEU A 389 " --> pdb=" O THR A 378 " (cutoff:3.500A) removed outlier: 5.219A 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: 6.283A pdb=" N LEU B 389 " --> pdb=" O THR B 378 " (cutoff:3.500A) removed outlier: 5.220A 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: 6.284A pdb=" N LEU C 389 " --> pdb=" O THR C 378 " (cutoff:3.500A) removed outlier: 5.219A 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: 6.284A pdb=" N LEU D 389 " --> pdb=" O THR D 378 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N THR D 378 " --> pdb=" O LEU D 389 " (cutoff:3.500A) 744 hydrogen bonds defined for protein. 2220 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: 6.02 Time building geometry restraints manager: 8.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3392 1.31 - 1.44: 5996 1.44 - 1.56: 12764 1.56 - 1.69: 60 1.69 - 1.81: 216 Bond restraints: 22428 Sorted by residual: bond pdb=" C21 POV A 901 " pdb=" O21 POV A 901 " ideal model delta sigma weight residual 1.330 1.426 -0.096 2.00e-02 2.50e+03 2.28e+01 bond pdb=" C21 POV A 908 " pdb=" O21 POV A 908 " ideal model delta sigma weight residual 1.330 1.425 -0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" C21 POV B 902 " pdb=" O21 POV B 902 " ideal model delta sigma weight residual 1.330 1.425 -0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" C31 POV A 903 " pdb=" O31 POV A 903 " ideal model delta sigma weight residual 1.327 1.422 -0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" C21 POV C 902 " pdb=" O21 POV C 902 " ideal model delta sigma weight residual 1.330 1.425 -0.095 2.00e-02 2.50e+03 2.25e+01 ... (remaining 22423 not shown) Histogram of bond angle deviations from ideal: 99.28 - 106.25: 433 106.25 - 113.22: 12130 113.22 - 120.19: 8427 120.19 - 127.16: 8885 127.16 - 134.12: 193 Bond angle restraints: 30068 Sorted by residual: angle pdb=" N LEU A 513 " pdb=" CA LEU A 513 " pdb=" C LEU A 513 " ideal model delta sigma weight residual 114.56 106.69 7.87 1.27e+00 6.20e-01 3.84e+01 angle pdb=" N LEU C 513 " pdb=" CA LEU C 513 " pdb=" C LEU C 513 " ideal model delta sigma weight residual 114.56 106.70 7.86 1.27e+00 6.20e-01 3.83e+01 angle pdb=" N LEU B 513 " pdb=" CA LEU B 513 " pdb=" C LEU B 513 " ideal model delta sigma weight residual 114.56 106.70 7.86 1.27e+00 6.20e-01 3.83e+01 angle pdb=" N LEU D 513 " pdb=" CA LEU D 513 " pdb=" C LEU D 513 " ideal model delta sigma weight residual 114.56 106.71 7.85 1.27e+00 6.20e-01 3.82e+01 angle pdb=" N ILE C 644 " pdb=" CA ILE C 644 " pdb=" C ILE C 644 " ideal model delta sigma weight residual 113.10 108.24 4.86 9.70e-01 1.06e+00 2.51e+01 ... (remaining 30063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 13147 35.82 - 71.63: 411 71.63 - 107.45: 66 107.45 - 143.26: 13 143.26 - 179.08: 3 Dihedral angle restraints: 13640 sinusoidal: 6144 harmonic: 7496 Sorted by residual: dihedral pdb=" CB CYS A 612 " pdb=" SG CYS A 612 " pdb=" SG CYS A 619 " pdb=" CB CYS A 619 " ideal model delta sinusoidal sigma weight residual -86.00 -165.67 79.67 1 1.00e+01 1.00e-02 7.88e+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 -86.00 -165.66 79.66 1 1.00e+01 1.00e-02 7.88e+01 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 -86.00 -165.63 79.63 1 1.00e+01 1.00e-02 7.87e+01 ... (remaining 13637 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2714 0.058 - 0.116: 503 0.116 - 0.173: 43 0.173 - 0.231: 0 0.231 - 0.289: 12 Chirality restraints: 3272 Sorted by residual: chirality pdb=" CA GLU A 423 " pdb=" N GLU A 423 " pdb=" C GLU A 423 " pdb=" CB GLU A 423 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA GLU B 423 " pdb=" N GLU B 423 " pdb=" C GLU B 423 " pdb=" CB GLU B 423 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CA GLU D 423 " pdb=" N GLU D 423 " pdb=" C GLU D 423 " pdb=" CB GLU D 423 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.03e+00 ... (remaining 3269 not shown) Planarity restraints: 3668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 509 " 0.040 5.00e-02 4.00e+02 6.16e-02 6.07e+00 pdb=" N PRO D 510 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO D 510 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 510 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 509 " 0.040 5.00e-02 4.00e+02 6.12e-02 6.00e+00 pdb=" N PRO C 510 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO C 510 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 510 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 509 " 0.040 5.00e-02 4.00e+02 6.11e-02 5.98e+00 pdb=" N PRO A 510 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 510 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 510 " 0.034 5.00e-02 4.00e+02 ... (remaining 3665 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 5831 2.80 - 3.32: 18182 3.32 - 3.85: 35741 3.85 - 4.37: 44230 4.37 - 4.90: 73673 Nonbonded interactions: 177657 Sorted by model distance: nonbonded pdb=" O GLU C 308 " pdb=" O HOH C1001 " model vdw 2.274 2.440 nonbonded pdb=" O GLU B 308 " pdb=" O HOH B1001 " model vdw 2.274 2.440 nonbonded pdb=" O GLU D 308 " pdb=" O HOH D1001 " model vdw 2.276 2.440 nonbonded pdb=" O GLU A 308 " pdb=" O HOH A1001 " model vdw 2.311 2.440 nonbonded pdb=" O HIS D 417 " pdb=" OG1 THR D 421 " model vdw 2.314 2.440 ... (remaining 177652 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 62 through 751 or resid 901 or resid 904 or resid 906)) selection = (chain 'B' and (resid 62 through 751 or resid 901 or resid 904 or resid 906)) selection = (chain 'C' and (resid 62 through 751 or resid 901 or resid 904 or resid 906)) selection = (chain 'D' and (resid 62 through 751 or resid 901 or resid 904 or resid 906)) } 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=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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.260 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 54.790 Find NCS groups from input model: 1.860 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 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 : 0.008 0.096 22428 Z= 0.471 Angle : 1.216 12.999 30068 Z= 0.593 Chirality : 0.046 0.289 3272 Planarity : 0.005 0.062 3668 Dihedral : 16.896 179.078 8744 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -6.02 (0.11), residues: 2520 helix: -4.67 (0.04), residues: 1544 sheet: -0.30 (0.62), residues: 88 loop : -2.61 (0.18), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 559 HIS 0.006 0.001 HIS D 160 PHE 0.018 0.002 PHE B 447 TYR 0.010 0.001 TYR C 451 ARG 0.003 0.001 ARG D 714 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 561 time to evaluate : 2.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 GLU cc_start: 0.6801 (tt0) cc_final: 0.6466 (tp30) REVERT: A 332 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6845 (mt-10) REVERT: A 488 MET cc_start: 0.6624 (mtp) cc_final: 0.6061 (mmm) REVERT: A 501 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7633 (mm-30) REVERT: B 207 GLU cc_start: 0.7614 (pt0) cc_final: 0.7373 (pt0) REVERT: B 214 GLU cc_start: 0.6787 (tt0) cc_final: 0.6364 (tp30) REVERT: B 351 MET cc_start: 0.8730 (mtp) cc_final: 0.8510 (mtp) REVERT: B 488 MET cc_start: 0.6618 (mtp) cc_final: 0.5996 (mmm) REVERT: C 129 GLU cc_start: 0.6840 (mp0) cc_final: 0.6595 (mp0) REVERT: C 207 GLU cc_start: 0.7738 (pt0) cc_final: 0.7523 (pt0) REVERT: C 332 GLU cc_start: 0.7100 (mt-10) cc_final: 0.6798 (mt-10) REVERT: C 488 MET cc_start: 0.6628 (mtp) cc_final: 0.5994 (mmm) REVERT: D 129 GLU cc_start: 0.6827 (mp0) cc_final: 0.6605 (mp0) REVERT: D 207 GLU cc_start: 0.7572 (pt0) cc_final: 0.7367 (pt0) REVERT: D 488 MET cc_start: 0.6630 (mtp) cc_final: 0.6107 (mmp) outliers start: 0 outliers final: 0 residues processed: 561 average time/residue: 1.2030 time to fit residues: 771.3040 Evaluate side-chains 339 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 339 time to evaluate : 2.372 ------------------------------------------------------------------------------- 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: 4.9990 chunk 191 optimal weight: 8.9990 chunk 105 optimal weight: 9.9990 chunk 65 optimal weight: 20.0000 chunk 128 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 197 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 chunk 228 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 ASN A 242 ASN A 251 ASN A 274 GLN A 410 ASN A 412 ASN A 643 ASN A 646 GLN A 671 ASN A 735 ASN B 71 ASN B 182 ASN B 205 ASN B 242 ASN B 251 ASN B 412 ASN B 643 ASN B 646 GLN B 671 ASN C 71 ASN C 205 ASN ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 ASN C 251 ASN C 274 GLN C 412 ASN C 523 HIS C 643 ASN C 646 GLN C 671 ASN C 735 ASN D 71 ASN D 205 ASN D 242 ASN D 251 ASN D 274 GLN D 412 ASN D 523 HIS D 643 ASN D 646 GLN D 671 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 22428 Z= 0.471 Angle : 0.803 13.035 30068 Z= 0.392 Chirality : 0.049 0.224 3272 Planarity : 0.006 0.051 3668 Dihedral : 19.618 142.863 3724 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 4.51 % Allowed : 9.81 % Favored : 85.69 % Cbeta Deviations : 0.00 % 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: -3.04 (0.14), residues: 2520 helix: -1.81 (0.10), residues: 1572 sheet: 0.06 (0.61), residues: 84 loop : -2.35 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 739 HIS 0.007 0.002 HIS B 244 PHE 0.032 0.003 PHE A 259 TYR 0.018 0.003 TYR B 260 ARG 0.011 0.001 ARG B 225 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 349 time to evaluate : 2.373 Fit side-chains revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7809 (mptt) cc_final: 0.7475 (tttm) REVERT: A 289 ILE cc_start: 0.7868 (OUTLIER) cc_final: 0.7560 (mm) REVERT: A 320 MET cc_start: 0.8583 (mmt) cc_final: 0.8375 (mmt) REVERT: A 323 MET cc_start: 0.8111 (ttm) cc_final: 0.7908 (ttm) REVERT: A 488 MET cc_start: 0.6617 (mtp) cc_final: 0.5861 (mpm) REVERT: A 574 MET cc_start: 0.7695 (OUTLIER) cc_final: 0.6834 (ptm) REVERT: A 641 ASP cc_start: 0.7486 (t0) cc_final: 0.7285 (t70) REVERT: A 717 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.7443 (mmm) REVERT: A 719 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6973 (pm20) REVERT: A 750 ASN cc_start: 0.7081 (t160) cc_final: 0.6816 (t0) REVERT: B 145 LEU cc_start: 0.6881 (OUTLIER) cc_final: 0.6636 (mt) REVERT: B 289 ILE cc_start: 0.7868 (OUTLIER) cc_final: 0.7555 (mm) REVERT: B 315 ASP cc_start: 0.6524 (p0) cc_final: 0.6313 (p0) REVERT: B 320 MET cc_start: 0.8601 (mmt) cc_final: 0.8254 (mmt) REVERT: B 488 MET cc_start: 0.6680 (mtp) cc_final: 0.5941 (mpm) REVERT: B 641 ASP cc_start: 0.7537 (t0) cc_final: 0.7317 (t70) REVERT: B 717 MET cc_start: 0.7704 (OUTLIER) cc_final: 0.7372 (mmm) REVERT: B 719 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7163 (pm20) REVERT: C 182 ASN cc_start: 0.7481 (t0) cc_final: 0.7248 (t0) REVERT: C 289 ILE cc_start: 0.7879 (OUTLIER) cc_final: 0.7566 (mm) REVERT: C 320 MET cc_start: 0.8578 (mmt) cc_final: 0.8291 (mmt) REVERT: C 488 MET cc_start: 0.6645 (mtp) cc_final: 0.5918 (mpm) REVERT: C 641 ASP cc_start: 0.7524 (t0) cc_final: 0.7294 (t70) REVERT: C 717 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7401 (mmm) REVERT: D 121 LYS cc_start: 0.7740 (mptt) cc_final: 0.7498 (tttm) REVERT: D 145 LEU cc_start: 0.6934 (OUTLIER) cc_final: 0.6686 (mt) REVERT: D 289 ILE cc_start: 0.7853 (OUTLIER) cc_final: 0.7542 (mm) REVERT: D 320 MET cc_start: 0.8582 (mmt) cc_final: 0.8274 (mmt) REVERT: D 355 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6909 (pm20) REVERT: D 488 MET cc_start: 0.6714 (mtp) cc_final: 0.5957 (mpm) REVERT: D 641 ASP cc_start: 0.7527 (t0) cc_final: 0.7291 (t70) REVERT: D 717 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.7394 (mmm) outliers start: 102 outliers final: 34 residues processed: 421 average time/residue: 1.2410 time to fit residues: 598.8802 Evaluate side-chains 368 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 321 time to evaluate : 2.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain B residue 717 MET Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 743 LYS Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 713 SER Chi-restraints excluded: chain C residue 717 MET Chi-restraints excluded: chain C residue 743 LYS Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 713 SER Chi-restraints excluded: chain D residue 717 MET Chi-restraints excluded: chain D residue 719 GLU Chi-restraints excluded: chain D residue 743 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 0.0470 chunk 71 optimal weight: 6.9990 chunk 190 optimal weight: 8.9990 chunk 155 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 229 optimal weight: 9.9990 chunk 247 optimal weight: 0.8980 chunk 204 optimal weight: 0.9990 chunk 227 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 183 optimal weight: 0.9980 overall best weight: 0.9882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN B 227 GLN B 523 HIS B 735 ASN B 750 ASN ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 750 ASN D 735 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 22428 Z= 0.132 Angle : 0.479 7.482 30068 Z= 0.244 Chirality : 0.037 0.225 3272 Planarity : 0.003 0.047 3668 Dihedral : 17.507 116.887 3724 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.18 % Allowed : 12.85 % Favored : 83.97 % 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: -1.29 (0.16), residues: 2520 helix: -0.18 (0.12), residues: 1556 sheet: -0.37 (0.57), residues: 88 loop : -2.05 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 380 HIS 0.003 0.001 HIS C 439 PHE 0.012 0.001 PHE C 449 TYR 0.013 0.001 TYR A 451 ARG 0.003 0.000 ARG C 462 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 362 time to evaluate : 2.490 Fit side-chains REVERT: A 121 LYS cc_start: 0.7658 (mptt) cc_final: 0.7338 (tttm) REVERT: A 214 GLU cc_start: 0.7286 (tt0) cc_final: 0.6993 (tt0) REVERT: A 276 GLU cc_start: 0.6502 (OUTLIER) cc_final: 0.6113 (mp0) REVERT: A 289 ILE cc_start: 0.7836 (OUTLIER) cc_final: 0.7563 (mm) REVERT: A 412 ASN cc_start: 0.7712 (m-40) cc_final: 0.7498 (m-40) REVERT: A 423 GLU cc_start: 0.6357 (OUTLIER) cc_final: 0.6141 (pm20) REVERT: A 488 MET cc_start: 0.6665 (mtp) cc_final: 0.5904 (mpm) REVERT: A 655 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.7995 (tt) REVERT: A 672 MET cc_start: 0.8223 (ttm) cc_final: 0.7970 (mtp) REVERT: A 717 MET cc_start: 0.7638 (mpp) cc_final: 0.7392 (mmm) REVERT: A 719 GLU cc_start: 0.7241 (pt0) cc_final: 0.6920 (pm20) REVERT: B 129 GLU cc_start: 0.6377 (mp0) cc_final: 0.6095 (mp0) REVERT: B 145 LEU cc_start: 0.6902 (OUTLIER) cc_final: 0.6666 (mt) REVERT: B 182 ASN cc_start: 0.7054 (t0) cc_final: 0.6779 (t0) REVERT: B 229 ASP cc_start: 0.7435 (OUTLIER) cc_final: 0.7170 (p0) REVERT: B 320 MET cc_start: 0.8647 (mmt) cc_final: 0.8372 (mmt) REVERT: B 488 MET cc_start: 0.6659 (mtp) cc_final: 0.5919 (mpm) REVERT: B 717 MET cc_start: 0.7590 (mpp) cc_final: 0.7326 (mmm) REVERT: C 121 LYS cc_start: 0.7619 (mptt) cc_final: 0.7276 (tttm) REVERT: C 320 MET cc_start: 0.8608 (mmt) cc_final: 0.8367 (mmt) REVERT: C 488 MET cc_start: 0.6688 (mtp) cc_final: 0.5965 (mpm) REVERT: C 677 MET cc_start: 0.8445 (mtp) cc_final: 0.8244 (mtm) REVERT: C 717 MET cc_start: 0.7657 (mpp) cc_final: 0.7344 (mmm) REVERT: D 121 LYS cc_start: 0.7571 (mptt) cc_final: 0.7290 (tttm) REVERT: D 145 LEU cc_start: 0.6985 (OUTLIER) cc_final: 0.6735 (mt) REVERT: D 320 MET cc_start: 0.8627 (mmt) cc_final: 0.8333 (mmt) REVERT: D 355 GLU cc_start: 0.7091 (mm-30) cc_final: 0.6812 (pm20) REVERT: D 488 MET cc_start: 0.6674 (mtp) cc_final: 0.5936 (mpm) REVERT: D 717 MET cc_start: 0.7598 (mpp) cc_final: 0.7299 (mmm) REVERT: D 719 GLU cc_start: 0.7233 (pt0) cc_final: 0.6928 (pm20) outliers start: 72 outliers final: 24 residues processed: 400 average time/residue: 1.2184 time to fit residues: 559.2443 Evaluate side-chains 359 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 328 time to evaluate : 2.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 713 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 459 SER Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 588 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 9.9990 chunk 172 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 153 optimal weight: 9.9990 chunk 230 optimal weight: 0.9990 chunk 243 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 chunk 218 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 HIS ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 750 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 22428 Z= 0.195 Angle : 0.533 10.479 30068 Z= 0.264 Chirality : 0.039 0.214 3272 Planarity : 0.003 0.042 3668 Dihedral : 16.951 111.357 3724 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.37 % Allowed : 13.43 % Favored : 82.20 % 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: -0.71 (0.16), residues: 2520 helix: 0.36 (0.13), residues: 1584 sheet: -0.02 (0.58), residues: 84 loop : -2.07 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 559 HIS 0.004 0.001 HIS C 439 PHE 0.012 0.001 PHE D 569 TYR 0.016 0.001 TYR C 451 ARG 0.003 0.000 ARG D 225 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 327 time to evaluate : 2.256 Fit side-chains REVERT: A 121 LYS cc_start: 0.7602 (mptt) cc_final: 0.7174 (tttm) REVERT: A 129 GLU cc_start: 0.6762 (mp0) cc_final: 0.6462 (pt0) REVERT: A 276 GLU cc_start: 0.6506 (OUTLIER) cc_final: 0.6046 (mp0) REVERT: A 289 ILE cc_start: 0.7808 (OUTLIER) cc_final: 0.7520 (mm) REVERT: A 423 GLU cc_start: 0.6344 (OUTLIER) cc_final: 0.6046 (pm20) REVERT: A 488 MET cc_start: 0.6662 (mtp) cc_final: 0.5905 (mpm) REVERT: A 655 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8200 (tp) REVERT: A 717 MET cc_start: 0.7733 (mpp) cc_final: 0.7408 (mmm) REVERT: A 719 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.7011 (pm20) REVERT: B 129 GLU cc_start: 0.6409 (mp0) cc_final: 0.6133 (mp0) REVERT: B 145 LEU cc_start: 0.6974 (OUTLIER) cc_final: 0.6759 (mt) REVERT: B 182 ASN cc_start: 0.7176 (t0) cc_final: 0.6901 (t0) REVERT: B 229 ASP cc_start: 0.7470 (OUTLIER) cc_final: 0.7254 (p0) REVERT: B 289 ILE cc_start: 0.7803 (OUTLIER) cc_final: 0.7520 (mm) REVERT: B 320 MET cc_start: 0.8634 (mmt) cc_final: 0.8291 (mmt) REVERT: B 338 ASN cc_start: 0.7406 (m-40) cc_final: 0.6657 (m-40) REVERT: B 488 MET cc_start: 0.6633 (mtp) cc_final: 0.5950 (mpm) REVERT: B 717 MET cc_start: 0.7707 (mpp) cc_final: 0.7378 (mmm) REVERT: C 121 LYS cc_start: 0.7628 (mptt) cc_final: 0.7193 (tttm) REVERT: C 276 GLU cc_start: 0.6517 (OUTLIER) cc_final: 0.6231 (mp0) REVERT: C 289 ILE cc_start: 0.7802 (OUTLIER) cc_final: 0.7531 (mm) REVERT: C 320 MET cc_start: 0.8631 (mmt) cc_final: 0.8314 (mmt) REVERT: C 488 MET cc_start: 0.6713 (mtp) cc_final: 0.6024 (mpm) REVERT: C 717 MET cc_start: 0.7723 (mpp) cc_final: 0.7404 (mmm) REVERT: D 121 LYS cc_start: 0.7590 (mptt) cc_final: 0.7205 (tttm) REVERT: D 289 ILE cc_start: 0.7833 (OUTLIER) cc_final: 0.7554 (mm) REVERT: D 320 MET cc_start: 0.8623 (mmt) cc_final: 0.8254 (mmt) REVERT: D 355 GLU cc_start: 0.7137 (mm-30) cc_final: 0.6805 (pm20) REVERT: D 488 MET cc_start: 0.6697 (mtp) cc_final: 0.5993 (mpm) REVERT: D 717 MET cc_start: 0.7689 (mpp) cc_final: 0.7373 (mmm) REVERT: D 719 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6993 (pm20) outliers start: 99 outliers final: 51 residues processed: 394 average time/residue: 1.2017 time to fit residues: 546.3470 Evaluate side-chains 384 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 321 time to evaluate : 2.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 255 GLN Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 340 ASP Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 685 SER Chi-restraints excluded: chain C residue 713 SER Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 255 GLN Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 340 ASP Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 626 SER Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain D residue 713 SER Chi-restraints excluded: chain D residue 719 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 9.9990 chunk 138 optimal weight: 2.9990 chunk 3 optimal weight: 20.0000 chunk 181 optimal weight: 0.6980 chunk 100 optimal weight: 9.9990 chunk 207 optimal weight: 0.0470 chunk 168 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 124 optimal weight: 7.9990 chunk 218 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 overall best weight: 2.7484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 22428 Z= 0.228 Angle : 0.562 9.070 30068 Z= 0.277 Chirality : 0.040 0.215 3272 Planarity : 0.003 0.041 3668 Dihedral : 16.703 109.818 3724 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 4.02 % Allowed : 13.83 % Favored : 82.16 % 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: -0.40 (0.17), residues: 2520 helix: 0.62 (0.13), residues: 1580 sheet: 0.20 (0.58), residues: 84 loop : -1.98 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 521 HIS 0.004 0.001 HIS C 439 PHE 0.014 0.001 PHE B 259 TYR 0.016 0.002 TYR C 451 ARG 0.004 0.001 ARG B 225 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 334 time to evaluate : 2.341 Fit side-chains revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7736 (mptt) cc_final: 0.7207 (tttm) REVERT: A 276 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.6116 (mp0) REVERT: A 289 ILE cc_start: 0.7852 (OUTLIER) cc_final: 0.7556 (mm) REVERT: A 412 ASN cc_start: 0.7822 (m-40) cc_final: 0.7610 (m-40) REVERT: A 423 GLU cc_start: 0.6350 (OUTLIER) cc_final: 0.6010 (pm20) REVERT: A 488 MET cc_start: 0.6657 (mtp) cc_final: 0.5909 (mpm) REVERT: A 655 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8173 (tp) REVERT: A 717 MET cc_start: 0.7756 (mpp) cc_final: 0.7423 (mmm) REVERT: A 719 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6986 (pm20) REVERT: B 129 GLU cc_start: 0.6430 (mp0) cc_final: 0.6172 (mp0) REVERT: B 145 LEU cc_start: 0.7059 (OUTLIER) cc_final: 0.6825 (mt) REVERT: B 182 ASN cc_start: 0.7275 (t0) cc_final: 0.6980 (t0) REVERT: B 289 ILE cc_start: 0.7845 (OUTLIER) cc_final: 0.7542 (mm) REVERT: B 320 MET cc_start: 0.8634 (mmt) cc_final: 0.8227 (mmt) REVERT: B 412 ASN cc_start: 0.7899 (m-40) cc_final: 0.7656 (m-40) REVERT: B 488 MET cc_start: 0.6651 (mtp) cc_final: 0.5963 (mpm) REVERT: B 717 MET cc_start: 0.7743 (mpp) cc_final: 0.7365 (mmm) REVERT: B 722 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7515 (tmmt) REVERT: C 276 GLU cc_start: 0.6583 (OUTLIER) cc_final: 0.6162 (mp0) REVERT: C 289 ILE cc_start: 0.7811 (OUTLIER) cc_final: 0.7522 (mm) REVERT: C 320 MET cc_start: 0.8644 (mmt) cc_final: 0.8272 (mmt) REVERT: C 423 GLU cc_start: 0.6370 (OUTLIER) cc_final: 0.6076 (OUTLIER) REVERT: C 488 MET cc_start: 0.6645 (mtp) cc_final: 0.5963 (mpm) REVERT: C 717 MET cc_start: 0.7761 (mpp) cc_final: 0.7427 (mmm) REVERT: D 129 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6844 (mp0) REVERT: D 276 GLU cc_start: 0.6503 (OUTLIER) cc_final: 0.6055 (mp0) REVERT: D 289 ILE cc_start: 0.7812 (OUTLIER) cc_final: 0.7527 (mm) REVERT: D 320 MET cc_start: 0.8630 (mmt) cc_final: 0.8250 (mmt) REVERT: D 355 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6885 (pm20) REVERT: D 488 MET cc_start: 0.6659 (mtp) cc_final: 0.5927 (mpm) REVERT: D 546 GLU cc_start: 0.7007 (mp0) cc_final: 0.6758 (mp0) REVERT: D 717 MET cc_start: 0.7744 (mpp) cc_final: 0.7409 (mmm) REVERT: D 719 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6982 (pm20) outliers start: 91 outliers final: 49 residues processed: 394 average time/residue: 1.2160 time to fit residues: 549.4715 Evaluate side-chains 378 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 316 time to evaluate : 2.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 369 ARG Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain B residue 722 LYS Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 255 GLN Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 340 ASP Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 713 SER Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 255 GLN Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 340 ASP Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 626 SER Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain D residue 713 SER Chi-restraints excluded: chain D residue 719 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 0.4980 chunk 219 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 60 optimal weight: 8.9990 chunk 243 optimal weight: 6.9990 chunk 202 optimal weight: 9.9990 chunk 112 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 750 ASN ** C 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 22428 Z= 0.225 Angle : 0.552 8.776 30068 Z= 0.273 Chirality : 0.040 0.208 3272 Planarity : 0.003 0.039 3668 Dihedral : 16.469 107.487 3724 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.67 % Allowed : 14.36 % Favored : 81.98 % 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: -0.20 (0.17), residues: 2520 helix: 0.81 (0.13), residues: 1576 sheet: 0.20 (0.60), residues: 84 loop : -1.94 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 521 HIS 0.004 0.001 HIS B 439 PHE 0.013 0.001 PHE C 569 TYR 0.016 0.002 TYR C 451 ARG 0.004 0.000 ARG A 225 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 322 time to evaluate : 2.408 Fit side-chains REVERT: A 121 LYS cc_start: 0.7747 (mptt) cc_final: 0.7156 (tttm) REVERT: A 276 GLU cc_start: 0.6589 (OUTLIER) cc_final: 0.6196 (mp0) REVERT: A 289 ILE cc_start: 0.7869 (OUTLIER) cc_final: 0.7563 (mm) REVERT: A 412 ASN cc_start: 0.7838 (m-40) cc_final: 0.7623 (m-40) REVERT: A 488 MET cc_start: 0.6661 (mtp) cc_final: 0.5982 (mpm) REVERT: A 655 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8170 (tp) REVERT: A 717 MET cc_start: 0.7652 (mpp) cc_final: 0.7363 (mmm) REVERT: A 719 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6871 (pm20) REVERT: B 145 LEU cc_start: 0.7054 (OUTLIER) cc_final: 0.6837 (mt) REVERT: B 182 ASN cc_start: 0.7135 (t0) cc_final: 0.6899 (t0) REVERT: B 320 MET cc_start: 0.8618 (mmt) cc_final: 0.8220 (mmt) REVERT: B 412 ASN cc_start: 0.7895 (m-40) cc_final: 0.7672 (m-40) REVERT: B 488 MET cc_start: 0.6663 (mtp) cc_final: 0.5944 (mpm) REVERT: B 717 MET cc_start: 0.7664 (mpp) cc_final: 0.7347 (mmm) REVERT: B 719 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.7018 (pm20) REVERT: C 276 GLU cc_start: 0.6575 (OUTLIER) cc_final: 0.6133 (mp0) REVERT: C 289 ILE cc_start: 0.7850 (OUTLIER) cc_final: 0.7563 (mm) REVERT: C 320 MET cc_start: 0.8650 (mmt) cc_final: 0.8281 (mmt) REVERT: C 488 MET cc_start: 0.6654 (mtp) cc_final: 0.5977 (mpm) REVERT: C 717 MET cc_start: 0.7651 (mpp) cc_final: 0.7359 (mmm) REVERT: D 129 GLU cc_start: 0.7101 (mm-30) cc_final: 0.6799 (mm-30) REVERT: D 276 GLU cc_start: 0.6613 (OUTLIER) cc_final: 0.6195 (mp0) REVERT: D 289 ILE cc_start: 0.7848 (OUTLIER) cc_final: 0.7557 (mm) REVERT: D 320 MET cc_start: 0.8616 (mmt) cc_final: 0.8192 (mmt) REVERT: D 355 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6837 (pm20) REVERT: D 488 MET cc_start: 0.6653 (mtp) cc_final: 0.5925 (mpm) REVERT: D 546 GLU cc_start: 0.6964 (mp0) cc_final: 0.6753 (mp0) REVERT: D 717 MET cc_start: 0.7643 (mpp) cc_final: 0.7340 (mmm) REVERT: D 719 GLU cc_start: 0.7202 (pt0) cc_final: 0.6952 (pm20) outliers start: 83 outliers final: 57 residues processed: 375 average time/residue: 1.2819 time to fit residues: 552.2174 Evaluate side-chains 373 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 306 time to evaluate : 2.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 369 ARG Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 255 GLN Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 340 ASP Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 713 SER Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 255 GLN Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 340 ASP Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 626 SER Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain D residue 713 SER Chi-restraints excluded: chain D residue 720 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 178 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 205 optimal weight: 4.9990 chunk 136 optimal weight: 10.0000 chunk 242 optimal weight: 0.6980 chunk 152 optimal weight: 9.9990 chunk 148 optimal weight: 10.0000 chunk 112 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 227 GLN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 439 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.4838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 22428 Z= 0.126 Angle : 0.474 8.558 30068 Z= 0.235 Chirality : 0.037 0.181 3272 Planarity : 0.003 0.041 3668 Dihedral : 15.467 94.988 3724 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.92 % Allowed : 15.37 % Favored : 81.71 % 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: 0.27 (0.17), residues: 2520 helix: 1.26 (0.13), residues: 1564 sheet: -0.07 (0.61), residues: 88 loop : -1.86 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 380 HIS 0.003 0.001 HIS B 439 PHE 0.009 0.001 PHE C 522 TYR 0.012 0.001 TYR C 451 ARG 0.003 0.000 ARG A 698 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 333 time to evaluate : 2.154 Fit side-chains REVERT: A 121 LYS cc_start: 0.7700 (mptt) cc_final: 0.7100 (tttm) REVERT: A 276 GLU cc_start: 0.6492 (OUTLIER) cc_final: 0.6196 (mp0) REVERT: A 289 ILE cc_start: 0.7865 (OUTLIER) cc_final: 0.7582 (mm) REVERT: A 350 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7639 (ttmt) REVERT: A 488 MET cc_start: 0.6607 (mtp) cc_final: 0.5953 (mpm) REVERT: A 555 MET cc_start: 0.7814 (tmm) cc_final: 0.7356 (ttm) REVERT: A 719 GLU cc_start: 0.7166 (pt0) cc_final: 0.6895 (pm20) REVERT: B 320 MET cc_start: 0.8635 (mmt) cc_final: 0.8287 (mmt) REVERT: B 488 MET cc_start: 0.6635 (mtp) cc_final: 0.5929 (mpm) REVERT: B 555 MET cc_start: 0.7818 (tmm) cc_final: 0.7356 (ttm) REVERT: C 276 GLU cc_start: 0.6516 (OUTLIER) cc_final: 0.6296 (mp0) REVERT: C 289 ILE cc_start: 0.7822 (OUTLIER) cc_final: 0.7534 (mm) REVERT: C 320 MET cc_start: 0.8638 (mmt) cc_final: 0.8271 (mmt) REVERT: C 488 MET cc_start: 0.6630 (mtp) cc_final: 0.5929 (mpm) REVERT: C 555 MET cc_start: 0.7815 (tmm) cc_final: 0.7375 (ttm) REVERT: C 717 MET cc_start: 0.7486 (mpp) cc_final: 0.7281 (mmm) REVERT: D 129 GLU cc_start: 0.7052 (mm-30) cc_final: 0.6754 (mm-30) REVERT: D 289 ILE cc_start: 0.7839 (OUTLIER) cc_final: 0.7565 (mm) REVERT: D 320 MET cc_start: 0.8621 (mmt) cc_final: 0.8247 (mmt) REVERT: D 355 GLU cc_start: 0.7080 (mm-30) cc_final: 0.6763 (pm20) REVERT: D 488 MET cc_start: 0.6680 (mtp) cc_final: 0.5941 (mpm) REVERT: D 555 MET cc_start: 0.7809 (tmm) cc_final: 0.7386 (ttm) REVERT: D 717 MET cc_start: 0.7464 (mpp) cc_final: 0.7249 (mmm) REVERT: D 719 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6927 (pm20) outliers start: 66 outliers final: 38 residues processed: 371 average time/residue: 1.3193 time to fit residues: 556.4936 Evaluate side-chains 358 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 313 time to evaluate : 2.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 350 LYS Chi-restraints excluded: chain A residue 369 ARG Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 340 ASP Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 713 SER Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 340 ASP Chi-restraints excluded: chain D residue 369 ARG Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 626 SER Chi-restraints excluded: chain D residue 713 SER Chi-restraints excluded: chain D residue 719 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 0.3980 chunk 96 optimal weight: 9.9990 chunk 145 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 47 optimal weight: 8.9990 chunk 154 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 120 optimal weight: 0.2980 chunk 22 optimal weight: 4.9990 chunk 190 optimal weight: 20.0000 chunk 220 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.4925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 22428 Z= 0.203 Angle : 0.535 8.769 30068 Z= 0.264 Chirality : 0.039 0.201 3272 Planarity : 0.003 0.039 3668 Dihedral : 15.642 90.439 3724 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.18 % Allowed : 15.33 % Favored : 81.49 % 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: 0.18 (0.17), residues: 2520 helix: 1.14 (0.13), residues: 1584 sheet: 0.28 (0.63), residues: 84 loop : -1.90 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 692 HIS 0.003 0.001 HIS B 439 PHE 0.013 0.001 PHE C 569 TYR 0.016 0.002 TYR C 451 ARG 0.003 0.000 ARG B 225 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 316 time to evaluate : 2.662 Fit side-chains REVERT: A 121 LYS cc_start: 0.7751 (mptt) cc_final: 0.7110 (tttm) REVERT: A 276 GLU cc_start: 0.6595 (OUTLIER) cc_final: 0.6184 (mp0) REVERT: A 488 MET cc_start: 0.6614 (mtp) cc_final: 0.5955 (mpm) REVERT: A 719 GLU cc_start: 0.7208 (pt0) cc_final: 0.6900 (pm20) REVERT: B 276 GLU cc_start: 0.6509 (OUTLIER) cc_final: 0.5972 (mp0) REVERT: B 320 MET cc_start: 0.8625 (mmt) cc_final: 0.8235 (mmt) REVERT: B 488 MET cc_start: 0.6613 (mtp) cc_final: 0.6132 (mmp) REVERT: C 276 GLU cc_start: 0.6571 (OUTLIER) cc_final: 0.6241 (mp0) REVERT: C 320 MET cc_start: 0.8631 (mmt) cc_final: 0.8263 (mmt) REVERT: C 488 MET cc_start: 0.6626 (mtp) cc_final: 0.5933 (mpm) REVERT: C 717 MET cc_start: 0.7622 (mpp) cc_final: 0.7340 (mmm) REVERT: D 129 GLU cc_start: 0.7078 (mm-30) cc_final: 0.6743 (mm-30) REVERT: D 320 MET cc_start: 0.8621 (mmt) cc_final: 0.8244 (mmt) REVERT: D 355 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6839 (pm20) REVERT: D 488 MET cc_start: 0.6637 (mtp) cc_final: 0.6137 (mmp) REVERT: D 717 MET cc_start: 0.7584 (mpp) cc_final: 0.7306 (mmm) REVERT: D 719 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6903 (pm20) outliers start: 72 outliers final: 46 residues processed: 357 average time/residue: 1.2758 time to fit residues: 520.2283 Evaluate side-chains 355 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 305 time to evaluate : 2.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 369 ARG Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 340 ASP Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 713 SER Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 340 ASP Chi-restraints excluded: chain D residue 369 ARG Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 626 SER Chi-restraints excluded: chain D residue 713 SER Chi-restraints excluded: chain D residue 719 GLU Chi-restraints excluded: chain D residue 720 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 8.9990 chunk 212 optimal weight: 1.9990 chunk 226 optimal weight: 10.0000 chunk 136 optimal weight: 20.0000 chunk 98 optimal weight: 10.0000 chunk 177 optimal weight: 4.9990 chunk 69 optimal weight: 20.0000 chunk 204 optimal weight: 3.9990 chunk 214 optimal weight: 1.9990 chunk 225 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN ** C 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.5035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 22428 Z= 0.297 Angle : 0.609 8.983 30068 Z= 0.300 Chirality : 0.043 0.216 3272 Planarity : 0.004 0.040 3668 Dihedral : 16.287 87.881 3724 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.83 % Allowed : 15.55 % Favored : 81.63 % 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 (0.17), residues: 2520 helix: 0.94 (0.13), residues: 1584 sheet: 0.24 (0.64), residues: 84 loop : -1.87 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 521 HIS 0.006 0.001 HIS C 301 PHE 0.016 0.002 PHE C 569 TYR 0.017 0.002 TYR A 451 ARG 0.005 0.001 ARG D 225 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 322 time to evaluate : 2.284 Fit side-chains REVERT: A 182 ASN cc_start: 0.7321 (t0) cc_final: 0.6993 (t0) REVERT: A 276 GLU cc_start: 0.6676 (OUTLIER) cc_final: 0.6158 (mp0) REVERT: A 488 MET cc_start: 0.6667 (mtp) cc_final: 0.5948 (mpm) REVERT: A 555 MET cc_start: 0.7955 (tmm) cc_final: 0.7401 (ttm) REVERT: A 682 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7692 (pt0) REVERT: A 719 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6908 (pm20) REVERT: B 129 GLU cc_start: 0.6742 (mp0) cc_final: 0.6357 (pt0) REVERT: B 276 GLU cc_start: 0.6562 (OUTLIER) cc_final: 0.5949 (mp0) REVERT: B 320 MET cc_start: 0.8634 (mmt) cc_final: 0.8194 (mmt) REVERT: B 488 MET cc_start: 0.6663 (mtp) cc_final: 0.6191 (mmp) REVERT: B 555 MET cc_start: 0.7962 (tmm) cc_final: 0.7408 (ttm) REVERT: B 682 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7728 (pt0) REVERT: C 276 GLU cc_start: 0.6634 (OUTLIER) cc_final: 0.6185 (mp0) REVERT: C 320 MET cc_start: 0.8658 (mmt) cc_final: 0.8253 (mmt) REVERT: C 488 MET cc_start: 0.6666 (mtp) cc_final: 0.5981 (mpm) REVERT: C 717 MET cc_start: 0.7747 (mpp) cc_final: 0.7409 (mmm) REVERT: D 276 GLU cc_start: 0.6607 (OUTLIER) cc_final: 0.6186 (mp0) REVERT: D 320 MET cc_start: 0.8624 (mmt) cc_final: 0.8205 (mmt) REVERT: D 355 GLU cc_start: 0.7223 (mm-30) cc_final: 0.6879 (pm20) REVERT: D 488 MET cc_start: 0.6683 (mtp) cc_final: 0.6175 (mmp) REVERT: D 717 MET cc_start: 0.7699 (mpp) cc_final: 0.7361 (mmm) REVERT: D 719 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6988 (pm20) outliers start: 64 outliers final: 47 residues processed: 354 average time/residue: 1.2947 time to fit residues: 522.6194 Evaluate side-chains 361 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 306 time to evaluate : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 369 ARG Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 340 ASP Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 713 SER Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 340 ASP Chi-restraints excluded: chain D residue 369 ARG Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 626 SER Chi-restraints excluded: chain D residue 713 SER Chi-restraints excluded: chain D residue 719 GLU Chi-restraints excluded: chain D residue 720 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 10.0000 chunk 146 optimal weight: 0.8980 chunk 113 optimal weight: 8.9990 chunk 166 optimal weight: 9.9990 chunk 251 optimal weight: 6.9990 chunk 231 optimal weight: 9.9990 chunk 199 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 154 optimal weight: 7.9990 chunk 122 optimal weight: 6.9990 chunk 158 optimal weight: 0.2980 overall best weight: 4.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 439 HIS ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.5179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 22428 Z= 0.339 Angle : 0.648 11.575 30068 Z= 0.318 Chirality : 0.045 0.224 3272 Planarity : 0.004 0.036 3668 Dihedral : 16.702 89.836 3724 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.52 % Allowed : 16.21 % Favored : 81.27 % 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: -0.25 (0.17), residues: 2520 helix: 0.71 (0.13), residues: 1596 sheet: 0.19 (0.64), residues: 84 loop : -1.90 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 521 HIS 0.005 0.001 HIS C 439 PHE 0.018 0.002 PHE B 569 TYR 0.017 0.002 TYR C 451 ARG 0.006 0.001 ARG C 225 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 309 time to evaluate : 2.140 Fit side-chains REVERT: A 184 LYS cc_start: 0.7305 (ttpt) cc_final: 0.6988 (tptm) REVERT: A 276 GLU cc_start: 0.6778 (OUTLIER) cc_final: 0.6308 (mp0) REVERT: A 423 GLU cc_start: 0.6268 (OUTLIER) cc_final: 0.5970 (pm20) REVERT: A 488 MET cc_start: 0.6654 (mtp) cc_final: 0.5955 (mpm) REVERT: A 555 MET cc_start: 0.7990 (tmm) cc_final: 0.7427 (ttm) REVERT: A 682 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7691 (pt0) REVERT: A 719 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6973 (pm20) REVERT: B 129 GLU cc_start: 0.6720 (mp0) cc_final: 0.6416 (pt0) REVERT: B 276 GLU cc_start: 0.6574 (OUTLIER) cc_final: 0.6009 (mp0) REVERT: B 320 MET cc_start: 0.8623 (mmt) cc_final: 0.8185 (mmt) REVERT: B 423 GLU cc_start: 0.6363 (OUTLIER) cc_final: 0.6081 (OUTLIER) REVERT: B 488 MET cc_start: 0.6680 (mtp) cc_final: 0.5930 (mpm) REVERT: B 555 MET cc_start: 0.7990 (tmm) cc_final: 0.7426 (ttm) REVERT: B 682 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7729 (pt0) REVERT: C 276 GLU cc_start: 0.6672 (OUTLIER) cc_final: 0.6173 (mp0) REVERT: C 423 GLU cc_start: 0.6403 (OUTLIER) cc_final: 0.6109 (OUTLIER) REVERT: C 488 MET cc_start: 0.6663 (mtp) cc_final: 0.5971 (mpm) REVERT: C 555 MET cc_start: 0.7953 (tmm) cc_final: 0.7437 (ttm) REVERT: C 717 MET cc_start: 0.7764 (mpp) cc_final: 0.7391 (mmm) REVERT: C 738 LYS cc_start: 0.8423 (mttt) cc_final: 0.7847 (mtmm) REVERT: D 276 GLU cc_start: 0.6641 (OUTLIER) cc_final: 0.6199 (mp0) REVERT: D 355 GLU cc_start: 0.7256 (mm-30) cc_final: 0.6876 (pm20) REVERT: D 423 GLU cc_start: 0.6397 (OUTLIER) cc_final: 0.6105 (OUTLIER) REVERT: D 488 MET cc_start: 0.6707 (mtp) cc_final: 0.5927 (mpm) REVERT: D 555 MET cc_start: 0.7959 (tmm) cc_final: 0.7446 (ttm) REVERT: D 682 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7730 (pt0) REVERT: D 717 MET cc_start: 0.7740 (mpp) cc_final: 0.7365 (mmm) REVERT: D 719 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.7004 (pm20) outliers start: 57 outliers final: 46 residues processed: 336 average time/residue: 1.3011 time to fit residues: 497.7071 Evaluate side-chains 358 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 302 time to evaluate : 2.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 369 ARG Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 340 ASP Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 713 SER Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 369 ARG Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 626 SER Chi-restraints excluded: chain D residue 682 GLU Chi-restraints excluded: chain D residue 713 SER Chi-restraints excluded: chain D residue 719 GLU Chi-restraints excluded: chain D residue 720 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 184 optimal weight: 0.7980 chunk 29 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 205 optimal weight: 7.9990 chunk 25 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 175 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 439 HIS D 750 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.181659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.133611 restraints weight = 22066.905| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.77 r_work: 0.3239 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3083 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3078 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.5150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 22428 Z= 0.155 Angle : 0.520 10.826 30068 Z= 0.256 Chirality : 0.038 0.194 3272 Planarity : 0.003 0.041 3668 Dihedral : 15.703 87.287 3724 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.30 % Allowed : 16.61 % Favored : 81.10 % 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: 0.22 (0.17), residues: 2520 helix: 1.17 (0.13), residues: 1576 sheet: 0.26 (0.64), residues: 84 loop : -1.84 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 380 HIS 0.005 0.001 HIS C 439 PHE 0.010 0.001 PHE C 522 TYR 0.014 0.001 TYR C 451 ARG 0.002 0.000 ARG C 225 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9519.40 seconds wall clock time: 166 minutes 1.90 seconds (9961.90 seconds total)