Starting phenix.real_space_refine on Thu Mar 21 05:51:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qs6_4624/03_2024/6qs6_4624_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qs6_4624/03_2024/6qs6_4624.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/6qs6_4624/03_2024/6qs6_4624.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qs6_4624/03_2024/6qs6_4624.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qs6_4624/03_2024/6qs6_4624_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qs6_4624/03_2024/6qs6_4624_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= 0.008 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 812 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: 5 Type Number sf(0) Gaussians P 31 5.49 5 S 109 5.16 5 C 17822 2.51 5 N 5179 2.21 5 O 5416 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 TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A ARG 528": "NH1" <-> "NH2" Residue "A ARG 550": "NH1" <-> "NH2" Residue "A TYR 671": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 320": "NH1" <-> "NH2" Residue "F ARG 332": "NH1" <-> "NH2" Residue "F ARG 528": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28557 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4538 Classifications: {'peptide': 577} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 554} Chain breaks: 2 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: 4538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4538 Classifications: {'peptide': 577} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 554} Chain breaks: 2 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: 4538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4538 Classifications: {'peptide': 577} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 554} Chain breaks: 2 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: "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: 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} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.78, per 1000 atoms: 0.52 Number of scatterers: 28557 At special positions: 0 Unit cell: (123.9, 145.95, 150.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 109 16.00 P 31 15.00 O 5416 8.00 N 5179 7.00 C 17822 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=17, symmetry=0 Number of additional bonds: simple=17, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.82 Conformation dependent library (CDL) restraints added in 5.1 seconds 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6652 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 177 helices and 27 sheets defined 50.6% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.35 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 174 Processing helix chain 'A' and resid 184 through 195 Processing helix chain 'A' and resid 212 through 225 Processing helix chain 'A' and resid 243 through 245 No H-bonds generated for 'chain 'A' and resid 243 through 245' Processing helix chain 'A' and resid 255 through 268 Processing helix chain 'A' and resid 280 through 283 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 332 Processing helix chain 'A' and resid 343 through 358 Processing helix chain 'A' and resid 367 through 379 Processing helix chain 'A' and resid 388 through 405 Processing helix chain 'A' and resid 533 through 543 Processing helix chain 'A' and resid 555 through 560 Processing helix chain 'A' and resid 562 through 568 removed outlier: 3.755A pdb=" N HIS A 568 " --> pdb=" O GLN A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 588 Processing helix chain 'A' and resid 611 through 622 Processing helix chain 'A' and resid 634 through 636 No H-bonds generated for 'chain 'A' and resid 634 through 636' Processing helix chain 'A' and resid 640 through 647 Processing helix chain 'A' and resid 654 through 658 removed outlier: 4.574A pdb=" N GLU A 657 " --> pdb=" O VAL A 654 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU A 658 " --> pdb=" O GLY A 655 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 654 through 658' 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 728 Processing helix chain 'A' and resid 734 through 748 Processing helix chain 'A' and resid 751 through 755 Processing helix chain 'A' and resid 768 through 789 Processing helix chain 'A' and resid 797 through 806 Processing helix chain 'A' and resid 815 through 826 Processing helix chain 'A' and resid 828 through 833 Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 184 through 194 Processing helix chain 'B' and resid 212 through 225 Processing helix chain 'B' and resid 242 through 245 No H-bonds generated for 'chain 'B' and resid 242 through 245' Processing helix chain 'B' and resid 254 through 267 Processing helix chain 'B' and resid 280 through 284 Processing helix chain 'B' and resid 295 through 303 Proline residue: B 301 - end of helix Processing helix chain 'B' and resid 316 through 322 Processing helix chain 'B' and resid 327 through 332 Processing helix chain 'B' and resid 343 through 361 Processing helix chain 'B' and resid 367 through 380 Processing helix chain 'B' and resid 388 through 407 Processing helix chain 'B' and resid 533 through 543 Processing helix chain 'B' and resid 553 through 569 Processing helix chain 'B' and resid 574 through 589 Processing helix chain 'B' and resid 612 through 622 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: 3.651A pdb=" N VAL B 643 " --> pdb=" O LYS B 640 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER B 644 " --> pdb=" O HIS B 641 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL B 647 " --> pdb=" O SER B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 668 Processing helix chain 'B' and resid 679 through 681 No H-bonds generated for 'chain 'B' and resid 679 through 681' 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 727 Processing helix chain 'B' and resid 734 through 748 Processing helix chain 'B' and resid 768 through 789 Processing helix chain 'B' and resid 797 through 805 Processing helix chain 'B' and resid 815 through 835 Proline residue: B 828 - end of helix Processing helix chain 'C' and resid 160 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 213 through 225 Processing helix chain 'C' and resid 242 through 246 Processing helix chain 'C' and resid 254 through 268 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 299 through 304 Processing helix chain 'C' and resid 316 through 322 Processing helix chain 'C' and resid 327 through 331 Processing helix chain 'C' and resid 343 through 361 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 588 Processing helix chain 'C' and resid 611 through 622 Processing helix chain 'C' and resid 640 through 647 removed outlier: 3.871A pdb=" N VAL C 643 " --> pdb=" O LYS C 640 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ARG C 645 " --> pdb=" O SER C 642 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL C 647 " --> pdb=" O SER C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 656 No H-bonds generated for 'chain 'C' and resid 654 through 656' 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 753 through 756 No H-bonds generated for 'chain 'C' and resid 753 through 756' Processing helix chain 'C' and resid 768 through 789 removed outlier: 3.819A pdb=" N GLU C 788 " --> pdb=" O LYS C 784 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ARG C 789 " --> pdb=" O ARG C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 797 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 169 through 173 Processing helix chain 'D' and resid 184 through 194 Processing helix chain 'D' and resid 212 through 225 Processing helix chain 'D' and resid 242 through 248 removed outlier: 3.809A pdb=" N ALA D 247 " --> pdb=" O GLY D 243 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLY D 248 " --> pdb=" O ALA D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 268 Processing helix chain 'D' and resid 280 through 284 removed outlier: 3.751A pdb=" N VAL D 284 " --> pdb=" O LEU D 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 280 through 284' Processing helix chain 'D' and resid 300 through 305 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 379 Processing helix chain 'D' and resid 388 through 406 Processing helix chain 'D' and resid 410 through 426 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 567 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 645 Processing helix chain 'D' and resid 656 through 658 No H-bonds generated for 'chain 'D' and resid 656 through 658' 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 684 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 751 through 755 Processing helix chain 'D' and resid 768 through 789 Processing helix chain 'D' and resid 797 through 806 Processing helix chain 'D' and resid 815 through 824 Processing helix chain 'D' and resid 826 through 834 Processing helix chain 'E' and resid 168 through 174 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 243 through 247 Processing helix chain 'E' and resid 254 through 269 Processing helix chain 'E' and resid 280 through 284 Processing helix chain 'E' and resid 299 through 305 Processing helix chain 'E' and resid 316 through 322 Processing helix chain 'E' and resid 343 through 361 Processing helix chain 'E' and resid 367 through 379 Processing helix chain 'E' and resid 388 through 406 Processing helix chain 'E' and resid 533 through 541 Processing helix chain 'E' and resid 554 through 560 Processing helix chain 'E' and resid 562 through 569 Processing helix chain 'E' and resid 574 through 589 Processing helix chain 'E' and resid 611 through 623 removed outlier: 3.921A pdb=" N CYS E 615 " --> pdb=" O LYS E 611 " (cutoff:3.500A) Processing helix chain 'E' and resid 634 through 636 No H-bonds generated for 'chain 'E' and resid 634 through 636' Processing helix chain 'E' and resid 641 through 646 Processing helix chain 'E' and resid 664 through 667 No H-bonds generated for 'chain 'E' and resid 664 through 667' 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 684 through 696 Processing helix chain 'E' and resid 722 through 728 Processing helix chain 'E' and resid 735 through 748 Processing helix chain 'E' and resid 751 through 755 Processing helix chain 'E' and resid 768 through 789 Processing helix chain 'E' and resid 797 through 806 Processing helix chain 'E' and resid 815 through 833 Proline residue: E 828 - end of helix Processing helix chain 'F' and resid 169 through 173 Processing helix chain 'F' and resid 184 through 195 Processing helix chain 'F' and resid 212 through 225 Processing helix chain 'F' and resid 242 through 247 Processing helix chain 'F' and resid 255 through 269 Processing helix chain 'F' and resid 280 through 284 Processing helix chain 'F' and resid 300 through 305 removed outlier: 3.679A pdb=" N ARG F 305 " --> pdb=" O PRO F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 322 Processing helix chain 'F' and resid 343 through 360 Processing helix chain 'F' and resid 367 through 380 Processing helix chain 'F' and resid 388 through 405 Processing helix chain 'F' and resid 533 through 542 Processing helix chain 'F' and resid 556 through 569 removed outlier: 3.529A pdb=" N HIS F 568 " --> pdb=" O GLN F 564 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG F 569 " --> pdb=" O GLU F 565 " (cutoff:3.500A) Processing helix chain 'F' and resid 574 through 589 Processing helix chain 'F' and resid 611 through 622 Processing helix chain 'F' and resid 640 through 645 Processing helix chain 'F' and resid 654 through 656 No H-bonds generated for 'chain 'F' and resid 654 through 656' Processing helix chain 'F' and resid 664 through 667 No H-bonds generated for 'chain 'F' and resid 664 through 667' 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 696 Processing helix chain 'F' and resid 722 through 726 Processing helix chain 'F' and resid 734 through 748 Processing helix chain 'F' and resid 751 through 756 Processing helix chain 'F' and resid 768 through 789 Processing helix chain 'F' and resid 797 through 807 Processing helix chain 'F' and resid 814 through 835 Proline residue: F 828 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 165 through 167 Processing sheet with id= B, first strand: chain 'A' and resid 311 through 314 removed outlier: 7.817A pdb=" N THR A 314 " --> pdb=" O PRO A 202 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N LEU A 204 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N GLN A 334 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE A 205 " --> pdb=" O GLN A 334 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL A 336 " --> pdb=" O ILE A 205 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 759 through 762 removed outlier: 3.658A pdb=" N GLU A 759 " --> pdb=" O SER A 600 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU A 602 " --> pdb=" O GLU A 759 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 604 " --> pdb=" O VAL A 761 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLY A 599 " --> pdb=" O THR A 712 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N SER A 672 " --> pdb=" O VAL A 713 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N ILE A 715 " --> pdb=" O SER A 672 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE A 674 " --> pdb=" O ILE A 715 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N THR A 717 " --> pdb=" O ILE A 674 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU A 676 " --> pdb=" O THR A 717 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 698 through 700 removed outlier: 3.561A pdb=" N LEU A 699 " --> pdb=" O VAL A 707 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 792 through 795 Processing sheet with id= F, first strand: chain 'B' and resid 165 through 167 removed outlier: 5.432A pdb=" N ASP B 278 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL B 311 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLN B 334 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ILE B 205 " --> pdb=" O GLN B 334 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL B 336 " --> pdb=" O ILE B 205 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 601 through 603 removed outlier: 7.061A pdb=" N GLU B 759 " --> pdb=" O LEU B 602 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 630 through 633 removed outlier: 6.070A pdb=" N VAL B 713 " --> pdb=" O ILE B 674 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N LEU B 676 " --> pdb=" O VAL B 713 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE B 715 " --> pdb=" O LEU B 676 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 698 through 701 removed outlier: 3.868A pdb=" N ARG B 705 " --> pdb=" O ASP B 701 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 793 through 795 removed outlier: 6.330A pdb=" N ILE B 844 " --> pdb=" O HIS B 794 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 165 through 167 removed outlier: 4.850A pdb=" N ASP C 278 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N VAL C 311 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N THR C 314 " --> pdb=" O PRO C 202 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N LEU C 204 " --> pdb=" O THR C 314 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N GLN C 334 " --> pdb=" O VAL C 203 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE C 205 " --> pdb=" O GLN C 334 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N VAL C 336 " --> pdb=" O ILE C 205 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 759 through 762 removed outlier: 3.559A pdb=" N LEU C 602 " --> pdb=" O GLU C 759 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 698 through 700 Processing sheet with id= N, first strand: chain 'C' and resid 792 through 795 Processing sheet with id= O, first strand: chain 'D' and resid 165 through 167 removed outlier: 5.099A pdb=" N ASP D 278 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL D 311 " --> pdb=" O ILE D 277 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 759 through 761 removed outlier: 3.507A pdb=" N GLU D 759 " --> pdb=" O SER D 600 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU D 602 " --> pdb=" O GLU D 759 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR D 717 " --> pdb=" O LEU D 676 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL D 630 " --> pdb=" O LEU D 675 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ASP D 677 " --> pdb=" O VAL D 630 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE D 632 " --> pdb=" O ASP D 677 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 845 through 848 removed outlier: 3.693A pdb=" N ARG D 845 " --> pdb=" O VAL D 856 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 335 through 337 removed outlier: 6.579A pdb=" N VAL E 203 " --> pdb=" O VAL E 336 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA E 313 " --> pdb=" O ILE E 277 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 236 through 238 removed outlier: 3.585A pdb=" N LEU E 238 " --> pdb=" O ILE E 274 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 599 through 603 removed outlier: 3.697A pdb=" N THR E 717 " --> pdb=" O LEU E 676 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL E 630 " --> pdb=" O LEU E 675 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ASP E 677 " --> pdb=" O VAL E 630 " (cutoff:3.500A) removed outlier: 6.954A 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 792 through 795 removed outlier: 3.557A 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 Processing sheet with id= X, first strand: chain 'F' and resid 334 through 337 removed outlier: 6.937A pdb=" N GLY F 312 " --> pdb=" O LEU F 204 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N GLY F 206 " --> pdb=" O GLY F 312 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N THR F 314 " --> pdb=" O GLY F 206 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 599 through 603 removed outlier: 3.802A pdb=" N MET F 716 " --> pdb=" O PHE F 601 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 698 through 700 removed outlier: 3.501A pdb=" N VAL F 707 " --> pdb=" O LEU F 699 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 793 through 795 removed outlier: 6.238A pdb=" N ILE F 844 " --> pdb=" O HIS F 794 " (cutoff:3.500A) 1212 hydrogen bonds defined for protein. 3612 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: 9.57 Time building geometry restraints manager: 12.72 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: 10116 1.36 - 1.50: 8035 1.50 - 1.65: 10640 1.65 - 1.80: 152 1.80 - 1.94: 45 Bond restraints: 28988 Sorted by residual: bond pdb=" CB GLN C 692 " pdb=" CG GLN C 692 " ideal model delta sigma weight residual 1.520 1.424 0.096 3.00e-02 1.11e+03 1.02e+01 bond pdb=" CB VAL D 580 " pdb=" CG1 VAL D 580 " ideal model delta sigma weight residual 1.521 1.417 0.104 3.30e-02 9.18e+02 1.00e+01 bond pdb=" CG GLN C 692 " pdb=" CD GLN C 692 " ideal model delta sigma weight residual 1.516 1.440 0.076 2.50e-02 1.60e+03 9.23e+00 bond pdb=" CB LEU D 618 " pdb=" CG LEU D 618 " ideal model delta sigma weight residual 1.530 1.470 0.060 2.00e-02 2.50e+03 8.90e+00 bond pdb=" CB GLN B 692 " pdb=" CG GLN B 692 " ideal model delta sigma weight residual 1.520 1.439 0.081 3.00e-02 1.11e+03 7.37e+00 ... (remaining 28983 not shown) Histogram of bond angle deviations from ideal: 94.87 - 103.72: 415 103.72 - 112.58: 15252 112.58 - 121.44: 16808 121.44 - 130.29: 6571 130.29 - 139.15: 139 Bond angle restraints: 39185 Sorted by residual: angle pdb=" N VAL B 686 " pdb=" CA VAL B 686 " pdb=" C VAL B 686 " ideal model delta sigma weight residual 112.96 106.52 6.44 1.00e+00 1.00e+00 4.14e+01 angle pdb=" N VAL E 666 " pdb=" CA VAL E 666 " pdb=" C VAL E 666 " ideal model delta sigma weight residual 112.96 107.50 5.46 1.00e+00 1.00e+00 2.98e+01 angle pdb=" CB LYS B 199 " pdb=" CG LYS B 199 " pdb=" CD LYS B 199 " ideal model delta sigma weight residual 111.30 100.17 11.13 2.30e+00 1.89e-01 2.34e+01 angle pdb=" C LEU B 386 " pdb=" N PRO B 387 " pdb=" CA PRO B 387 " ideal model delta sigma weight residual 127.00 136.59 -9.59 2.40e+00 1.74e-01 1.60e+01 angle pdb=" N ARG D 815 " pdb=" CA ARG D 815 " pdb=" C ARG D 815 " ideal model delta sigma weight residual 109.81 118.48 -8.67 2.21e+00 2.05e-01 1.54e+01 ... (remaining 39180 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.10: 17596 32.10 - 64.19: 242 64.19 - 96.29: 19 96.29 - 128.39: 2 128.39 - 160.48: 2 Dihedral angle restraints: 17861 sinusoidal: 7544 harmonic: 10317 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 180.00 142.77 37.23 0 5.00e+00 4.00e-02 5.55e+01 dihedral pdb=" O1B ADP A1002 " pdb=" O3A ADP A1002 " pdb=" PB ADP A1002 " pdb=" PA ADP A1002 " ideal model delta sinusoidal sigma weight residual 300.00 139.51 160.48 1 2.00e+01 2.50e-03 4.66e+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 -60.00 72.63 -132.62 1 2.00e+01 2.50e-03 4.03e+01 ... (remaining 17858 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3330 0.067 - 0.134: 962 0.134 - 0.200: 133 0.200 - 0.267: 8 0.267 - 0.334: 3 Chirality restraints: 4436 Sorted by residual: chirality pdb=" CB ILE B 205 " pdb=" CA ILE B 205 " pdb=" CG1 ILE B 205 " pdb=" CG2 ILE B 205 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CB THR C 282 " pdb=" CA THR C 282 " pdb=" OG1 THR C 282 " pdb=" CG2 THR C 282 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.30 2.00e-01 2.50e+01 2.20e+00 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 -2.35 -0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 4433 not shown) Planarity restraints: 5114 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 683 " 0.059 5.00e-02 4.00e+02 8.94e-02 1.28e+01 pdb=" N PRO D 684 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO D 684 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO D 684 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 763 " 0.018 2.00e-02 2.50e+03 2.42e-02 1.03e+01 pdb=" CG PHE C 763 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE C 763 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE C 763 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE C 763 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 PHE C 763 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE C 763 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ADP A1002 " 0.014 2.00e-02 2.50e+03 1.87e-02 9.58e+00 pdb=" C2 ADP A1002 " 0.009 2.00e-02 2.50e+03 pdb=" C4 ADP A1002 " -0.051 2.00e-02 2.50e+03 pdb=" C5 ADP A1002 " 0.002 2.00e-02 2.50e+03 pdb=" C6 ADP A1002 " -0.001 2.00e-02 2.50e+03 pdb=" C8 ADP A1002 " 0.013 2.00e-02 2.50e+03 pdb=" N1 ADP A1002 " 0.001 2.00e-02 2.50e+03 pdb=" N3 ADP A1002 " 0.020 2.00e-02 2.50e+03 pdb=" N6 ADP A1002 " -0.000 2.00e-02 2.50e+03 pdb=" N7 ADP A1002 " 0.009 2.00e-02 2.50e+03 pdb=" N9 ADP A1002 " -0.016 2.00e-02 2.50e+03 ... (remaining 5111 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 2520 2.73 - 3.27: 27663 3.27 - 3.81: 47126 3.81 - 4.36: 56622 4.36 - 4.90: 96502 Nonbonded interactions: 230433 Sorted by model distance: nonbonded pdb=" O2A AGS D 902 " pdb=" O2B AGS D 902 " model vdw 2.187 2.440 nonbonded pdb=" O1B AGS C1002 " pdb=" O2G AGS C1002 " model vdw 2.226 2.440 nonbonded pdb=" O1B AGS B1002 " pdb=" O2G AGS B1002 " model vdw 2.231 2.440 nonbonded pdb=" O2A AGS C1002 " pdb=" O2B AGS C1002 " model vdw 2.236 2.440 nonbonded pdb=" O1B AGS B1001 " pdb=" O2G AGS B1001 " model vdw 2.238 2.440 ... (remaining 230428 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 858)) selection = (chain 'C' and (resid 159 through 287 or resid 293 through 408 or resid 527 thro \ ugh 858)) selection = (chain 'D' and (resid 159 through 408 or resid 527 through 858)) selection = (chain 'E' and resid 159 through 858) selection = (chain 'F' and resid 159 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: 0.010 Normalize map: mean=0, sd=1: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.180 Construct map_model_manager: 0.030 Extract box with map and model: 6.960 Check model and map are aligned: 0.500 Set scattering table: 0.280 Process input model: 74.280 Find NCS groups from input model: 2.370 Set up NCS constraints: 0.120 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:3.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4645 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 0.104 28988 Z= 0.704 Angle : 1.090 13.526 39185 Z= 0.578 Chirality : 0.061 0.334 4436 Planarity : 0.008 0.089 5114 Dihedral : 11.075 160.483 11209 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 0.07 % Allowed : 1.07 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -4.07 (0.11), residues: 3532 helix: -2.38 (0.09), residues: 1931 sheet: -3.20 (0.24), residues: 372 loop : -2.74 (0.15), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.005 TRP B 543 HIS 0.015 0.002 HIS C 567 PHE 0.050 0.005 PHE C 763 TYR 0.026 0.003 TYR C 357 ARG 0.022 0.001 ARG D 815 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1028 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1026 time to evaluate : 3.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 169 THR cc_start: 0.5676 (p) cc_final: 0.4319 (p) REVERT: A 391 ILE cc_start: 0.5904 (mt) cc_final: 0.5660 (tp) REVERT: A 394 ILE cc_start: 0.5916 (mm) cc_final: 0.4792 (mt) REVERT: B 783 TYR cc_start: 0.6315 (m-10) cc_final: 0.6115 (m-10) REVERT: B 821 ILE cc_start: 0.7067 (mt) cc_final: 0.6712 (mt) REVERT: C 800 LEU cc_start: 0.8488 (tt) cc_final: 0.7619 (mp) REVERT: D 459 GLU cc_start: 0.5364 (tt0) cc_final: 0.5050 (tp30) REVERT: D 578 ASP cc_start: 0.2146 (m-30) cc_final: 0.1886 (m-30) REVERT: D 598 ILE cc_start: 0.7147 (mt) cc_final: 0.6862 (tp) REVERT: D 808 TYR cc_start: 0.3433 (t80) cc_final: 0.3066 (t80) REVERT: E 406 ASP cc_start: 0.3797 (t0) cc_final: 0.3135 (t70) REVERT: E 744 VAL cc_start: 0.6902 (t) cc_final: 0.6581 (t) REVERT: F 297 ASN cc_start: 0.7041 (m110) cc_final: 0.6645 (m-40) REVERT: F 392 ASP cc_start: 0.5669 (m-30) cc_final: 0.4962 (m-30) REVERT: F 536 ILE cc_start: 0.6083 (mm) cc_final: 0.5861 (mm) REVERT: F 707 VAL cc_start: 0.1847 (t) cc_final: 0.1616 (t) REVERT: F 795 ILE cc_start: 0.6473 (tt) cc_final: 0.6256 (tt) outliers start: 2 outliers final: 0 residues processed: 1028 average time/residue: 0.4669 time to fit residues: 710.9916 Evaluate side-chains 577 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 577 time to evaluate : 3.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 300 optimal weight: 1.9990 chunk 269 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 182 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 279 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 169 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 323 optimal weight: 9.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN A 281 HIS ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 HIS ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 747 HIS A 794 HIS A 849 ASN B 195 GLN B 281 HIS B 297 ASN ** B 567 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 822 GLN B 823 GLN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN C 641 HIS ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 858 HIS D 192 GLN D 692 GLN D 806 ASN D 822 GLN E 309 HIS E 334 GLN ** E 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 567 HIS E 574 ASN E 688 ASN ** E 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 858 HIS F 195 GLN ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 726 GLN F 849 ASN ** F 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5433 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 28988 Z= 0.257 Angle : 0.782 16.438 39185 Z= 0.390 Chirality : 0.048 0.234 4436 Planarity : 0.006 0.068 5114 Dihedral : 10.110 140.337 4163 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.29 % Favored : 94.68 % Rotamer: Outliers : 2.96 % Allowed : 10.95 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -2.51 (0.13), residues: 3532 helix: -0.90 (0.11), residues: 1933 sheet: -2.79 (0.25), residues: 394 loop : -2.32 (0.16), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 462 HIS 0.009 0.001 HIS E 568 PHE 0.034 0.002 PHE E 255 TYR 0.029 0.002 TYR F 783 ARG 0.009 0.001 ARG A 528 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 740 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 652 time to evaluate : 3.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 THR cc_start: 0.6644 (p) cc_final: 0.6422 (p) REVERT: B 169 THR cc_start: 0.6493 (p) cc_final: 0.6272 (p) REVERT: B 294 ASP cc_start: 0.3065 (OUTLIER) cc_final: 0.2144 (p0) REVERT: B 401 ILE cc_start: 0.7278 (mm) cc_final: 0.6925 (mm) REVERT: C 282 THR cc_start: 0.7153 (m) cc_final: 0.6936 (p) REVERT: C 293 MET cc_start: 0.6453 (mmm) cc_final: 0.5790 (mmm) REVERT: C 340 GLU cc_start: 0.6063 (pm20) cc_final: 0.5667 (pt0) REVERT: C 359 LEU cc_start: 0.7463 (pp) cc_final: 0.7075 (pp) REVERT: C 641 HIS cc_start: 0.4580 (OUTLIER) cc_final: 0.4153 (m-70) REVERT: C 815 ARG cc_start: 0.6979 (ttp-110) cc_final: 0.6501 (ttm110) REVERT: D 281 HIS cc_start: 0.4575 (p-80) cc_final: 0.4236 (p-80) REVERT: D 305 ARG cc_start: 0.6722 (mmm160) cc_final: 0.6449 (ptp-170) REVERT: E 752 GLU cc_start: 0.6616 (mp0) cc_final: 0.6416 (mp0) REVERT: F 167 ASP cc_start: 0.7238 (t0) cc_final: 0.7002 (t0) REVERT: F 186 GLU cc_start: 0.5982 (mp0) cc_final: 0.5230 (mt-10) REVERT: F 314 THR cc_start: 0.5919 (t) cc_final: 0.4092 (p) REVERT: F 399 SER cc_start: 0.5425 (m) cc_final: 0.4981 (p) REVERT: F 626 ASP cc_start: 0.5596 (OUTLIER) cc_final: 0.5100 (t0) REVERT: F 795 ILE cc_start: 0.6325 (tt) cc_final: 0.6104 (tt) outliers start: 88 outliers final: 41 residues processed: 700 average time/residue: 0.4391 time to fit residues: 475.3534 Evaluate side-chains 539 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 495 time to evaluate : 3.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain B residue 269 GLN Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 672 SER Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 717 THR Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 625 SER Chi-restraints excluded: chain C residue 641 HIS Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain C residue 761 VAL Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 442 ASP Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 674 ILE Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 737 MET Chi-restraints excluded: chain D residue 802 LEU Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 318 GLU Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 843 VAL Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 626 ASP Chi-restraints excluded: chain F residue 677 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 179 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 269 optimal weight: 3.9990 chunk 220 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 chunk 323 optimal weight: 30.0000 chunk 349 optimal weight: 7.9990 chunk 288 optimal weight: 0.3980 chunk 321 optimal weight: 8.9990 chunk 110 optimal weight: 8.9990 chunk 259 optimal weight: 6.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 778 GLN ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 822 GLN C 159 GLN ** C 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 620 ASN E 361 HIS E 806 ASN E 824 GLN ** E 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 GLN F 297 ASN F 688 ASN F 726 GLN ** F 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6374 moved from start: 0.6506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 28988 Z= 0.341 Angle : 0.848 14.540 39185 Z= 0.423 Chirality : 0.048 0.216 4436 Planarity : 0.007 0.077 5114 Dihedral : 9.836 149.527 4163 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.51 % Favored : 93.43 % Rotamer: Outliers : 4.13 % Allowed : 13.43 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -1.90 (0.13), residues: 3532 helix: -0.47 (0.11), residues: 1939 sheet: -2.14 (0.25), residues: 386 loop : -2.09 (0.17), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP C 462 HIS 0.070 0.002 HIS C 641 PHE 0.031 0.003 PHE B 729 TYR 0.027 0.002 TYR F 322 ARG 0.025 0.001 ARG E 356 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 628 time to evaluate : 3.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 MET cc_start: 0.6815 (pmm) cc_final: 0.6007 (mtp) REVERT: A 316 LEU cc_start: 0.6463 (pp) cc_final: 0.5745 (tp) REVERT: A 552 MET cc_start: 0.5530 (mmp) cc_final: 0.4199 (pmm) REVERT: A 622 MET cc_start: 0.7861 (tmm) cc_final: 0.7272 (ppp) REVERT: A 745 VAL cc_start: 0.8001 (t) cc_final: 0.7738 (m) REVERT: A 761 VAL cc_start: 0.8113 (OUTLIER) cc_final: 0.7881 (p) REVERT: A 783 TYR cc_start: 0.5981 (m-10) cc_final: 0.5761 (m-80) REVERT: B 181 ILE cc_start: 0.8266 (mp) cc_final: 0.8044 (mt) REVERT: C 293 MET cc_start: 0.6999 (mmm) cc_final: 0.5344 (mmm) REVERT: D 257 GLU cc_start: 0.5952 (tm-30) cc_final: 0.5672 (tm-30) REVERT: D 551 MET cc_start: 0.5941 (mpp) cc_final: 0.5203 (mtm) REVERT: F 186 GLU cc_start: 0.5997 (mp0) cc_final: 0.5029 (mt-10) REVERT: F 399 SER cc_start: 0.5447 (m) cc_final: 0.5182 (p) REVERT: F 535 GLU cc_start: 0.7166 (tp30) cc_final: 0.6674 (tp30) REVERT: F 626 ASP cc_start: 0.6031 (OUTLIER) cc_final: 0.5817 (t0) outliers start: 123 outliers final: 65 residues processed: 703 average time/residue: 0.4032 time to fit residues: 449.0351 Evaluate side-chains 562 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 495 time to evaluate : 3.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 729 PHE Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 778 GLN Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 310 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 641 HIS Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 442 ASP Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 632 ILE Chi-restraints excluded: chain D residue 674 ILE Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 802 LEU Chi-restraints excluded: chain E residue 176 LYS Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 318 GLU Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain E residue 632 ILE Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 742 LEU Chi-restraints excluded: chain E residue 760 VAL Chi-restraints excluded: chain E residue 843 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 269 GLN Chi-restraints excluded: chain F residue 559 LEU Chi-restraints excluded: chain F residue 607 THR Chi-restraints excluded: chain F residue 626 ASP Chi-restraints excluded: chain F residue 632 ILE Chi-restraints excluded: chain F residue 714 VAL Chi-restraints excluded: chain F residue 761 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 319 optimal weight: 4.9990 chunk 243 optimal weight: 9.9990 chunk 168 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 154 optimal weight: 0.9980 chunk 217 optimal weight: 3.9990 chunk 325 optimal weight: 3.9990 chunk 344 optimal weight: 20.0000 chunk 169 optimal weight: 0.9980 chunk 308 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 GLN ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 778 GLN B 334 GLN ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 692 GLN ** E 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 857 GLN ** F 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 688 ASN F 692 GLN F 726 GLN F 857 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.7856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 28988 Z= 0.250 Angle : 0.737 13.583 39185 Z= 0.364 Chirality : 0.046 0.270 4436 Planarity : 0.006 0.064 5114 Dihedral : 9.463 144.450 4163 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.66 % Allowed : 18.03 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -1.32 (0.14), residues: 3532 helix: 0.00 (0.12), residues: 1905 sheet: -1.96 (0.25), residues: 391 loop : -1.75 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 462 HIS 0.024 0.001 HIS C 641 PHE 0.024 0.002 PHE B 276 TYR 0.026 0.002 TYR D 734 ARG 0.016 0.001 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 555 time to evaluate : 3.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 MET cc_start: 0.5518 (tpt) cc_final: 0.5236 (tpt) REVERT: A 622 MET cc_start: 0.8105 (tmm) cc_final: 0.7867 (tmm) REVERT: A 819 ARG cc_start: 0.5437 (OUTLIER) cc_final: 0.4690 (ttt180) REVERT: B 276 PHE cc_start: 0.7511 (t80) cc_final: 0.7285 (t80) REVERT: C 293 MET cc_start: 0.7396 (mmm) cc_final: 0.6262 (mmm) REVERT: C 317 ASP cc_start: 0.6272 (OUTLIER) cc_final: 0.5819 (t0) REVERT: C 637 PHE cc_start: 0.7769 (m-10) cc_final: 0.7392 (m-10) REVERT: D 257 GLU cc_start: 0.6173 (tm-30) cc_final: 0.5904 (tm-30) REVERT: D 551 MET cc_start: 0.6163 (mpp) cc_final: 0.5682 (mtm) REVERT: D 598 ILE cc_start: 0.8315 (mt) cc_final: 0.7645 (tp) REVERT: E 562 MET cc_start: 0.2453 (tpt) cc_final: 0.1782 (tpt) REVERT: E 708 ASP cc_start: 0.5738 (t0) cc_final: 0.4922 (p0) REVERT: E 726 GLN cc_start: 0.7715 (mt0) cc_final: 0.7263 (pp30) REVERT: E 818 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7544 (mtpp) REVERT: F 186 GLU cc_start: 0.6186 (mp0) cc_final: 0.5308 (mt-10) REVERT: F 399 SER cc_start: 0.5592 (m) cc_final: 0.5336 (p) REVERT: F 737 MET cc_start: 0.4476 (mmm) cc_final: 0.4152 (mmm) outliers start: 109 outliers final: 67 residues processed: 626 average time/residue: 0.4128 time to fit residues: 415.5733 Evaluate side-chains 554 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 484 time to evaluate : 3.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 819 ARG Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 310 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 562 MET Chi-restraints excluded: chain C residue 700 THR Chi-restraints excluded: chain C residue 717 THR Chi-restraints excluded: chain C residue 773 SER Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 442 ASP Chi-restraints excluded: chain D residue 674 ILE Chi-restraints excluded: chain D residue 700 THR Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 773 SER Chi-restraints excluded: chain D residue 802 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 318 GLU Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 701 ASP Chi-restraints excluded: chain E residue 737 MET Chi-restraints excluded: chain E residue 742 LEU Chi-restraints excluded: chain E residue 760 VAL Chi-restraints excluded: chain E residue 770 HIS Chi-restraints excluded: chain E residue 818 LYS Chi-restraints excluded: chain E residue 843 VAL Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 714 VAL Chi-restraints excluded: chain F residue 741 VAL Chi-restraints excluded: chain F residue 761 VAL Chi-restraints excluded: chain F residue 812 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 286 optimal weight: 0.0070 chunk 195 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 256 optimal weight: 8.9990 chunk 141 optimal weight: 2.9990 chunk 293 optimal weight: 1.9990 chunk 237 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 175 optimal weight: 0.6980 chunk 308 optimal weight: 0.0980 chunk 86 optimal weight: 8.9990 overall best weight: 0.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN A 595 ASN ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 GLN C 726 GLN ** E 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 683 HIS E 747 HIS ** E 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 831 GLN E 849 ASN ** F 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 726 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 moved from start: 0.8320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28988 Z= 0.185 Angle : 0.680 14.520 39185 Z= 0.329 Chirality : 0.044 0.194 4436 Planarity : 0.005 0.059 5114 Dihedral : 9.193 144.088 4163 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 18.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.09 % Allowed : 19.44 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -0.98 (0.14), residues: 3532 helix: 0.28 (0.12), residues: 1902 sheet: -1.74 (0.24), residues: 396 loop : -1.61 (0.18), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 462 HIS 0.013 0.001 HIS E 568 PHE 0.033 0.002 PHE B 729 TYR 0.028 0.001 TYR A 380 ARG 0.008 0.001 ARG C 815 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 535 time to evaluate : 3.402 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 712 THR cc_start: 0.6900 (p) cc_final: 0.6681 (p) REVERT: A 819 ARG cc_start: 0.5232 (OUTLIER) cc_final: 0.4719 (ttt180) REVERT: B 323 ILE cc_start: 0.8382 (mt) cc_final: 0.8129 (mt) REVERT: B 376 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8371 (mt) REVERT: B 693 VAL cc_start: 0.8517 (t) cc_final: 0.8292 (t) REVERT: C 298 MET cc_start: 0.7818 (mpp) cc_final: 0.7410 (mpp) REVERT: C 317 ASP cc_start: 0.6266 (OUTLIER) cc_final: 0.5859 (t0) REVERT: C 726 GLN cc_start: 0.7304 (OUTLIER) cc_final: 0.6783 (pp30) REVERT: C 754 ILE cc_start: 0.7674 (pt) cc_final: 0.7197 (mt) REVERT: D 257 GLU cc_start: 0.6147 (tm-30) cc_final: 0.5886 (tm-30) REVERT: D 396 GLU cc_start: 0.4929 (tp30) cc_final: 0.4607 (tp30) REVERT: D 551 MET cc_start: 0.6262 (mpp) cc_final: 0.5816 (mtm) REVERT: D 598 ILE cc_start: 0.8548 (mt) cc_final: 0.7920 (tp) REVERT: D 675 LEU cc_start: 0.8101 (tp) cc_final: 0.7773 (tp) REVERT: E 186 GLU cc_start: 0.6351 (mp0) cc_final: 0.5640 (mp0) REVERT: E 708 ASP cc_start: 0.5663 (t0) cc_final: 0.4942 (p0) REVERT: E 726 GLN cc_start: 0.7848 (mt0) cc_final: 0.7354 (tm-30) REVERT: E 826 GLU cc_start: 0.7381 (mm-30) cc_final: 0.6907 (mt-10) REVERT: F 186 GLU cc_start: 0.6215 (mp0) cc_final: 0.5222 (mt-10) REVERT: F 399 SER cc_start: 0.5658 (m) cc_final: 0.5396 (p) REVERT: F 737 MET cc_start: 0.4494 (mmm) cc_final: 0.3938 (mmm) outliers start: 92 outliers final: 54 residues processed: 595 average time/residue: 0.3793 time to fit residues: 361.1878 Evaluate side-chains 530 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 472 time to evaluate : 3.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 595 ASN Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 819 ARG Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 310 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain C residue 562 MET Chi-restraints excluded: chain C residue 726 GLN Chi-restraints excluded: chain C residue 800 LEU Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 853 ILE Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 442 ASP Chi-restraints excluded: chain D residue 578 ASP Chi-restraints excluded: chain D residue 609 VAL Chi-restraints excluded: chain D residue 683 HIS Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 773 SER Chi-restraints excluded: chain D residue 774 ILE Chi-restraints excluded: chain D residue 802 LEU Chi-restraints excluded: chain E residue 176 LYS Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 318 GLU Chi-restraints excluded: chain E residue 536 ILE Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 701 ASP Chi-restraints excluded: chain E residue 742 LEU Chi-restraints excluded: chain E residue 760 VAL Chi-restraints excluded: chain E residue 770 HIS Chi-restraints excluded: chain E residue 843 VAL Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 714 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 115 optimal weight: 10.0000 chunk 309 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 202 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 344 optimal weight: 4.9990 chunk 285 optimal weight: 7.9990 chunk 159 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 113 optimal weight: 0.0770 chunk 180 optimal weight: 7.9990 overall best weight: 2.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN A 362 HIS ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 GLN B 641 HIS ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN E 269 GLN E 574 ASN E 778 GLN E 822 GLN F 159 GLN F 692 GLN F 726 GLN ** F 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.9974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 28988 Z= 0.334 Angle : 0.796 13.750 39185 Z= 0.396 Chirality : 0.048 0.319 4436 Planarity : 0.006 0.098 5114 Dihedral : 9.409 143.762 4163 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 21.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 4.26 % Allowed : 19.85 % Favored : 75.89 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.48 % 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: -1.07 (0.14), residues: 3532 helix: 0.09 (0.12), residues: 1921 sheet: -1.60 (0.24), residues: 395 loop : -1.54 (0.18), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 462 HIS 0.010 0.002 HIS E 858 PHE 0.032 0.003 PHE B 729 TYR 0.020 0.002 TYR B 671 ARG 0.015 0.001 ARG D 384 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 565 time to evaluate : 3.110 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 750 ARG cc_start: 0.6597 (mtt180) cc_final: 0.6311 (mtt180) REVERT: A 819 ARG cc_start: 0.5666 (OUTLIER) cc_final: 0.4905 (ttt180) REVERT: B 293 MET cc_start: 0.7499 (mmp) cc_final: 0.6784 (tpp) REVERT: B 383 ASP cc_start: 0.7022 (m-30) cc_final: 0.6767 (m-30) REVERT: B 622 MET cc_start: 0.7220 (mpp) cc_final: 0.6890 (ptp) REVERT: B 629 MET cc_start: 0.7168 (ppp) cc_final: 0.6496 (ppp) REVERT: C 224 ILE cc_start: 0.7700 (mm) cc_final: 0.7443 (mm) REVERT: C 266 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.6875 (tt) REVERT: C 298 MET cc_start: 0.8115 (mpp) cc_final: 0.7651 (mpp) REVERT: C 317 ASP cc_start: 0.7106 (t0) cc_final: 0.6674 (t0) REVERT: C 717 THR cc_start: 0.9256 (OUTLIER) cc_final: 0.8958 (p) REVERT: C 754 ILE cc_start: 0.8715 (pt) cc_final: 0.8292 (mt) REVERT: D 257 GLU cc_start: 0.6611 (tm-30) cc_final: 0.6283 (tm-30) REVERT: D 403 MET cc_start: 0.6979 (ptm) cc_final: 0.6724 (ptm) REVERT: D 551 MET cc_start: 0.6816 (mpp) cc_final: 0.6335 (mtm) REVERT: D 637 PHE cc_start: 0.8233 (m-80) cc_final: 0.7808 (m-10) REVERT: D 700 THR cc_start: 0.8074 (OUTLIER) cc_final: 0.7853 (p) REVERT: E 186 GLU cc_start: 0.6454 (mp0) cc_final: 0.5993 (mp0) REVERT: E 322 TYR cc_start: 0.6688 (m-80) cc_final: 0.6430 (m-80) REVERT: E 395 ASP cc_start: 0.5655 (t0) cc_final: 0.5398 (t0) REVERT: E 708 ASP cc_start: 0.5951 (t0) cc_final: 0.5295 (p0) REVERT: E 726 GLN cc_start: 0.8107 (mt0) cc_final: 0.7763 (tm-30) REVERT: F 399 SER cc_start: 0.5994 (m) cc_final: 0.5763 (p) outliers start: 127 outliers final: 73 residues processed: 645 average time/residue: 0.3736 time to fit residues: 387.5375 Evaluate side-chains 534 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 457 time to evaluate : 3.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 819 ARG Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 758 ASP Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 307 GLU Chi-restraints excluded: chain C residue 310 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 562 MET Chi-restraints excluded: chain C residue 641 HIS Chi-restraints excluded: chain C residue 717 THR Chi-restraints excluded: chain C residue 761 VAL Chi-restraints excluded: chain C residue 773 SER Chi-restraints excluded: chain C residue 800 LEU Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 853 ILE Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 638 MET Chi-restraints excluded: chain D residue 700 THR Chi-restraints excluded: chain D residue 773 SER Chi-restraints excluded: chain D residue 802 LEU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 318 GLU Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain E residue 536 ILE Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 701 ASP Chi-restraints excluded: chain E residue 742 LEU Chi-restraints excluded: chain E residue 760 VAL Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 293 MET Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 559 LEU Chi-restraints excluded: chain F residue 607 THR Chi-restraints excluded: chain F residue 714 VAL Chi-restraints excluded: chain F residue 741 VAL Chi-restraints excluded: chain F residue 761 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 332 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 196 optimal weight: 0.7980 chunk 251 optimal weight: 0.4980 chunk 194 optimal weight: 0.1980 chunk 289 optimal weight: 3.9990 chunk 192 optimal weight: 0.9980 chunk 343 optimal weight: 8.9990 chunk 214 optimal weight: 2.9990 chunk 209 optimal weight: 10.0000 chunk 158 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 688 ASN A 822 GLN B 192 GLN B 195 GLN B 726 GLN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 778 GLN ** D 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 822 GLN F 159 GLN F 225 ASN ** F 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 334 GLN F 692 GLN F 726 GLN F 824 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 1.0264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 28988 Z= 0.201 Angle : 0.727 22.098 39185 Z= 0.352 Chirality : 0.046 0.194 4436 Planarity : 0.005 0.064 5114 Dihedral : 9.029 142.998 4163 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.70 % Favored : 95.27 % Rotamer: Outliers : 2.82 % Allowed : 23.00 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -0.68 (0.14), residues: 3532 helix: 0.43 (0.12), residues: 1907 sheet: -1.40 (0.24), residues: 397 loop : -1.41 (0.18), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP C 462 HIS 0.014 0.001 HIS E 568 PHE 0.028 0.002 PHE B 729 TYR 0.019 0.002 TYR F 656 ARG 0.012 0.001 ARG D 197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 509 time to evaluate : 3.765 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 320 ARG cc_start: 0.6679 (OUTLIER) cc_final: 0.6431 (ttp80) REVERT: A 662 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7320 (tp) REVERT: A 819 ARG cc_start: 0.5380 (OUTLIER) cc_final: 0.4851 (ttt180) REVERT: B 293 MET cc_start: 0.7623 (mmp) cc_final: 0.6880 (tpp) REVERT: B 325 LYS cc_start: 0.7814 (mmmt) cc_final: 0.7179 (mmtt) REVERT: B 383 ASP cc_start: 0.6557 (m-30) cc_final: 0.6355 (m-30) REVERT: B 629 MET cc_start: 0.6738 (ppp) cc_final: 0.6145 (ppp) REVERT: B 737 MET cc_start: 0.7424 (mmm) cc_final: 0.7166 (tpt) REVERT: B 812 TYR cc_start: 0.6123 (m-80) cc_final: 0.5904 (m-80) REVERT: C 298 MET cc_start: 0.8069 (mpp) cc_final: 0.7417 (mpp) REVERT: C 329 LEU cc_start: 0.8947 (tp) cc_final: 0.8704 (tp) REVERT: C 403 MET cc_start: 0.6712 (mmm) cc_final: 0.6499 (mmm) REVERT: C 754 ILE cc_start: 0.8766 (pt) cc_final: 0.7818 (mt) REVERT: C 766 LEU cc_start: 0.7107 (mt) cc_final: 0.6884 (mt) REVERT: C 834 LEU cc_start: 0.8399 (pp) cc_final: 0.8119 (mt) REVERT: D 212 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7410 (mmtp) REVERT: D 257 GLU cc_start: 0.6485 (tm-30) cc_final: 0.6125 (tm-30) REVERT: D 551 MET cc_start: 0.6786 (mpp) cc_final: 0.6457 (mtm) REVERT: D 637 PHE cc_start: 0.8241 (m-80) cc_final: 0.7890 (m-10) REVERT: D 658 GLU cc_start: 0.7198 (pm20) cc_final: 0.6706 (pm20) REVERT: D 700 THR cc_start: 0.8043 (OUTLIER) cc_final: 0.7805 (p) REVERT: E 240 LEU cc_start: 0.5779 (pt) cc_final: 0.5270 (pp) REVERT: E 322 TYR cc_start: 0.6902 (m-80) cc_final: 0.6564 (m-80) REVERT: E 708 ASP cc_start: 0.5895 (t0) cc_final: 0.5300 (p0) REVERT: E 726 GLN cc_start: 0.8146 (mt0) cc_final: 0.7856 (tm-30) REVERT: F 323 ILE cc_start: 0.7768 (mp) cc_final: 0.7307 (mm) REVERT: F 354 LYS cc_start: 0.6341 (OUTLIER) cc_final: 0.5612 (pttt) REVERT: F 737 MET cc_start: 0.4492 (mmm) cc_final: 0.4087 (mmm) outliers start: 84 outliers final: 44 residues processed: 558 average time/residue: 0.3776 time to fit residues: 343.3443 Evaluate side-chains 501 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 451 time to evaluate : 3.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 819 ARG Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 310 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain C residue 800 LEU Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain D residue 638 MET Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 700 THR Chi-restraints excluded: chain D residue 773 SER Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 318 GLU Chi-restraints excluded: chain E residue 536 ILE Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 676 LEU Chi-restraints excluded: chain E residue 742 LEU Chi-restraints excluded: chain E residue 760 VAL Chi-restraints excluded: chain F residue 354 LYS Chi-restraints excluded: chain F residue 741 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 212 optimal weight: 4.9990 chunk 137 optimal weight: 0.0970 chunk 204 optimal weight: 10.0000 chunk 103 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 218 optimal weight: 6.9990 chunk 233 optimal weight: 1.9990 chunk 169 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 chunk 269 optimal weight: 5.9990 overall best weight: 1.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 688 ASN ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 822 GLN B 195 GLN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 GLN ** C 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN ** E 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 361 HIS F 159 GLN F 225 ASN F 726 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 1.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 28988 Z= 0.248 Angle : 0.741 17.945 39185 Z= 0.361 Chirality : 0.046 0.217 4436 Planarity : 0.005 0.058 5114 Dihedral : 9.027 145.852 4163 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 19.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.09 % Allowed : 23.64 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -0.63 (0.14), residues: 3532 helix: 0.46 (0.12), residues: 1899 sheet: -1.46 (0.24), residues: 408 loop : -1.32 (0.19), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 462 HIS 0.015 0.001 HIS D 683 PHE 0.047 0.003 PHE B 621 TYR 0.025 0.002 TYR A 783 ARG 0.008 0.001 ARG B 631 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 488 time to evaluate : 3.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 ARG cc_start: 0.7002 (ttp-170) cc_final: 0.6769 (ttp80) REVERT: A 391 ILE cc_start: 0.8221 (mm) cc_final: 0.7793 (tp) REVERT: A 662 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7327 (tp) REVERT: A 783 TYR cc_start: 0.5605 (m-80) cc_final: 0.5270 (m-80) REVERT: A 819 ARG cc_start: 0.5650 (OUTLIER) cc_final: 0.5009 (ttt180) REVERT: B 293 MET cc_start: 0.7536 (mmp) cc_final: 0.6898 (tpp) REVERT: B 325 LYS cc_start: 0.8092 (mmmt) cc_final: 0.7490 (mmtt) REVERT: B 383 ASP cc_start: 0.6584 (m-30) cc_final: 0.6320 (m-30) REVERT: B 552 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.7569 (tmm) REVERT: C 298 MET cc_start: 0.8182 (mpp) cc_final: 0.7555 (mpp) REVERT: C 329 LEU cc_start: 0.9082 (tp) cc_final: 0.8855 (tp) REVERT: C 754 ILE cc_start: 0.9000 (pt) cc_final: 0.8539 (mt) REVERT: C 800 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8095 (mp) REVERT: D 257 GLU cc_start: 0.6631 (tm-30) cc_final: 0.6280 (tm-30) REVERT: D 637 PHE cc_start: 0.8134 (m-80) cc_final: 0.7889 (m-10) REVERT: D 700 THR cc_start: 0.8250 (OUTLIER) cc_final: 0.8024 (p) REVERT: E 322 TYR cc_start: 0.6948 (m-80) cc_final: 0.6548 (m-80) REVERT: E 708 ASP cc_start: 0.6290 (t0) cc_final: 0.5532 (p0) REVERT: E 726 GLN cc_start: 0.8327 (mt0) cc_final: 0.7967 (tm-30) REVERT: F 354 LYS cc_start: 0.6425 (OUTLIER) cc_final: 0.5660 (pttt) REVERT: F 365 ILE cc_start: 0.6151 (mt) cc_final: 0.5585 (mp) REVERT: F 616 LYS cc_start: 0.7996 (mmtt) cc_final: 0.7692 (mmtm) REVERT: F 638 MET cc_start: 0.5256 (mmm) cc_final: 0.4135 (mmm) REVERT: F 737 MET cc_start: 0.4683 (mmm) cc_final: 0.4078 (mmm) outliers start: 92 outliers final: 57 residues processed: 540 average time/residue: 0.3744 time to fit residues: 333.2808 Evaluate side-chains 497 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 434 time to evaluate : 3.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 819 ARG Chi-restraints excluded: chain A residue 858 HIS Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 690 LEU Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 310 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain C residue 658 GLU Chi-restraints excluded: chain C residue 711 ASN Chi-restraints excluded: chain C residue 800 LEU Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 598 ILE Chi-restraints excluded: chain D residue 638 MET Chi-restraints excluded: chain D residue 644 SER Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 700 THR Chi-restraints excluded: chain D residue 773 SER Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 318 GLU Chi-restraints excluded: chain E residue 536 ILE Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain E residue 602 LEU Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 676 LEU Chi-restraints excluded: chain E residue 693 VAL Chi-restraints excluded: chain E residue 742 LEU Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 293 MET Chi-restraints excluded: chain F residue 354 LYS Chi-restraints excluded: chain F residue 607 THR Chi-restraints excluded: chain F residue 714 VAL Chi-restraints excluded: chain F residue 741 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 312 optimal weight: 7.9990 chunk 328 optimal weight: 7.9990 chunk 299 optimal weight: 5.9990 chunk 319 optimal weight: 0.0980 chunk 192 optimal weight: 6.9990 chunk 139 optimal weight: 10.0000 chunk 251 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 288 optimal weight: 0.0000 chunk 302 optimal weight: 3.9990 chunk 318 optimal weight: 8.9990 overall best weight: 2.0190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 688 ASN ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 822 GLN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 GLN ** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN ** E 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 1.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 28988 Z= 0.252 Angle : 0.736 18.070 39185 Z= 0.361 Chirality : 0.046 0.285 4436 Planarity : 0.005 0.056 5114 Dihedral : 8.967 149.366 4163 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 19.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.65 % Allowed : 24.78 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -0.55 (0.14), residues: 3532 helix: 0.49 (0.12), residues: 1895 sheet: -1.14 (0.26), residues: 379 loop : -1.33 (0.18), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 462 HIS 0.016 0.001 HIS D 683 PHE 0.029 0.002 PHE B 729 TYR 0.022 0.002 TYR B 783 ARG 0.013 0.001 ARG E 667 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 478 time to evaluate : 3.500 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 391 ILE cc_start: 0.8331 (mm) cc_final: 0.8001 (tp) REVERT: A 634 MET cc_start: 0.7748 (mtp) cc_final: 0.7048 (mmm) REVERT: A 662 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7477 (tp) REVERT: A 783 TYR cc_start: 0.5656 (m-80) cc_final: 0.5319 (m-80) REVERT: A 819 ARG cc_start: 0.5566 (OUTLIER) cc_final: 0.4983 (ttt180) REVERT: B 293 MET cc_start: 0.7703 (mmp) cc_final: 0.7161 (tpp) REVERT: B 325 LYS cc_start: 0.8128 (mmmt) cc_final: 0.7648 (mmtt) REVERT: B 383 ASP cc_start: 0.6678 (m-30) cc_final: 0.6397 (m-30) REVERT: B 638 MET cc_start: 0.7025 (mpt) cc_final: 0.6762 (mpp) REVERT: C 298 MET cc_start: 0.8232 (mpp) cc_final: 0.7706 (mpp) REVERT: C 754 ILE cc_start: 0.9058 (pt) cc_final: 0.8552 (mt) REVERT: C 800 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8088 (mp) REVERT: D 251 TYR cc_start: 0.7026 (m-80) cc_final: 0.6777 (m-80) REVERT: D 257 GLU cc_start: 0.6864 (tm-30) cc_final: 0.6555 (tm-30) REVERT: D 637 PHE cc_start: 0.8430 (m-80) cc_final: 0.8010 (m-10) REVERT: D 700 THR cc_start: 0.8418 (OUTLIER) cc_final: 0.8049 (p) REVERT: D 766 LEU cc_start: 0.7497 (mt) cc_final: 0.7138 (mp) REVERT: D 803 LEU cc_start: 0.8841 (mt) cc_final: 0.8604 (mt) REVERT: E 322 TYR cc_start: 0.6904 (m-80) cc_final: 0.6578 (m-80) REVERT: E 708 ASP cc_start: 0.6445 (t0) cc_final: 0.5937 (p0) REVERT: E 737 MET cc_start: 0.5948 (mmt) cc_final: 0.5508 (mmm) REVERT: F 354 LYS cc_start: 0.6449 (OUTLIER) cc_final: 0.5767 (pttt) REVERT: F 365 ILE cc_start: 0.6202 (mt) cc_final: 0.5829 (mp) REVERT: F 638 MET cc_start: 0.5641 (mmm) cc_final: 0.5135 (mmm) outliers start: 79 outliers final: 54 residues processed: 523 average time/residue: 0.3870 time to fit residues: 331.7440 Evaluate side-chains 493 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 434 time to evaluate : 3.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 819 ARG Chi-restraints excluded: chain A residue 858 HIS Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 777 ILE Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 310 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 562 MET Chi-restraints excluded: chain C residue 625 SER Chi-restraints excluded: chain C residue 711 ASN Chi-restraints excluded: chain C residue 800 LEU Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 310 CYS Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 638 MET Chi-restraints excluded: chain D residue 644 SER Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 700 THR Chi-restraints excluded: chain D residue 717 THR Chi-restraints excluded: chain D residue 773 SER Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 318 GLU Chi-restraints excluded: chain E residue 536 ILE Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 676 LEU Chi-restraints excluded: chain E residue 742 LEU Chi-restraints excluded: chain E residue 766 LEU Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 354 LYS Chi-restraints excluded: chain F residue 559 LEU Chi-restraints excluded: chain F residue 607 THR Chi-restraints excluded: chain F residue 714 VAL Chi-restraints excluded: chain F residue 741 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 209 optimal weight: 0.4980 chunk 338 optimal weight: 20.0000 chunk 206 optimal weight: 2.9990 chunk 160 optimal weight: 0.0570 chunk 235 optimal weight: 9.9990 chunk 354 optimal weight: 30.0000 chunk 326 optimal weight: 10.0000 chunk 282 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 218 optimal weight: 2.9990 chunk 173 optimal weight: 0.9990 overall best weight: 1.1104 ------------------------------------------------------------------------------- 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 822 GLN B 778 GLN B 806 ASN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 GLN ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 GLN ** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 1.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28988 Z= 0.211 Angle : 0.732 17.236 39185 Z= 0.356 Chirality : 0.046 0.203 4436 Planarity : 0.005 0.057 5114 Dihedral : 8.831 150.898 4163 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.08 % Allowed : 25.39 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -0.46 (0.14), residues: 3532 helix: 0.60 (0.12), residues: 1887 sheet: -1.26 (0.25), residues: 400 loop : -1.27 (0.18), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 462 HIS 0.031 0.001 HIS E 309 PHE 0.037 0.002 PHE B 621 TYR 0.025 0.001 TYR F 661 ARG 0.010 0.001 ARG D 750 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 472 time to evaluate : 3.423 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: A 391 ILE cc_start: 0.8337 (mm) cc_final: 0.8052 (tp) REVERT: A 551 MET cc_start: 0.7305 (tpp) cc_final: 0.7030 (tpp) REVERT: A 634 MET cc_start: 0.7767 (mtp) cc_final: 0.7092 (mmm) REVERT: A 662 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7449 (tp) REVERT: A 783 TYR cc_start: 0.5481 (m-80) cc_final: 0.5155 (m-80) REVERT: A 819 ARG cc_start: 0.5466 (OUTLIER) cc_final: 0.4940 (ttt180) REVERT: B 293 MET cc_start: 0.7692 (mmp) cc_final: 0.7190 (tpp) REVERT: B 318 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7591 (mt-10) REVERT: B 325 LYS cc_start: 0.8109 (mmmt) cc_final: 0.7521 (mmtt) REVERT: B 562 MET cc_start: 0.6017 (tmm) cc_final: 0.5754 (tmm) REVERT: C 298 MET cc_start: 0.8045 (mpp) cc_final: 0.7716 (mtm) REVERT: C 800 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8089 (mt) REVERT: D 207 GLU cc_start: 0.6697 (mp0) cc_final: 0.6468 (mp0) REVERT: D 257 GLU cc_start: 0.6949 (tm-30) cc_final: 0.6638 (tm-30) REVERT: D 700 THR cc_start: 0.8321 (OUTLIER) cc_final: 0.8073 (p) REVERT: D 734 TYR cc_start: 0.6911 (t80) cc_final: 0.6530 (t80) REVERT: D 766 LEU cc_start: 0.7500 (mt) cc_final: 0.7184 (mp) REVERT: D 803 LEU cc_start: 0.8778 (mt) cc_final: 0.8532 (mt) REVERT: E 322 TYR cc_start: 0.6874 (m-80) cc_final: 0.6565 (m-80) REVERT: E 686 VAL cc_start: 0.7196 (OUTLIER) cc_final: 0.6943 (t) REVERT: E 708 ASP cc_start: 0.6487 (t0) cc_final: 0.5911 (p0) REVERT: F 354 LYS cc_start: 0.6427 (OUTLIER) cc_final: 0.5773 (pttt) REVERT: F 365 ILE cc_start: 0.6206 (mt) cc_final: 0.5941 (mp) REVERT: F 638 MET cc_start: 0.5674 (mmm) cc_final: 0.4587 (mmm) REVERT: F 639 GLU cc_start: 0.6412 (mp0) cc_final: 0.6018 (mp0) REVERT: F 737 MET cc_start: 0.3841 (mmm) cc_final: 0.3404 (mmm) outliers start: 62 outliers final: 44 residues processed: 505 average time/residue: 0.3642 time to fit residues: 306.6017 Evaluate side-chains 487 residues out of total 2994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 437 time to evaluate : 3.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 819 ARG Chi-restraints excluded: chain A residue 858 HIS Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 195 GLN Chi-restraints excluded: chain C residue 310 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 800 LEU Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain D residue 310 CYS Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 638 MET Chi-restraints excluded: chain D residue 644 SER Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 700 THR Chi-restraints excluded: chain D residue 717 THR Chi-restraints excluded: chain D residue 773 SER Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 318 GLU Chi-restraints excluded: chain E residue 536 ILE Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 676 LEU Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain E residue 766 LEU Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 354 LYS Chi-restraints excluded: chain F residue 607 THR Chi-restraints excluded: chain F residue 714 VAL Chi-restraints excluded: chain F residue 741 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 224 optimal weight: 4.9990 chunk 300 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 260 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 282 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 chunk 290 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 52 optimal weight: 0.0670 overall best weight: 0.8922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 688 ASN ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 822 GLN B 736 HIS ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 GLN ** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.124109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.100441 restraints weight = 71623.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.102504 restraints weight = 42223.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.103839 restraints weight = 29103.096| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 1.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.343 28988 Z= 0.320 Angle : 0.828 65.868 39185 Z= 0.435 Chirality : 0.045 0.365 4436 Planarity : 0.006 0.232 5114 Dihedral : 8.825 150.897 4163 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 22.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.91 % Allowed : 26.06 % Favored : 72.03 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.48 % 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: -0.45 (0.14), residues: 3532 helix: 0.61 (0.12), residues: 1887 sheet: -1.22 (0.25), residues: 394 loop : -1.28 (0.18), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 462 HIS 0.020 0.001 HIS E 309 PHE 0.029 0.002 PHE B 621 TYR 0.023 0.001 TYR F 661 ARG 0.007 0.000 ARG D 750 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7219.00 seconds wall clock time: 130 minutes 2.37 seconds (7802.37 seconds total)