Starting phenix.real_space_refine on Wed Feb 21 08:24:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qs8_4627/02_2024/6qs8_4627_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qs8_4627/02_2024/6qs8_4627.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qs8_4627/02_2024/6qs8_4627.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qs8_4627/02_2024/6qs8_4627.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qs8_4627/02_2024/6qs8_4627_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qs8_4627/02_2024/6qs8_4627_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1218 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 32 5.49 5 Mg 8 5.21 5 S 108 5.16 5 C 18010 2.51 5 N 5230 2.21 5 O 5487 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 320": "NH1" <-> "NH2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A ARG 528": "NH1" <-> "NH2" Residue "B ARG 252": "NH1" <-> "NH2" Residue "B ARG 332": "NH1" <-> "NH2" Residue "B ARG 528": "NH1" <-> "NH2" Residue "B ARG 550": "NH1" <-> "NH2" Residue "C ARG 252": "NH1" <-> "NH2" Residue "C ARG 332": "NH1" <-> "NH2" Residue "C ARG 528": "NH1" <-> "NH2" Residue "C ARG 550": "NH1" <-> "NH2" Residue "D ARG 332": "NH1" <-> "NH2" Residue "D ARG 528": "NH1" <-> "NH2" Residue "D ARG 550": "NH1" <-> "NH2" Residue "E ARG 332": "NH1" <-> "NH2" Residue "E ARG 528": "NH1" <-> "NH2" Residue "E ARG 550": "NH1" <-> "NH2" Residue "F ARG 252": "NH1" <-> "NH2" Residue "F ARG 332": "NH1" <-> "NH2" Residue "F ARG 528": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 28875 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4472 Classifications: {'peptide': 568} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 546} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 4562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4562 Classifications: {'peptide': 582} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 559} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 4976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 4976 Classifications: {'peptide': 630} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 606} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 4952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 4952 Classifications: {'peptide': 625} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 601} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 4952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 4952 Classifications: {'peptide': 625} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 601} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 4496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4496 Classifications: {'peptide': 573} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 551} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "S" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'TRANS': 23} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'UNK:plan-1': 24} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'AGS': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 15.99, per 1000 atoms: 0.55 Number of scatterers: 28875 At special positions: 0 Unit cell: (119.7, 143.85, 157.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 108 16.00 P 32 15.00 Mg 8 11.99 O 5487 8.00 N 5230 7.00 C 18010 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.89 Conformation dependent library (CDL) restraints added in 5.1 seconds 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6724 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 178 helices and 25 sheets defined 50.4% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.92 Creating SS restraints... Processing helix chain 'A' and resid 161 through 164 No H-bonds generated for 'chain 'A' and resid 161 through 164' Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 184 through 193 Processing helix chain 'A' and resid 212 through 225 Processing helix chain 'A' and resid 242 through 245 No H-bonds generated for 'chain 'A' and resid 242 through 245' Processing helix chain 'A' and resid 255 through 268 Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 296 through 304 Proline residue: A 301 - end of helix Processing helix chain 'A' and resid 316 through 322 Processing helix chain 'A' and resid 327 through 331 Processing helix chain 'A' and resid 343 through 352 Processing helix chain 'A' and resid 354 through 360 Processing helix chain 'A' and resid 367 through 380 Processing helix chain 'A' and resid 388 through 407 Processing helix chain 'A' and resid 533 through 542 Processing helix chain 'A' and resid 555 through 560 Processing helix chain 'A' and resid 562 through 567 Processing helix chain 'A' and resid 574 through 588 Processing helix chain 'A' and resid 611 through 622 Processing helix chain 'A' and resid 640 through 647 Processing helix chain 'A' and resid 662 through 668 Processing helix chain 'A' and resid 679 through 681 No H-bonds generated for 'chain 'A' and resid 679 through 681' Processing helix chain 'A' and resid 686 through 696 Processing helix chain 'A' and resid 722 through 726 Processing helix chain 'A' and resid 735 through 748 Processing helix chain 'A' and resid 768 through 789 Processing helix chain 'A' and resid 797 through 804 Processing helix chain 'A' and resid 814 through 826 Processing helix chain 'A' and resid 828 through 834 Processing helix chain 'B' and resid 168 through 174 Processing helix chain 'B' and resid 184 through 194 Processing helix chain 'B' and resid 213 through 225 Processing helix chain 'B' and resid 242 through 246 Processing helix chain 'B' and resid 255 through 268 Processing helix chain 'B' and resid 280 through 284 Processing helix chain 'B' and resid 295 through 304 Proline residue: B 301 - end of helix removed outlier: 3.761A pdb=" N ALA B 304 " --> pdb=" O LYS B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 322 Processing helix chain 'B' and resid 327 through 331 Processing helix chain 'B' and resid 343 through 352 Processing helix chain 'B' and resid 354 through 361 Processing helix chain 'B' and resid 367 through 379 Processing helix chain 'B' and resid 388 through 406 Processing helix chain 'B' and resid 533 through 544 Processing helix chain 'B' and resid 553 through 560 Processing helix chain 'B' and resid 562 through 567 Processing helix chain 'B' and resid 574 through 589 Processing helix chain 'B' and resid 611 through 623 Processing helix chain 'B' and resid 634 through 636 No H-bonds generated for 'chain 'B' and resid 634 through 636' Processing helix chain 'B' and resid 640 through 647 removed outlier: 3.675A pdb=" N VAL B 643 " --> pdb=" O LYS B 640 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL B 647 " --> pdb=" O SER B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 658 No H-bonds generated for 'chain 'B' and resid 656 through 658' Processing helix chain 'B' and resid 661 through 668 Processing helix chain 'B' and resid 684 through 686 No H-bonds generated for 'chain 'B' and resid 684 through 686' Processing helix chain 'B' and resid 688 through 696 Processing helix chain 'B' and resid 722 through 728 Processing helix chain 'B' and resid 734 through 748 Processing helix chain 'B' and resid 753 through 756 No H-bonds generated for 'chain 'B' and resid 753 through 756' Processing helix chain 'B' and resid 768 through 789 Processing helix chain 'B' and resid 797 through 806 Processing helix chain 'B' and resid 815 through 833 Proline residue: B 828 - end of helix Processing helix chain 'C' and resid 161 through 164 No H-bonds generated for 'chain 'C' and resid 161 through 164' Processing helix chain 'C' and resid 168 through 173 Processing helix chain 'C' and resid 184 through 194 Processing helix chain 'C' and resid 212 through 225 removed outlier: 3.579A pdb=" N VAL C 216 " --> pdb=" O LYS C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 247 Processing helix chain 'C' and resid 254 through 269 removed outlier: 3.584A pdb=" N GLN C 269 " --> pdb=" O ASP C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 282 No H-bonds generated for 'chain 'C' and resid 280 through 282' Processing helix chain 'C' and resid 300 through 304 Processing helix chain 'C' and resid 318 through 322 Processing helix chain 'C' and resid 327 through 330 No H-bonds generated for 'chain 'C' and resid 327 through 330' Processing helix chain 'C' and resid 343 through 361 removed outlier: 3.872A pdb=" N GLY C 352 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N GLU C 355 " --> pdb=" O ARG C 351 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ARG C 356 " --> pdb=" O GLY C 352 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR C 357 " --> pdb=" O LEU C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 380 Processing helix chain 'C' and resid 388 through 406 Processing helix chain 'C' and resid 410 through 428 Processing helix chain 'C' and resid 445 through 464 Processing helix chain 'C' and resid 533 through 543 Processing helix chain 'C' and resid 553 through 560 Processing helix chain 'C' and resid 562 through 566 Processing helix chain 'C' and resid 574 through 589 Processing helix chain 'C' and resid 611 through 623 Processing helix chain 'C' and resid 642 through 647 Processing helix chain 'C' and resid 661 through 668 Processing helix chain 'C' and resid 679 through 681 No H-bonds generated for 'chain 'C' and resid 679 through 681' Processing helix chain 'C' and resid 684 through 686 No H-bonds generated for 'chain 'C' and resid 684 through 686' Processing helix chain 'C' and resid 689 through 696 Processing helix chain 'C' and resid 722 through 728 Processing helix chain 'C' and resid 734 through 748 Processing helix chain 'C' and resid 768 through 787 Processing helix chain 'C' and resid 799 through 806 Processing helix chain 'C' and resid 815 through 833 Proline residue: C 828 - end of helix Processing helix chain 'D' and resid 161 through 164 No H-bonds generated for 'chain 'D' and resid 161 through 164' Processing helix chain 'D' and resid 168 through 173 Processing helix chain 'D' and resid 184 through 194 Processing helix chain 'D' and resid 213 through 225 Processing helix chain 'D' and resid 242 through 248 Processing helix chain 'D' and resid 254 through 269 Processing helix chain 'D' and resid 280 through 283 Processing helix chain 'D' and resid 297 through 303 Proline residue: D 301 - end of helix No H-bonds generated for 'chain 'D' and resid 297 through 303' Processing helix chain 'D' and resid 318 through 322 Processing helix chain 'D' and resid 327 through 331 Processing helix chain 'D' and resid 343 through 361 Processing helix chain 'D' and resid 367 through 380 Processing helix chain 'D' and resid 388 through 406 Processing helix chain 'D' and resid 410 through 428 Processing helix chain 'D' and resid 445 through 464 Processing helix chain 'D' and resid 533 through 543 Processing helix chain 'D' and resid 553 through 560 Processing helix chain 'D' and resid 562 through 566 Processing helix chain 'D' and resid 574 through 588 Processing helix chain 'D' and resid 611 through 623 Processing helix chain 'D' and resid 634 through 636 No H-bonds generated for 'chain 'D' and resid 634 through 636' Processing helix chain 'D' and resid 642 through 646 Processing helix chain 'D' and resid 654 through 656 No H-bonds generated for 'chain 'D' and resid 654 through 656' Processing helix chain 'D' and resid 662 through 668 Processing helix chain 'D' and resid 679 through 681 No H-bonds generated for 'chain 'D' and resid 679 through 681' Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 722 through 728 Processing helix chain 'D' and resid 734 through 748 Processing helix chain 'D' and resid 753 through 755 No H-bonds generated for 'chain 'D' and resid 753 through 755' Processing helix chain 'D' and resid 768 through 789 Processing helix chain 'D' and resid 797 through 805 Processing helix chain 'D' and resid 815 through 834 Proline residue: D 828 - end of helix Processing helix chain 'E' and resid 161 through 164 No H-bonds generated for 'chain 'E' and resid 161 through 164' Processing helix chain 'E' and resid 169 through 173 Processing helix chain 'E' and resid 184 through 194 Processing helix chain 'E' and resid 212 through 225 Processing helix chain 'E' and resid 230 through 232 No H-bonds generated for 'chain 'E' and resid 230 through 232' Processing helix chain 'E' and resid 242 through 245 No H-bonds generated for 'chain 'E' and resid 242 through 245' Processing helix chain 'E' and resid 254 through 269 Processing helix chain 'E' and resid 280 through 284 Processing helix chain 'E' and resid 296 through 303 Proline residue: E 301 - end of helix Processing helix chain 'E' and resid 316 through 322 Processing helix chain 'E' and resid 327 through 332 removed outlier: 3.831A pdb=" N GLU E 330 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ARG E 331 " --> pdb=" O ALA E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 361 removed outlier: 4.550A pdb=" N LEU E 359 " --> pdb=" O GLU E 355 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N HIS E 360 " --> pdb=" O ARG E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 380 Processing helix chain 'E' and resid 388 through 406 Processing helix chain 'E' and resid 410 through 428 Processing helix chain 'E' and resid 445 through 465 Processing helix chain 'E' and resid 533 through 544 Processing helix chain 'E' and resid 553 through 566 Processing helix chain 'E' and resid 574 through 588 Processing helix chain 'E' and resid 611 through 623 Processing helix chain 'E' and resid 642 through 646 Processing helix chain 'E' and resid 662 through 668 Processing helix chain 'E' and resid 679 through 681 No H-bonds generated for 'chain 'E' and resid 679 through 681' Processing helix chain 'E' and resid 687 through 696 Processing helix chain 'E' and resid 722 through 728 Processing helix chain 'E' and resid 734 through 748 Processing helix chain 'E' and resid 768 through 787 Processing helix chain 'E' and resid 799 through 806 Processing helix chain 'E' and resid 815 through 834 Proline residue: E 828 - end of helix Processing helix chain 'F' and resid 161 through 164 No H-bonds generated for 'chain 'F' and resid 161 through 164' Processing helix chain 'F' and resid 168 through 173 Processing helix chain 'F' and resid 184 through 194 Processing helix chain 'F' and resid 212 through 225 removed outlier: 3.807A pdb=" N VAL F 216 " --> pdb=" O LYS F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 232 No H-bonds generated for 'chain 'F' and resid 230 through 232' Processing helix chain 'F' and resid 242 through 245 No H-bonds generated for 'chain 'F' and resid 242 through 245' Processing helix chain 'F' and resid 255 through 269 Processing helix chain 'F' and resid 280 through 284 Processing helix chain 'F' and resid 296 through 303 Proline residue: F 301 - end of helix Processing helix chain 'F' and resid 316 through 322 Processing helix chain 'F' and resid 328 through 331 No H-bonds generated for 'chain 'F' and resid 328 through 331' Processing helix chain 'F' and resid 343 through 352 Processing helix chain 'F' and resid 354 through 361 Processing helix chain 'F' and resid 367 through 380 Processing helix chain 'F' and resid 388 through 406 Processing helix chain 'F' and resid 533 through 542 Processing helix chain 'F' and resid 555 through 569 removed outlier: 4.487A pdb=" N HIS F 567 " --> pdb=" O GLU F 563 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N HIS F 568 " --> pdb=" O GLN F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 574 through 588 Processing helix chain 'F' and resid 611 through 622 Processing helix chain 'F' and resid 643 through 646 No H-bonds generated for 'chain 'F' and resid 643 through 646' Processing helix chain 'F' and resid 663 through 668 Processing helix chain 'F' and resid 679 through 681 No H-bonds generated for 'chain 'F' and resid 679 through 681' Processing helix chain 'F' and resid 684 through 695 removed outlier: 4.401A pdb=" N ASN F 688 " --> pdb=" O PRO F 684 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ILE F 689 " --> pdb=" O ASP F 685 " (cutoff:3.500A) Processing helix chain 'F' and resid 722 through 728 Processing helix chain 'F' and resid 735 through 748 Processing helix chain 'F' and resid 769 through 789 Processing helix chain 'F' and resid 797 through 807 Processing helix chain 'F' and resid 815 through 833 Proline residue: F 828 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 165 through 167 removed outlier: 4.610A pdb=" N ASP A 278 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL A 311 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N GLN A 334 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ILE A 205 " --> pdb=" O GLN A 334 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL A 336 " --> pdb=" O ILE A 205 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 599 through 603 removed outlier: 6.506A pdb=" N VAL A 630 " --> pdb=" O LEU A 675 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ASP A 677 " --> pdb=" O VAL A 630 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE A 632 " --> pdb=" O ASP A 677 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 698 through 700 Processing sheet with id= D, first strand: chain 'A' and resid 793 through 795 removed outlier: 6.172A pdb=" N ILE A 844 " --> pdb=" O HIS A 794 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 165 through 167 removed outlier: 5.385A pdb=" N ASP B 278 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N VAL B 311 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLY B 206 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N GLN B 334 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE B 205 " --> pdb=" O GLN B 334 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N VAL B 336 " --> pdb=" O ILE B 205 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 759 through 762 removed outlier: 3.571A pdb=" N GLU B 759 " --> pdb=" O SER B 600 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY B 599 " --> pdb=" O THR B 712 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N SER B 672 " --> pdb=" O VAL B 713 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N ILE B 715 " --> pdb=" O SER B 672 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE B 674 " --> pdb=" O ILE B 715 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N THR B 717 " --> pdb=" O ILE B 674 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N LEU B 676 " --> pdb=" O THR B 717 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL B 630 " --> pdb=" O LEU B 675 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N ASP B 677 " --> pdb=" O VAL B 630 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE B 632 " --> pdb=" O ASP B 677 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 698 through 700 Processing sheet with id= H, first strand: chain 'B' and resid 793 through 795 removed outlier: 5.870A pdb=" N ILE B 844 " --> pdb=" O HIS B 794 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG B 845 " --> pdb=" O VAL B 856 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 165 through 167 removed outlier: 4.987A pdb=" N ASP C 278 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL C 311 " --> pdb=" O ILE C 277 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 202 through 205 removed outlier: 5.703A pdb=" N GLN C 334 " --> pdb=" O VAL C 203 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE C 205 " --> pdb=" O GLN C 334 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N VAL C 336 " --> pdb=" O ILE C 205 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 759 through 762 removed outlier: 3.561A pdb=" N GLU C 759 " --> pdb=" O SER C 600 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL C 630 " --> pdb=" O LEU C 675 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ASP C 677 " --> pdb=" O VAL C 630 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ILE C 632 " --> pdb=" O ASP C 677 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 698 through 700 Processing sheet with id= M, first strand: chain 'C' and resid 792 through 795 removed outlier: 3.635A pdb=" N ARG C 845 " --> pdb=" O VAL C 856 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 165 through 167 removed outlier: 5.303A pdb=" N ASP D 278 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY D 206 " --> pdb=" O THR D 314 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N GLN D 334 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILE D 205 " --> pdb=" O GLN D 334 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N VAL D 336 " --> pdb=" O ILE D 205 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 759 through 762 removed outlier: 3.627A pdb=" N GLU D 759 " --> pdb=" O SER D 600 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY D 599 " --> pdb=" O THR D 712 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N SER D 672 " --> pdb=" O VAL D 713 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ILE D 715 " --> pdb=" O SER D 672 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ILE D 674 " --> pdb=" O ILE D 715 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N THR D 717 " --> pdb=" O ILE D 674 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU D 676 " --> pdb=" O THR D 717 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL D 630 " --> pdb=" O LEU D 675 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N ASP D 677 " --> pdb=" O VAL D 630 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE D 632 " --> pdb=" O ASP D 677 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 698 through 700 Processing sheet with id= Q, first strand: chain 'D' and resid 792 through 795 Processing sheet with id= R, first strand: chain 'E' and resid 165 through 167 removed outlier: 3.648A pdb=" N LEU E 238 " --> pdb=" O ILE E 274 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 333 through 337 removed outlier: 7.587A pdb=" N ASN E 201 " --> pdb=" O GLN E 334 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N VAL E 336 " --> pdb=" O ASN E 201 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL E 203 " --> pdb=" O VAL E 336 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA E 313 " --> pdb=" O ILE E 277 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 759 through 762 removed outlier: 3.738A pdb=" N LEU E 602 " --> pdb=" O GLU E 759 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL E 630 " --> pdb=" O LEU E 675 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ASP E 677 " --> pdb=" O VAL E 630 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE E 632 " --> pdb=" O ASP E 677 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 698 through 700 Processing sheet with id= V, first strand: chain 'E' and resid 844 through 848 removed outlier: 3.933A pdb=" N ARG E 845 " --> pdb=" O VAL E 856 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 165 through 167 removed outlier: 3.619A pdb=" N LEU F 238 " --> pdb=" O ILE F 274 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU F 240 " --> pdb=" O PHE F 276 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ASP F 278 " --> pdb=" O LEU F 240 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL F 311 " --> pdb=" O ILE F 277 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N THR F 314 " --> pdb=" O PRO F 202 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N LEU F 204 " --> pdb=" O THR F 314 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 599 through 604 removed outlier: 3.727A pdb=" N GLY F 599 " --> pdb=" O THR F 712 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE F 601 " --> pdb=" O VAL F 714 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N SER F 672 " --> pdb=" O VAL F 713 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N ILE F 715 " --> pdb=" O SER F 672 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE F 674 " --> pdb=" O ILE F 715 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N THR F 717 " --> pdb=" O ILE F 674 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LEU F 676 " --> pdb=" O THR F 717 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL F 630 " --> pdb=" O LEU F 675 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ASP F 677 " --> pdb=" O VAL F 630 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE F 632 " --> pdb=" O ASP F 677 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 792 through 795 1208 hydrogen bonds defined for protein. 3603 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: 10.60 Time building geometry restraints manager: 12.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 10263 1.36 - 1.51: 8656 1.51 - 1.65: 10184 1.65 - 1.80: 174 1.80 - 1.95: 20 Bond restraints: 29297 Sorted by residual: bond pdb=" CG1 ILE B 584 " pdb=" CD1 ILE B 584 " ideal model delta sigma weight residual 1.513 1.380 0.133 3.90e-02 6.57e+02 1.16e+01 bond pdb=" CG1 ILE D 584 " pdb=" CD1 ILE D 584 " ideal model delta sigma weight residual 1.513 1.381 0.132 3.90e-02 6.57e+02 1.15e+01 bond pdb=" CG1 ILE C 584 " pdb=" CD1 ILE C 584 " ideal model delta sigma weight residual 1.513 1.391 0.122 3.90e-02 6.57e+02 9.77e+00 bond pdb=" CB GLU B 752 " pdb=" CG GLU B 752 " ideal model delta sigma weight residual 1.520 1.430 0.090 3.00e-02 1.11e+03 8.97e+00 bond pdb=" CB PRO B 650 " pdb=" CG PRO B 650 " ideal model delta sigma weight residual 1.492 1.352 0.140 5.00e-02 4.00e+02 7.81e+00 ... (remaining 29292 not shown) Histogram of bond angle deviations from ideal: 96.23 - 104.11: 435 104.11 - 112.00: 14014 112.00 - 119.89: 12455 119.89 - 127.77: 12464 127.77 - 135.66: 226 Bond angle restraints: 39594 Sorted by residual: angle pdb=" C LEU A 299 " pdb=" N LYS A 300 " pdb=" CA LYS A 300 " ideal model delta sigma weight residual 120.09 126.79 -6.70 1.25e+00 6.40e-01 2.87e+01 angle pdb=" C SER C 644 " pdb=" N ARG C 645 " pdb=" CA ARG C 645 " ideal model delta sigma weight residual 121.58 112.42 9.16 1.95e+00 2.63e-01 2.21e+01 angle pdb=" CB LYS B 199 " pdb=" CG LYS B 199 " pdb=" CD LYS B 199 " ideal model delta sigma weight residual 111.30 100.76 10.54 2.30e+00 1.89e-01 2.10e+01 angle pdb=" C ALA C 247 " pdb=" N GLY C 248 " pdb=" CA GLY C 248 " ideal model delta sigma weight residual 121.82 111.65 10.17 2.30e+00 1.89e-01 1.95e+01 angle pdb=" CA LEU D 646 " pdb=" CB LEU D 646 " pdb=" CG LEU D 646 " ideal model delta sigma weight residual 116.30 131.25 -14.95 3.50e+00 8.16e-02 1.82e+01 ... (remaining 39589 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.36: 17624 26.36 - 52.72: 383 52.72 - 79.09: 52 79.09 - 105.45: 4 105.45 - 131.81: 2 Dihedral angle restraints: 18065 sinusoidal: 7643 harmonic: 10422 Sorted by residual: dihedral pdb=" CA MET C 293 " pdb=" C MET C 293 " pdb=" N ASP C 294 " pdb=" CA ASP C 294 " ideal model delta harmonic sigma weight residual 180.00 141.73 38.27 0 5.00e+00 4.00e-02 5.86e+01 dihedral pdb=" C5' ADP F1001 " pdb=" O5' ADP F1001 " pdb=" PA ADP F1001 " pdb=" O2A ADP F1001 " ideal model delta sinusoidal sigma weight residual 300.00 168.19 131.81 1 2.00e+01 2.50e-03 4.00e+01 dihedral pdb=" CA ASP A 624 " pdb=" C ASP A 624 " pdb=" N SER A 625 " pdb=" CA SER A 625 " ideal model delta harmonic sigma weight residual -180.00 -148.79 -31.21 0 5.00e+00 4.00e-02 3.90e+01 ... (remaining 18062 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 3441 0.070 - 0.141: 928 0.141 - 0.211: 103 0.211 - 0.281: 4 0.281 - 0.351: 3 Chirality restraints: 4479 Sorted by residual: chirality pdb=" CB VAL B 679 " pdb=" CA VAL B 679 " pdb=" CG1 VAL B 679 " pdb=" CG2 VAL B 679 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" CB VAL C 679 " pdb=" CA VAL C 679 " pdb=" CG1 VAL C 679 " pdb=" CG2 VAL C 679 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CG LEU B 694 " pdb=" CB LEU B 694 " pdb=" CD1 LEU B 694 " pdb=" CD2 LEU B 694 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 4476 not shown) Planarity restraints: 5168 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 763 " 0.020 2.00e-02 2.50e+03 2.52e-02 1.11e+01 pdb=" CG PHE D 763 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE D 763 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE D 763 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE D 763 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE D 763 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE D 763 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 763 " 0.019 2.00e-02 2.50e+03 2.51e-02 1.10e+01 pdb=" CG PHE B 763 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE B 763 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE B 763 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 763 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE B 763 " 0.014 2.00e-02 2.50e+03 pdb=" CZ PHE B 763 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 763 " 0.018 2.00e-02 2.50e+03 2.38e-02 9.88e+00 pdb=" CG PHE C 763 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE C 763 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 PHE C 763 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE C 763 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 PHE C 763 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE C 763 " 0.005 2.00e-02 2.50e+03 ... (remaining 5165 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 270 2.59 - 3.17: 23431 3.17 - 3.75: 44444 3.75 - 4.32: 63078 4.32 - 4.90: 103385 Nonbonded interactions: 234608 Sorted by model distance: nonbonded pdb=" O1B AGS D 902 " pdb="MG MG D 904 " model vdw 2.018 2.170 nonbonded pdb=" O2G AGS E1002 " pdb="MG MG E1003 " model vdw 2.024 2.170 nonbonded pdb=" OG1 THR E 612 " pdb="MG MG E1003 " model vdw 2.045 2.170 nonbonded pdb=" O1B AGS C1001 " pdb="MG MG C1003 " model vdw 2.062 2.170 nonbonded pdb=" O1B AGS D 901 " pdb="MG MG D 903 " model vdw 2.066 2.170 ... (remaining 234603 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 159 through 858) selection = (chain 'B' and (resid 159 through 287 or resid 293 through 543 or resid 553 thro \ ugh 858)) selection = (chain 'C' and (resid 159 through 287 or resid 293 through 408 or resid 527 thro \ ugh 543 or resid 553 through 858)) selection = (chain 'D' and (resid 159 through 408 or resid 527 through 543 or resid 553 thro \ ugh 858)) selection = (chain 'E' and (resid 159 through 408 or resid 527 through 543 or resid 553 thro \ ugh 858)) selection = (chain 'F' and (resid 159 through 287 or resid 293 through 858)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.040 Extract box with map and model: 6.850 Check model and map are aligned: 0.410 Set scattering table: 0.250 Process input model: 78.850 Find NCS groups from input model: 2.500 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 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 : 0.011 0.140 29297 Z= 0.728 Angle : 1.047 14.947 39594 Z= 0.565 Chirality : 0.061 0.351 4479 Planarity : 0.008 0.072 5168 Dihedral : 11.141 131.810 11341 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 0.17 % Allowed : 1.23 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.91 (0.11), residues: 3561 helix: -2.48 (0.08), residues: 1986 sheet: -2.65 (0.24), residues: 352 loop : -2.38 (0.16), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.006 TRP D 543 HIS 0.017 0.003 HIS F 747 PHE 0.053 0.005 PHE D 763 TYR 0.039 0.003 TYR B 357 ARG 0.017 0.002 ARG C 351 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 917 residues out of total 3026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 912 time to evaluate : 3.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 LEU cc_start: 0.8601 (mt) cc_final: 0.8368 (tp) REVERT: A 700 THR cc_start: 0.8518 (m) cc_final: 0.8116 (p) REVERT: B 314 THR cc_start: 0.8952 (t) cc_final: 0.8618 (p) REVERT: B 399 SER cc_start: 0.8394 (m) cc_final: 0.8182 (p) REVERT: C 737 MET cc_start: 0.7515 (tpp) cc_final: 0.7313 (tpp) REVERT: C 761 VAL cc_start: 0.9465 (m) cc_final: 0.8699 (p) REVERT: C 817 LEU cc_start: 0.8590 (tp) cc_final: 0.8142 (tp) REVERT: D 622 MET cc_start: 0.7406 (ttm) cc_final: 0.7139 (mtm) REVERT: D 677 ASP cc_start: 0.8076 (t0) cc_final: 0.7827 (t70) REVERT: E 277 ILE cc_start: 0.8599 (mt) cc_final: 0.8042 (pt) REVERT: E 293 MET cc_start: 0.3039 (tpt) cc_final: 0.2668 (tpt) REVERT: E 685 ASP cc_start: 0.7145 (p0) cc_final: 0.6285 (t0) REVERT: F 713 VAL cc_start: 0.5930 (t) cc_final: 0.5458 (t) outliers start: 5 outliers final: 0 residues processed: 916 average time/residue: 0.5080 time to fit residues: 680.3013 Evaluate side-chains 433 residues out of total 3026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 433 time to evaluate : 3.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 0.7980 chunk 272 optimal weight: 0.9980 chunk 151 optimal weight: 3.9990 chunk 93 optimal weight: 8.9990 chunk 184 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 282 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 171 optimal weight: 6.9990 chunk 210 optimal weight: 0.4980 chunk 326 optimal weight: 9.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 HIS ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 GLN ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 GLN B 195 GLN B 281 HIS B 297 ASN B 360 HIS ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 HIS B 849 ASN B 858 HIS C 201 ASN C 297 ASN C 421 GLN ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 GLN ** D 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 641 HIS ** D 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 692 GLN D 748 ASN D 806 ASN D 822 GLN D 857 GLN E 192 GLN E 567 HIS E 641 HIS E 692 GLN E 703 GLN F 281 HIS F 309 HIS F 378 HIS F 573 GLN F 711 ASN F 726 GLN F 747 HIS F 794 HIS F 831 GLN F 849 ASN F 858 HIS Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 29297 Z= 0.237 Angle : 0.681 10.046 39594 Z= 0.343 Chirality : 0.045 0.213 4479 Planarity : 0.005 0.056 5168 Dihedral : 9.565 93.445 4207 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.66 % Allowed : 10.77 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.13), residues: 3561 helix: -0.78 (0.11), residues: 1950 sheet: -2.28 (0.24), residues: 385 loop : -1.74 (0.17), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 543 HIS 0.011 0.001 HIS F 567 PHE 0.031 0.002 PHE D 729 TYR 0.023 0.002 TYR C 656 ARG 0.014 0.001 ARG B 351 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 3026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 473 time to evaluate : 3.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 562 MET cc_start: 0.4580 (tpp) cc_final: 0.4017 (tpp) REVERT: A 700 THR cc_start: 0.8655 (m) cc_final: 0.8172 (p) REVERT: A 748 ASN cc_start: 0.8322 (m110) cc_final: 0.8069 (t0) REVERT: B 266 LEU cc_start: 0.8647 (mt) cc_final: 0.8408 (mt) REVERT: B 399 SER cc_start: 0.8551 (m) cc_final: 0.8321 (p) REVERT: B 689 ILE cc_start: 0.8676 (mm) cc_final: 0.8404 (mp) REVERT: B 737 MET cc_start: 0.7852 (ttm) cc_final: 0.7538 (ttp) REVERT: B 784 LYS cc_start: 0.8530 (tmmt) cc_final: 0.8262 (tmmt) REVERT: C 413 ASP cc_start: 0.7406 (t0) cc_final: 0.7166 (t0) REVERT: C 453 ARG cc_start: 0.7584 (ttp80) cc_final: 0.7343 (ttp80) REVERT: C 715 ILE cc_start: 0.9211 (mt) cc_final: 0.8991 (mt) REVERT: D 329 LEU cc_start: 0.8908 (tp) cc_final: 0.8657 (tp) REVERT: D 424 LEU cc_start: 0.8664 (mt) cc_final: 0.8293 (tt) REVERT: D 642 SER cc_start: 0.8291 (m) cc_final: 0.7647 (p) REVERT: D 822 GLN cc_start: 0.7471 (tt0) cc_final: 0.7131 (tp40) REVERT: E 329 LEU cc_start: 0.8457 (tp) cc_final: 0.8244 (tp) REVERT: E 685 ASP cc_start: 0.7142 (p0) cc_final: 0.6697 (p0) REVERT: F 217 GLU cc_start: 0.6175 (pt0) cc_final: 0.5831 (pt0) REVERT: F 629 MET cc_start: 0.5420 (pmm) cc_final: 0.4597 (mtm) outliers start: 80 outliers final: 46 residues processed: 523 average time/residue: 0.4613 time to fit residues: 379.9539 Evaluate side-chains 411 residues out of total 3026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 365 time to evaluate : 3.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 562 MET Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 383 ASP Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 551 MET Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 747 HIS Chi-restraints excluded: chain C residue 752 GLU Chi-restraints excluded: chain C residue 804 SER Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 446 GLU Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 700 THR Chi-restraints excluded: chain D residue 744 VAL Chi-restraints excluded: chain D residue 806 ASN Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 276 PHE Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 703 GLN Chi-restraints excluded: chain E residue 714 VAL Chi-restraints excluded: chain E residue 797 ASP Chi-restraints excluded: chain E residue 803 LEU Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 297 ASN Chi-restraints excluded: chain F residue 543 TRP Chi-restraints excluded: chain F residue 615 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 272 optimal weight: 5.9990 chunk 222 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 327 optimal weight: 0.0670 chunk 353 optimal weight: 0.0170 chunk 291 optimal weight: 2.9990 chunk 324 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 262 optimal weight: 3.9990 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN A 334 GLN ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 719 ASN ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 GLN ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 HIS C 195 GLN C 421 GLN C 426 GLN C 445 ASN C 641 HIS ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 748 ASN D 806 ASN ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 427 GLN E 574 ASN E 703 GLN ** F 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 378 HIS ** F 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 858 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29297 Z= 0.178 Angle : 0.621 10.006 39594 Z= 0.309 Chirality : 0.043 0.212 4479 Planarity : 0.005 0.066 5168 Dihedral : 9.053 77.582 4207 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.39 % Allowed : 13.07 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.20 (0.14), residues: 3561 helix: 0.02 (0.11), residues: 1939 sheet: -2.24 (0.23), residues: 404 loop : -1.44 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 543 HIS 0.011 0.001 HIS F 378 PHE 0.023 0.001 PHE D 729 TYR 0.019 0.001 TYR F 671 ARG 0.008 0.001 ARG D 453 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 3026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 413 time to evaluate : 3.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 562 MET cc_start: 0.4502 (tpp) cc_final: 0.3788 (tpp) REVERT: A 629 MET cc_start: 0.6469 (ppp) cc_final: 0.6035 (ppp) REVERT: A 700 THR cc_start: 0.8623 (m) cc_final: 0.8169 (p) REVERT: B 399 SER cc_start: 0.8568 (m) cc_final: 0.8325 (p) REVERT: B 737 MET cc_start: 0.7803 (ttm) cc_final: 0.7602 (ttp) REVERT: B 784 LYS cc_start: 0.8444 (tmmt) cc_final: 0.8198 (tmmt) REVERT: C 413 ASP cc_start: 0.7444 (t0) cc_final: 0.7098 (t0) REVERT: C 453 ARG cc_start: 0.7537 (ttp80) cc_final: 0.7297 (ttp80) REVERT: C 562 MET cc_start: 0.7985 (ttt) cc_final: 0.7754 (ttt) REVERT: C 634 MET cc_start: 0.7633 (mmm) cc_final: 0.7362 (mmm) REVERT: D 329 LEU cc_start: 0.8953 (tp) cc_final: 0.8710 (tp) REVERT: D 418 ARG cc_start: 0.7549 (mmm160) cc_final: 0.7302 (tpt90) REVERT: D 424 LEU cc_start: 0.8639 (mt) cc_final: 0.8289 (tt) REVERT: D 642 SER cc_start: 0.8171 (m) cc_final: 0.7615 (p) REVERT: E 318 GLU cc_start: 0.6513 (mp0) cc_final: 0.5781 (mp0) REVERT: E 685 ASP cc_start: 0.7252 (p0) cc_final: 0.6807 (p0) REVERT: F 217 GLU cc_start: 0.6039 (pt0) cc_final: 0.5803 (pt0) REVERT: F 303 LEU cc_start: 0.7396 (pp) cc_final: 0.6908 (mp) outliers start: 72 outliers final: 47 residues processed: 456 average time/residue: 0.4169 time to fit residues: 303.8262 Evaluate side-chains 395 residues out of total 3026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 348 time to evaluate : 3.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain A residue 763 PHE Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 794 HIS Chi-restraints excluded: chain C residue 195 GLN Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 421 GLN Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 551 MET Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 752 GLU Chi-restraints excluded: chain C residue 804 SER Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 446 GLU Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 700 THR Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain D residue 851 ASP Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 644 SER Chi-restraints excluded: chain E residue 695 ASP Chi-restraints excluded: chain E residue 797 ASP Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 378 HIS Chi-restraints excluded: chain F residue 543 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 5.9990 chunk 246 optimal weight: 9.9990 chunk 169 optimal weight: 8.9990 chunk 36 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 219 optimal weight: 8.9990 chunk 328 optimal weight: 9.9990 chunk 347 optimal weight: 5.9990 chunk 171 optimal weight: 9.9990 chunk 311 optimal weight: 20.0000 chunk 93 optimal weight: 1.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 ASN A 309 HIS A 360 HIS A 567 HIS ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 858 HIS B 159 GLN B 620 ASN ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 HIS ** B 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 GLN C 445 ASN ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 822 GLN ** D 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 748 ASN ** D 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 831 GLN E 427 GLN F 823 GLN F 858 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 29297 Z= 0.309 Angle : 0.651 10.263 39594 Z= 0.326 Chirality : 0.045 0.303 4479 Planarity : 0.005 0.055 5168 Dihedral : 8.786 76.093 4207 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.26 % Allowed : 13.63 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.75 (0.14), residues: 3561 helix: 0.42 (0.12), residues: 1951 sheet: -2.08 (0.22), residues: 442 loop : -1.25 (0.19), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 543 HIS 0.010 0.001 HIS C 794 PHE 0.020 0.002 PHE D 729 TYR 0.018 0.002 TYR B 251 ARG 0.007 0.001 ARG E 645 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 3026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 354 time to evaluate : 3.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 562 MET cc_start: 0.4546 (tpp) cc_final: 0.3887 (tpp) REVERT: A 629 MET cc_start: 0.6783 (ppp) cc_final: 0.6470 (ppp) REVERT: A 700 THR cc_start: 0.8577 (m) cc_final: 0.8243 (p) REVERT: B 266 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8429 (mt) REVERT: B 326 ASP cc_start: 0.7822 (t0) cc_final: 0.7540 (t0) REVERT: B 399 SER cc_start: 0.8578 (m) cc_final: 0.8367 (p) REVERT: B 737 MET cc_start: 0.7909 (ttm) cc_final: 0.7683 (ttp) REVERT: C 453 ARG cc_start: 0.7657 (ttp80) cc_final: 0.7348 (ttp80) REVERT: C 634 MET cc_start: 0.7805 (mmm) cc_final: 0.7510 (mmm) REVERT: D 329 LEU cc_start: 0.8985 (tp) cc_final: 0.8744 (tp) REVERT: D 418 ARG cc_start: 0.7649 (mmm160) cc_final: 0.7364 (tpt90) REVERT: D 424 LEU cc_start: 0.8647 (mt) cc_final: 0.8270 (tt) REVERT: D 642 SER cc_start: 0.8172 (m) cc_final: 0.7725 (p) REVERT: E 293 MET cc_start: 0.2937 (tpp) cc_final: 0.2514 (tpt) REVERT: E 685 ASP cc_start: 0.7309 (p0) cc_final: 0.6795 (p0) outliers start: 98 outliers final: 62 residues processed: 414 average time/residue: 0.3926 time to fit residues: 262.6020 Evaluate side-chains 384 residues out of total 3026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 321 time to evaluate : 3.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 763 PHE Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 794 HIS Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 551 MET Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 747 HIS Chi-restraints excluded: chain C residue 761 VAL Chi-restraints excluded: chain C residue 779 LEU Chi-restraints excluded: chain C residue 804 SER Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 446 GLU Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 700 THR Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 588 ARG Chi-restraints excluded: chain E residue 644 SER Chi-restraints excluded: chain E residue 696 ASP Chi-restraints excluded: chain E residue 760 VAL Chi-restraints excluded: chain E residue 797 ASP Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 297 ASN Chi-restraints excluded: chain F residue 320 ARG Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 543 TRP Chi-restraints excluded: chain F residue 620 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 1.9990 chunk 197 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 259 optimal weight: 5.9990 chunk 143 optimal weight: 10.0000 chunk 296 optimal weight: 0.0040 chunk 240 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 177 optimal weight: 10.0000 chunk 312 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 overall best weight: 3.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 HIS ** B 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 GLN ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 HIS ** D 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 748 ASN D 824 GLN F 378 HIS F 641 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.4738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 29297 Z= 0.281 Angle : 0.634 11.103 39594 Z= 0.315 Chirality : 0.044 0.236 4479 Planarity : 0.004 0.060 5168 Dihedral : 8.527 74.339 4207 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.32 % Allowed : 14.76 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.47 (0.14), residues: 3561 helix: 0.66 (0.12), residues: 1941 sheet: -2.04 (0.22), residues: 436 loop : -1.10 (0.19), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 543 HIS 0.009 0.001 HIS F 378 PHE 0.018 0.002 PHE D 729 TYR 0.015 0.002 TYR F 671 ARG 0.012 0.001 ARG B 785 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 3026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 340 time to evaluate : 3.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 562 MET cc_start: 0.4564 (tpp) cc_final: 0.4225 (tpp) REVERT: A 629 MET cc_start: 0.7115 (ppp) cc_final: 0.6586 (ppp) REVERT: A 700 THR cc_start: 0.8565 (m) cc_final: 0.8164 (p) REVERT: B 326 ASP cc_start: 0.7942 (t0) cc_final: 0.7666 (t0) REVERT: B 710 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7460 (mtt90) REVERT: B 737 MET cc_start: 0.7973 (ttm) cc_final: 0.7661 (ttp) REVERT: C 453 ARG cc_start: 0.7590 (ttp80) cc_final: 0.7246 (ttp80) REVERT: C 634 MET cc_start: 0.7761 (mmm) cc_final: 0.7547 (mmm) REVERT: C 692 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8456 (mt0) REVERT: D 424 LEU cc_start: 0.8630 (mt) cc_final: 0.8267 (tt) REVERT: D 642 SER cc_start: 0.8051 (m) cc_final: 0.7646 (p) REVERT: E 293 MET cc_start: 0.2618 (tpp) cc_final: 0.2269 (tpt) REVERT: E 562 MET cc_start: 0.6819 (tpp) cc_final: 0.6528 (tpp) REVERT: E 685 ASP cc_start: 0.7356 (p0) cc_final: 0.6810 (p0) REVERT: F 217 GLU cc_start: 0.6327 (pt0) cc_final: 0.5823 (pt0) REVERT: F 737 MET cc_start: 0.4440 (tpt) cc_final: 0.3801 (mmp) outliers start: 100 outliers final: 65 residues processed: 404 average time/residue: 0.4078 time to fit residues: 264.8270 Evaluate side-chains 372 residues out of total 3026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 305 time to evaluate : 3.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 763 PHE Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 710 ARG Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 794 HIS Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 551 MET Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 692 GLN Chi-restraints excluded: chain C residue 754 ILE Chi-restraints excluded: chain C residue 761 VAL Chi-restraints excluded: chain C residue 804 SER Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 446 GLU Chi-restraints excluded: chain D residue 538 GLU Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 700 THR Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 318 GLU Chi-restraints excluded: chain E residue 588 ARG Chi-restraints excluded: chain E residue 644 SER Chi-restraints excluded: chain E residue 656 TYR Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 696 ASP Chi-restraints excluded: chain E residue 760 VAL Chi-restraints excluded: chain E residue 797 ASP Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 297 ASN Chi-restraints excluded: chain F residue 316 LEU Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 543 TRP Chi-restraints excluded: chain F residue 553 GLU Chi-restraints excluded: chain F residue 615 CYS Chi-restraints excluded: chain F residue 620 ASN Chi-restraints excluded: chain F residue 719 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 7.9990 chunk 313 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 204 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 348 optimal weight: 0.0670 chunk 289 optimal weight: 7.9990 chunk 161 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 chunk 182 optimal weight: 1.9990 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 ASN ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 HIS B 831 GLN C 264 ASN ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 GLN ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 747 HIS C 794 HIS ** D 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 823 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.4937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29297 Z= 0.181 Angle : 0.588 17.536 39594 Z= 0.289 Chirality : 0.042 0.174 4479 Planarity : 0.004 0.060 5168 Dihedral : 8.217 72.716 4207 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.53 % Allowed : 16.36 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.15 (0.14), residues: 3561 helix: 0.91 (0.12), residues: 1947 sheet: -1.88 (0.23), residues: 435 loop : -0.94 (0.19), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 543 HIS 0.009 0.001 HIS C 747 PHE 0.019 0.001 PHE D 729 TYR 0.016 0.001 TYR F 671 ARG 0.006 0.000 ARG C 414 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 347 time to evaluate : 4.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 562 MET cc_start: 0.4389 (tpp) cc_final: 0.4119 (tpp) REVERT: A 629 MET cc_start: 0.6939 (ppp) cc_final: 0.6502 (ppp) REVERT: A 700 THR cc_start: 0.8614 (m) cc_final: 0.8201 (p) REVERT: B 326 ASP cc_start: 0.7866 (t0) cc_final: 0.7651 (t0) REVERT: B 562 MET cc_start: 0.7844 (tpt) cc_final: 0.7588 (tpt) REVERT: B 737 MET cc_start: 0.7899 (ttm) cc_final: 0.7679 (ttp) REVERT: C 186 GLU cc_start: 0.6693 (mp0) cc_final: 0.6409 (mp0) REVERT: D 424 LEU cc_start: 0.8632 (mt) cc_final: 0.8248 (tt) REVERT: D 642 SER cc_start: 0.8173 (m) cc_final: 0.7754 (p) REVERT: E 303 LEU cc_start: 0.7695 (pp) cc_final: 0.7470 (mt) REVERT: E 535 GLU cc_start: 0.7350 (mp0) cc_final: 0.7052 (mm-30) REVERT: E 562 MET cc_start: 0.6576 (tpp) cc_final: 0.6257 (tpp) REVERT: E 624 ASP cc_start: 0.6931 (m-30) cc_final: 0.6671 (m-30) REVERT: E 685 ASP cc_start: 0.7345 (p0) cc_final: 0.6748 (p0) REVERT: E 783 TYR cc_start: 0.6878 (m-80) cc_final: 0.6625 (m-80) REVERT: F 217 GLU cc_start: 0.6301 (pt0) cc_final: 0.5850 (pt0) REVERT: F 737 MET cc_start: 0.4393 (tpt) cc_final: 0.3863 (mmp) outliers start: 76 outliers final: 54 residues processed: 396 average time/residue: 0.3755 time to fit residues: 242.8662 Evaluate side-chains 371 residues out of total 3026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 317 time to evaluate : 3.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 763 PHE Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 794 HIS Chi-restraints excluded: chain B residue 831 GLN Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 551 MET Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 747 HIS Chi-restraints excluded: chain C residue 761 VAL Chi-restraints excluded: chain C residue 804 SER Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 446 GLU Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain D residue 809 ASP Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 294 ASP Chi-restraints excluded: chain E residue 318 GLU Chi-restraints excluded: chain E residue 403 MET Chi-restraints excluded: chain E residue 588 ARG Chi-restraints excluded: chain E residue 644 SER Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 656 TYR Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 797 ASP Chi-restraints excluded: chain E residue 802 LEU Chi-restraints excluded: chain E residue 803 LEU Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 316 LEU Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 543 TRP Chi-restraints excluded: chain F residue 620 ASN Chi-restraints excluded: chain F residue 761 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 chunk 198 optimal weight: 3.9990 chunk 254 optimal weight: 3.9990 chunk 197 optimal weight: 8.9990 chunk 293 optimal weight: 0.9990 chunk 194 optimal weight: 4.9990 chunk 346 optimal weight: 20.0000 chunk 217 optimal weight: 6.9990 chunk 211 optimal weight: 8.9990 chunk 160 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 GLN ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 747 HIS ** D 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 378 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.5114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 29297 Z= 0.259 Angle : 0.629 17.328 39594 Z= 0.308 Chirality : 0.043 0.241 4479 Planarity : 0.004 0.061 5168 Dihedral : 8.225 72.479 4207 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.89 % Allowed : 16.32 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.07 (0.14), residues: 3561 helix: 0.98 (0.12), residues: 1936 sheet: -1.89 (0.23), residues: 447 loop : -0.86 (0.19), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 543 HIS 0.019 0.001 HIS C 747 PHE 0.016 0.001 PHE C 729 TYR 0.015 0.001 TYR F 671 ARG 0.008 0.000 ARG F 320 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 320 time to evaluate : 3.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 562 MET cc_start: 0.4381 (tpp) cc_final: 0.4069 (tpp) REVERT: A 629 MET cc_start: 0.7084 (ppp) cc_final: 0.6633 (ppp) REVERT: A 700 THR cc_start: 0.8703 (m) cc_final: 0.8252 (p) REVERT: B 326 ASP cc_start: 0.7939 (t0) cc_final: 0.7712 (t0) REVERT: B 562 MET cc_start: 0.7941 (tpt) cc_final: 0.7726 (tpt) REVERT: B 710 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7495 (mtt90) REVERT: B 737 MET cc_start: 0.7889 (ttm) cc_final: 0.7663 (ttp) REVERT: C 186 GLU cc_start: 0.6733 (mp0) cc_final: 0.6458 (mp0) REVERT: C 750 ARG cc_start: 0.6993 (OUTLIER) cc_final: 0.6779 (mtm110) REVERT: D 424 LEU cc_start: 0.8664 (mt) cc_final: 0.8247 (tt) REVERT: D 642 SER cc_start: 0.8047 (m) cc_final: 0.7714 (p) REVERT: E 293 MET cc_start: 0.3126 (tpp) cc_final: 0.1228 (ttm) REVERT: E 303 LEU cc_start: 0.7599 (pp) cc_final: 0.7355 (mt) REVERT: E 408 LYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7136 (mtmm) REVERT: E 535 GLU cc_start: 0.7368 (mp0) cc_final: 0.7102 (mm-30) REVERT: E 624 ASP cc_start: 0.6963 (m-30) cc_final: 0.6723 (m-30) REVERT: E 685 ASP cc_start: 0.7313 (p0) cc_final: 0.6668 (p0) REVERT: F 217 GLU cc_start: 0.6321 (pt0) cc_final: 0.5875 (pt0) REVERT: F 737 MET cc_start: 0.4703 (tpt) cc_final: 0.4075 (mmp) outliers start: 87 outliers final: 66 residues processed: 375 average time/residue: 0.3952 time to fit residues: 240.1974 Evaluate side-chains 374 residues out of total 3026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 305 time to evaluate : 3.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 763 PHE Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 710 ARG Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 794 HIS Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 421 GLN Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 747 HIS Chi-restraints excluded: chain C residue 750 ARG Chi-restraints excluded: chain C residue 761 VAL Chi-restraints excluded: chain C residue 779 LEU Chi-restraints excluded: chain C residue 804 SER Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 446 GLU Chi-restraints excluded: chain D residue 538 GLU Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain D residue 809 ASP Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 294 ASP Chi-restraints excluded: chain E residue 318 GLU Chi-restraints excluded: chain E residue 403 MET Chi-restraints excluded: chain E residue 408 LYS Chi-restraints excluded: chain E residue 588 ARG Chi-restraints excluded: chain E residue 644 SER Chi-restraints excluded: chain E residue 656 TYR Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 693 VAL Chi-restraints excluded: chain E residue 761 VAL Chi-restraints excluded: chain E residue 797 ASP Chi-restraints excluded: chain E residue 802 LEU Chi-restraints excluded: chain E residue 803 LEU Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 297 ASN Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 378 HIS Chi-restraints excluded: chain F residue 543 TRP Chi-restraints excluded: chain F residue 761 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 214 optimal weight: 9.9990 chunk 138 optimal weight: 0.8980 chunk 207 optimal weight: 0.9990 chunk 104 optimal weight: 9.9990 chunk 68 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 220 optimal weight: 3.9990 chunk 236 optimal weight: 3.9990 chunk 171 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 272 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN C 421 GLN ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 747 HIS ** C 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 378 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.5238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29297 Z= 0.199 Angle : 0.611 17.725 39594 Z= 0.299 Chirality : 0.042 0.214 4479 Planarity : 0.004 0.061 5168 Dihedral : 8.067 71.472 4207 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.76 % Allowed : 16.86 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.04 (0.15), residues: 3561 helix: 1.05 (0.12), residues: 1941 sheet: -1.82 (0.23), residues: 448 loop : -0.79 (0.19), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 543 HIS 0.017 0.001 HIS F 378 PHE 0.016 0.001 PHE D 729 TYR 0.015 0.001 TYR F 671 ARG 0.012 0.000 ARG F 320 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 328 time to evaluate : 3.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 562 MET cc_start: 0.4553 (tpp) cc_final: 0.4266 (tpp) REVERT: A 629 MET cc_start: 0.6974 (ppp) cc_final: 0.6533 (ppp) REVERT: B 326 ASP cc_start: 0.7933 (t0) cc_final: 0.7699 (t0) REVERT: B 710 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7511 (mtt90) REVERT: B 737 MET cc_start: 0.7848 (ttm) cc_final: 0.7638 (ttp) REVERT: C 186 GLU cc_start: 0.6715 (mp0) cc_final: 0.6484 (mp0) REVERT: C 750 ARG cc_start: 0.6944 (OUTLIER) cc_final: 0.6719 (mtm110) REVERT: D 424 LEU cc_start: 0.8599 (mt) cc_final: 0.8245 (tt) REVERT: D 642 SER cc_start: 0.8066 (m) cc_final: 0.7687 (p) REVERT: E 303 LEU cc_start: 0.7567 (pp) cc_final: 0.7322 (mt) REVERT: E 408 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.7171 (mtmm) REVERT: E 535 GLU cc_start: 0.7308 (mp0) cc_final: 0.7075 (mm-30) REVERT: E 685 ASP cc_start: 0.7298 (p0) cc_final: 0.6618 (p0) REVERT: F 217 GLU cc_start: 0.6338 (pt0) cc_final: 0.6059 (pt0) REVERT: F 737 MET cc_start: 0.4672 (tpt) cc_final: 0.4079 (mmp) outliers start: 83 outliers final: 68 residues processed: 382 average time/residue: 0.3849 time to fit residues: 240.7636 Evaluate side-chains 375 residues out of total 3026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 304 time to evaluate : 3.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 763 PHE Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 710 ARG Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 794 HIS Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 421 GLN Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 747 HIS Chi-restraints excluded: chain C residue 750 ARG Chi-restraints excluded: chain C residue 761 VAL Chi-restraints excluded: chain C residue 779 LEU Chi-restraints excluded: chain C residue 804 SER Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 446 GLU Chi-restraints excluded: chain D residue 538 GLU Chi-restraints excluded: chain D residue 552 MET Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 641 HIS Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain D residue 761 VAL Chi-restraints excluded: chain D residue 809 ASP Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 294 ASP Chi-restraints excluded: chain E residue 318 GLU Chi-restraints excluded: chain E residue 403 MET Chi-restraints excluded: chain E residue 408 LYS Chi-restraints excluded: chain E residue 644 SER Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 656 TYR Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 693 VAL Chi-restraints excluded: chain E residue 761 VAL Chi-restraints excluded: chain E residue 797 ASP Chi-restraints excluded: chain E residue 803 LEU Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 297 ASN Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 378 HIS Chi-restraints excluded: chain F residue 533 ASP Chi-restraints excluded: chain F residue 543 TRP Chi-restraints excluded: chain F residue 761 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 8.9990 chunk 332 optimal weight: 8.9990 chunk 303 optimal weight: 4.9990 chunk 323 optimal weight: 9.9990 chunk 194 optimal weight: 0.9980 chunk 140 optimal weight: 6.9990 chunk 253 optimal weight: 8.9990 chunk 99 optimal weight: 3.9990 chunk 292 optimal weight: 4.9990 chunk 305 optimal weight: 6.9990 chunk 322 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 HIS B 806 ASN ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 GLN ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 747 HIS D 334 GLN ** D 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 378 HIS F 823 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.5429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 29297 Z= 0.345 Angle : 0.691 16.251 39594 Z= 0.340 Chirality : 0.045 0.213 4479 Planarity : 0.005 0.061 5168 Dihedral : 8.278 73.351 4207 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.69 % Allowed : 17.35 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.11 (0.14), residues: 3561 helix: 0.90 (0.12), residues: 1949 sheet: -1.84 (0.22), residues: 460 loop : -0.83 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 543 HIS 0.023 0.001 HIS C 747 PHE 0.019 0.002 PHE E 333 TYR 0.014 0.002 TYR F 671 ARG 0.024 0.001 ARG F 320 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 303 time to evaluate : 3.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 562 MET cc_start: 0.4521 (tpp) cc_final: 0.4251 (tpp) REVERT: A 629 MET cc_start: 0.7126 (ppp) cc_final: 0.6922 (ppp) REVERT: B 677 ASP cc_start: 0.7829 (m-30) cc_final: 0.7558 (m-30) REVERT: B 710 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7561 (mtt90) REVERT: B 737 MET cc_start: 0.7886 (ttm) cc_final: 0.7685 (ttp) REVERT: C 186 GLU cc_start: 0.6833 (mp0) cc_final: 0.6572 (mp0) REVERT: C 690 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8632 (mt) REVERT: D 424 LEU cc_start: 0.8600 (mt) cc_final: 0.8243 (tt) REVERT: D 642 SER cc_start: 0.8101 (m) cc_final: 0.7696 (p) REVERT: E 303 LEU cc_start: 0.7531 (pp) cc_final: 0.7296 (mt) REVERT: E 408 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7275 (mtmm) REVERT: E 535 GLU cc_start: 0.7378 (mp0) cc_final: 0.7136 (mm-30) REVERT: F 217 GLU cc_start: 0.6465 (pt0) cc_final: 0.6074 (pt0) REVERT: F 737 MET cc_start: 0.4652 (tpt) cc_final: 0.4178 (mmp) outliers start: 81 outliers final: 63 residues processed: 358 average time/residue: 0.3767 time to fit residues: 221.2577 Evaluate side-chains 358 residues out of total 3026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 292 time to evaluate : 3.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 763 PHE Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 710 ARG Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 794 HIS Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 421 GLN Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 747 HIS Chi-restraints excluded: chain C residue 761 VAL Chi-restraints excluded: chain C residue 779 LEU Chi-restraints excluded: chain C residue 804 SER Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 446 GLU Chi-restraints excluded: chain D residue 538 GLU Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain D residue 761 VAL Chi-restraints excluded: chain D residue 809 ASP Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 318 GLU Chi-restraints excluded: chain E residue 408 LYS Chi-restraints excluded: chain E residue 644 SER Chi-restraints excluded: chain E residue 656 TYR Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 693 VAL Chi-restraints excluded: chain E residue 761 VAL Chi-restraints excluded: chain E residue 797 ASP Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 297 ASN Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 533 ASP Chi-restraints excluded: chain F residue 543 TRP Chi-restraints excluded: chain F residue 620 ASN Chi-restraints excluded: chain F residue 761 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 0.7980 chunk 341 optimal weight: 0.2980 chunk 208 optimal weight: 0.7980 chunk 162 optimal weight: 0.5980 chunk 237 optimal weight: 2.9990 chunk 358 optimal weight: 20.0000 chunk 330 optimal weight: 9.9990 chunk 285 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 220 optimal weight: 0.7980 chunk 175 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 747 HIS ** C 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 378 HIS F 823 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.5502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29297 Z= 0.169 Angle : 0.625 17.597 39594 Z= 0.304 Chirality : 0.042 0.199 4479 Planarity : 0.004 0.061 5168 Dihedral : 7.846 70.169 4207 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.96 % Allowed : 18.09 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.15), residues: 3561 helix: 1.10 (0.12), residues: 1948 sheet: -1.70 (0.23), residues: 450 loop : -0.70 (0.20), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 462 HIS 0.020 0.001 HIS C 747 PHE 0.016 0.001 PHE D 729 TYR 0.016 0.001 TYR F 671 ARG 0.011 0.000 ARG F 320 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 338 time to evaluate : 3.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 562 MET cc_start: 0.4467 (tpp) cc_final: 0.4241 (tpp) REVERT: A 627 GLU cc_start: 0.7756 (pp20) cc_final: 0.7463 (pp20) REVERT: B 710 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7423 (mtt90) REVERT: B 737 MET cc_start: 0.7784 (ttm) cc_final: 0.7516 (ttp) REVERT: C 186 GLU cc_start: 0.6728 (mp0) cc_final: 0.6506 (mp0) REVERT: D 424 LEU cc_start: 0.8602 (mt) cc_final: 0.8244 (tt) REVERT: D 642 SER cc_start: 0.8157 (m) cc_final: 0.7745 (p) REVERT: E 408 LYS cc_start: 0.7599 (OUTLIER) cc_final: 0.7169 (mtmm) REVERT: E 535 GLU cc_start: 0.7245 (mp0) cc_final: 0.7035 (mm-30) REVERT: E 685 ASP cc_start: 0.7314 (p0) cc_final: 0.6520 (t0) REVERT: F 217 GLU cc_start: 0.6361 (pt0) cc_final: 0.5997 (pt0) REVERT: F 737 MET cc_start: 0.4533 (tpt) cc_final: 0.4089 (mmp) REVERT: F 827 ASN cc_start: 0.8274 (m-40) cc_final: 0.8020 (m110) outliers start: 59 outliers final: 48 residues processed: 379 average time/residue: 0.4051 time to fit residues: 250.7599 Evaluate side-chains 359 residues out of total 3026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 309 time to evaluate : 3.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 763 PHE Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 710 ARG Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 794 HIS Chi-restraints excluded: chain B residue 822 GLN Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 334 GLN Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 761 VAL Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 446 GLU Chi-restraints excluded: chain D residue 538 GLU Chi-restraints excluded: chain D residue 552 MET Chi-restraints excluded: chain D residue 641 HIS Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain D residue 761 VAL Chi-restraints excluded: chain D residue 809 ASP Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 318 GLU Chi-restraints excluded: chain E residue 408 LYS Chi-restraints excluded: chain E residue 656 TYR Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 693 VAL Chi-restraints excluded: chain E residue 761 VAL Chi-restraints excluded: chain E residue 797 ASP Chi-restraints excluded: chain E residue 803 LEU Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 297 ASN Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 543 TRP Chi-restraints excluded: chain F residue 615 CYS Chi-restraints excluded: chain F residue 761 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 4.9990 chunk 304 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 263 optimal weight: 6.9990 chunk 42 optimal weight: 8.9990 chunk 79 optimal weight: 9.9990 chunk 286 optimal weight: 0.4980 chunk 119 optimal weight: 0.6980 chunk 293 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 HIS ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.106728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.082535 restraints weight = 75480.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.084160 restraints weight = 46078.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.085486 restraints weight = 26654.625| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.5538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.225 29297 Z= 0.283 Angle : 0.760 59.121 39594 Z= 0.400 Chirality : 0.043 0.259 4479 Planarity : 0.004 0.061 5168 Dihedral : 7.841 70.037 4207 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.06 % Allowed : 18.45 % Favored : 79.49 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.15), residues: 3561 helix: 1.09 (0.12), residues: 1947 sheet: -1.64 (0.23), residues: 444 loop : -0.71 (0.20), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 462 HIS 0.018 0.001 HIS A 747 PHE 0.016 0.001 PHE D 729 TYR 0.031 0.001 TYR C 671 ARG 0.051 0.000 ARG D 588 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6173.76 seconds wall clock time: 113 minutes 6.45 seconds (6786.45 seconds total)