Starting phenix.real_space_refine on Thu Mar 21 00:29:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qs4_4621/03_2024/6qs4_4621_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qs4_4621/03_2024/6qs4_4621.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qs4_4621/03_2024/6qs4_4621.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qs4_4621/03_2024/6qs4_4621.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qs4_4621/03_2024/6qs4_4621_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qs4_4621/03_2024/6qs4_4621_updated.pdb" } resolution = 4.2 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 31 5.49 5 S 107 5.16 5 C 17996 2.51 5 N 5225 2.21 5 O 5480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 320": "NH1" <-> "NH2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A ARG 528": "NH1" <-> "NH2" Residue "B ARG 252": "NH1" <-> "NH2" Residue "B ARG 332": "NH1" <-> "NH2" Residue "B ARG 528": "NH1" <-> "NH2" Residue "B ARG 550": "NH1" <-> "NH2" Residue "C ARG 252": "NH1" <-> "NH2" Residue "C ARG 332": "NH1" <-> "NH2" Residue "C ARG 528": "NH1" <-> "NH2" Residue "C ARG 550": "NH1" <-> "NH2" Residue "D ARG 332": "NH1" <-> "NH2" Residue "D ARG 528": "NH1" <-> "NH2" Residue "D ARG 550": "NH1" <-> "NH2" Residue "E ARG 332": "NH1" <-> "NH2" Residue "E ARG 528": "NH1" <-> "NH2" Residue "E ARG 550": "NH1" <-> "NH2" Residue "F ARG 252": "NH1" <-> "NH2" Residue "F ARG 332": "NH1" <-> "NH2" Residue "F ARG 528": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28839 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4472 Classifications: {'peptide': 568} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 546} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 4562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4562 Classifications: {'peptide': 582} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 559} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 4976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 4976 Classifications: {'peptide': 630} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 606} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 4952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 4952 Classifications: {'peptide': 625} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 601} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 4952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 4952 Classifications: {'peptide': 625} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 601} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 4472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4472 Classifications: {'peptide': 568} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 546} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "B" 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: "C" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {'AGS': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {'AGS': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 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: 14.91, per 1000 atoms: 0.52 Number of scatterers: 28839 At special positions: 0 Unit cell: (117.6, 142.8, 156.45, 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 107 16.00 P 31 15.00 O 5480 8.00 N 5225 7.00 C 17996 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.16 Conformation dependent library (CDL) restraints added in 4.6 seconds 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6716 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 182 helices and 27 sheets defined 51.4% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.74 Creating SS restraints... Processing helix chain 'A' and resid 161 through 164 No H-bonds generated for 'chain 'A' and resid 161 through 164' Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 184 through 194 Processing helix chain 'A' and resid 212 through 224 Processing helix chain 'A' and resid 255 through 269 Processing helix chain 'A' and resid 280 through 284 removed outlier: 3.779A pdb=" N VAL A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 284' Processing helix chain 'A' and resid 296 through 305 Proline residue: A 301 - end of helix Processing helix chain 'A' and resid 316 through 322 Processing helix chain 'A' and resid 327 through 330 No H-bonds generated for 'chain 'A' and resid 327 through 330' Processing helix chain 'A' and resid 343 through 361 removed outlier: 4.733A pdb=" N GLU A 355 " --> pdb=" O ARG A 351 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ARG A 356 " --> pdb=" O GLY A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 380 Processing helix chain 'A' and resid 388 through 405 Processing helix chain 'A' and resid 533 through 542 Processing helix chain 'A' and resid 556 through 560 Processing helix chain 'A' and resid 562 through 566 Processing helix chain 'A' and resid 574 through 589 Processing helix chain 'A' and resid 611 through 622 Processing helix chain 'A' and resid 640 through 646 Processing helix chain 'A' and resid 663 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 684 through 696 removed outlier: 3.603A pdb=" N ASP A 695 " --> pdb=" O GLN A 692 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP A 696 " --> pdb=" O VAL A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 726 Processing helix chain 'A' and resid 734 through 748 Processing helix chain 'A' and resid 751 through 756 removed outlier: 3.696A pdb=" N ARG A 756 " --> pdb=" O GLU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 789 Processing helix chain 'A' and resid 797 through 804 Processing helix chain 'A' and resid 815 through 834 removed outlier: 4.194A pdb=" N ASN A 827 " --> pdb=" O GLN A 823 " (cutoff:3.500A) Proline residue: A 828 - end of helix removed outlier: 3.620A pdb=" N GLN A 831 " --> pdb=" O ASN A 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 164 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 224 removed outlier: 3.703A pdb=" N VAL B 216 " --> pdb=" O LYS B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 232 No H-bonds generated for 'chain 'B' and resid 230 through 232' Processing helix chain 'B' and resid 243 through 246 No H-bonds generated for 'chain 'B' and resid 243 through 246' Processing helix chain 'B' and resid 254 through 268 Processing helix chain 'B' and resid 280 through 284 Processing helix chain 'B' and resid 296 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 330 No H-bonds generated for 'chain 'B' and resid 327 through 330' Processing helix chain 'B' and resid 343 through 352 Processing helix chain 'B' and resid 354 through 361 Processing helix chain 'B' and resid 367 through 379 Processing helix chain 'B' and resid 388 through 407 Processing helix chain 'B' and resid 533 through 543 Processing helix chain 'B' and resid 553 through 560 Processing helix chain 'B' and resid 562 through 568 Processing helix chain 'B' and resid 574 through 588 Processing helix chain 'B' and resid 611 through 623 Processing helix chain 'B' and resid 634 through 637 Processing helix chain 'B' and resid 641 through 647 removed outlier: 4.042A pdb=" N VAL B 647 " --> pdb=" O SER B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 658 No H-bonds generated for 'chain 'B' and resid 656 through 658' Processing helix chain 'B' and resid 661 through 668 Processing helix chain 'B' and resid 684 through 686 No H-bonds generated for 'chain 'B' and resid 684 through 686' Processing helix chain 'B' and resid 689 through 696 Processing helix chain 'B' and resid 722 through 728 Processing helix chain 'B' and resid 734 through 748 Processing helix chain 'B' and resid 751 through 755 Processing helix chain 'B' and resid 768 through 789 Processing helix chain 'B' and resid 797 through 806 Processing helix chain 'B' and resid 815 through 826 Processing helix chain 'B' and resid 828 through 834 Processing helix chain 'C' and resid 161 through 164 No H-bonds generated for 'chain 'C' and resid 161 through 164' Processing helix chain 'C' and resid 168 through 173 Processing helix chain 'C' and resid 184 through 194 Processing helix chain 'C' and resid 212 through 225 Processing helix chain 'C' and resid 230 through 232 No H-bonds generated for 'chain 'C' and resid 230 through 232' Processing helix chain 'C' and resid 242 through 248 removed outlier: 4.842A pdb=" N GLY C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) 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 296 through 304 Proline residue: C 301 - end of helix Processing helix chain 'C' and resid 317 through 322 removed outlier: 3.561A pdb=" N GLN C 321 " --> pdb=" O ASP C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 330 No H-bonds generated for 'chain 'C' and resid 327 through 330' Processing helix chain 'C' and resid 343 through 361 Processing helix chain 'C' and resid 367 through 379 Processing helix chain 'C' and resid 388 through 406 Processing helix chain 'C' and resid 410 through 429 Processing helix chain 'C' and resid 445 through 464 Processing helix chain 'C' and resid 533 through 541 Processing helix chain 'C' and resid 553 through 560 Processing helix chain 'C' and resid 562 through 568 removed outlier: 3.720A pdb=" N HIS C 567 " --> pdb=" O GLU C 563 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N HIS C 568 " --> pdb=" O GLN C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 589 Processing helix chain 'C' and resid 611 through 623 Processing helix chain 'C' and resid 634 through 636 No H-bonds generated for 'chain 'C' and resid 634 through 636' Processing helix chain 'C' and resid 643 through 647 Processing helix chain 'C' and resid 656 through 658 No H-bonds generated for 'chain 'C' and resid 656 through 658' Processing helix chain 'C' and resid 661 through 667 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 688 through 695 Processing helix chain 'C' and resid 722 through 728 Processing helix chain 'C' and resid 734 through 748 Processing helix chain 'C' and resid 751 through 754 No H-bonds generated for 'chain 'C' and resid 751 through 754' Processing helix chain 'C' and resid 768 through 789 removed outlier: 4.117A pdb=" N GLU C 788 " --> pdb=" O LYS C 784 " (cutoff:3.500A) Processing helix chain 'C' and resid 797 through 805 removed outlier: 3.658A pdb=" N LYS C 801 " --> pdb=" O ASP C 797 " (cutoff:3.500A) Processing helix chain 'C' and resid 815 through 833 Proline residue: C 828 - end of helix Processing helix chain 'D' and resid 161 through 164 No H-bonds generated for 'chain 'D' and resid 161 through 164' Processing helix chain 'D' and resid 168 through 173 Processing helix chain 'D' and resid 184 through 194 Processing helix chain 'D' and resid 212 through 225 removed outlier: 3.793A pdb=" N VAL D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 232 No H-bonds generated for 'chain 'D' and resid 230 through 232' Processing helix chain 'D' and resid 242 through 248 Processing helix chain 'D' and resid 255 through 266 Processing helix chain 'D' and resid 280 through 282 No H-bonds generated for 'chain 'D' and resid 280 through 282' Processing helix chain 'D' and resid 299 through 303 Processing helix chain 'D' and resid 316 through 322 removed outlier: 3.821A pdb=" N ARG D 320 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN D 321 " --> pdb=" O ASP D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 332 removed outlier: 4.434A pdb=" N ARG D 332 " --> pdb=" O ALA D 328 " (cutoff:3.500A) 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 428 Processing helix chain 'D' and resid 445 through 464 Processing helix chain 'D' and resid 533 through 543 Processing helix chain 'D' and resid 553 through 560 Processing helix chain 'D' and resid 562 through 568 removed outlier: 3.950A pdb=" N HIS D 568 " --> pdb=" O GLN D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 588 Processing helix chain 'D' and resid 611 through 622 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 643 through 646 No H-bonds generated for 'chain 'D' and resid 643 through 646' 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 686 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 removed outlier: 3.649A pdb=" N ASN D 755 " --> pdb=" O PRO D 751 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 751 through 755' Processing helix chain 'D' and resid 768 through 789 Processing helix chain 'D' and resid 797 through 805 Processing helix chain 'D' and resid 815 through 834 Proline residue: D 828 - end of helix Processing helix chain 'E' and resid 161 through 164 No H-bonds generated for 'chain 'E' and resid 161 through 164' Processing helix chain 'E' and resid 169 through 173 Processing helix chain 'E' and resid 184 through 194 Processing helix chain 'E' and resid 212 through 225 Processing helix chain 'E' and resid 230 through 232 No H-bonds generated for 'chain 'E' and resid 230 through 232' Processing helix chain 'E' and resid 242 through 248 removed outlier: 3.867A pdb=" N VAL E 246 " --> pdb=" O MET E 242 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N GLY E 248 " --> pdb=" O ALA E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 269 Processing helix chain 'E' and resid 296 through 305 Proline residue: E 301 - end of helix Processing helix chain 'E' and resid 316 through 321 Processing helix chain 'E' and resid 327 through 332 removed outlier: 4.266A pdb=" N ARG E 331 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ARG E 332 " --> pdb=" O ALA E 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 327 through 332' 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 410 through 429 Processing helix chain 'E' and resid 445 through 465 Processing helix chain 'E' and resid 533 through 543 Processing helix chain 'E' and resid 553 through 569 Processing helix chain 'E' and resid 574 through 588 Processing helix chain 'E' and resid 611 through 622 Processing helix chain 'E' and resid 640 through 646 removed outlier: 4.013A pdb=" N VAL E 643 " --> pdb=" O LYS E 640 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER E 644 " --> pdb=" O HIS E 641 " (cutoff:3.500A) Processing helix chain 'E' and resid 656 through 658 No H-bonds generated for 'chain 'E' and resid 656 through 658' Processing helix chain 'E' and resid 662 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 removed outlier: 3.525A pdb=" N PHE E 687 " --> pdb=" O PRO E 684 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ASN E 688 " --> pdb=" O ASP E 685 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU E 690 " --> pdb=" O PHE E 687 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU E 694 " --> pdb=" O LEU E 691 " (cutoff:3.500A) Processing helix chain 'E' and resid 722 through 728 Processing helix chain 'E' and resid 734 through 748 Processing helix chain 'E' and resid 751 through 756 removed outlier: 4.147A pdb=" N ASN E 755 " --> pdb=" O PRO E 751 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG E 756 " --> pdb=" O GLU E 752 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 751 through 756' Processing helix chain 'E' and resid 768 through 789 removed outlier: 3.564A pdb=" N ARG E 789 " --> pdb=" O ARG E 785 " (cutoff:3.500A) Processing helix chain 'E' and resid 798 through 806 Processing helix chain 'E' and resid 813 through 835 Proline residue: E 816 - end of helix removed outlier: 3.503A pdb=" N ILE E 821 " --> pdb=" O LYS E 818 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN E 823 " --> pdb=" O ALA E 820 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN E 824 " --> pdb=" O ILE E 821 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE E 825 " --> pdb=" O GLN E 822 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU E 826 " --> pdb=" O GLN E 823 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ASN E 827 " --> pdb=" O GLN E 824 " (cutoff:3.500A) Proline residue: E 828 - end of helix removed outlier: 3.864A pdb=" N LEU E 834 " --> pdb=" O GLN E 831 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 164 No H-bonds generated for 'chain 'F' and resid 161 through 164' Processing helix chain 'F' and resid 169 through 173 Processing helix chain 'F' and resid 184 through 194 Processing helix chain 'F' and resid 212 through 224 Processing helix chain 'F' and resid 230 through 232 No H-bonds generated for 'chain 'F' and resid 230 through 232' Processing helix chain 'F' and resid 242 through 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 295 through 303 Proline residue: F 301 - end of helix Processing helix chain 'F' and resid 316 through 321 Processing helix chain 'F' and resid 343 through 361 removed outlier: 4.971A pdb=" N GLU F 355 " --> pdb=" O ARG F 351 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ARG F 356 " --> pdb=" O GLY F 352 " (cutoff:3.500A) 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 559 through 569 removed outlier: 5.403A pdb=" N GLU F 563 " --> pdb=" O LEU F 560 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS F 567 " --> pdb=" O GLN F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 574 through 588 Processing helix chain 'F' and resid 611 through 622 Processing helix chain 'F' and resid 640 through 647 removed outlier: 3.804A pdb=" N VAL F 643 " --> pdb=" O LYS F 640 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER F 644 " --> pdb=" O HIS F 641 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL F 647 " --> pdb=" O SER F 644 " (cutoff:3.500A) Processing helix chain 'F' and resid 661 through 668 removed outlier: 3.532A pdb=" N ALA F 665 " --> pdb=" O TYR F 661 " (cutoff:3.500A) Processing helix chain 'F' and resid 684 through 696 Processing helix chain 'F' and resid 722 through 728 Processing helix chain 'F' and resid 735 through 748 Processing helix chain 'F' and resid 751 through 755 Processing helix chain 'F' and resid 768 through 789 Processing helix chain 'F' and resid 797 through 806 Processing helix chain 'F' and resid 815 through 834 Proline residue: F 828 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 334 through 337 removed outlier: 8.197A pdb=" N VAL A 311 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU A 275 " --> pdb=" O VAL A 311 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N ALA A 313 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE A 277 " --> pdb=" O ALA A 313 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N ARG A 236 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N PHE A 276 " --> pdb=" O ARG A 236 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU A 238 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ASP A 278 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N LEU A 240 " --> pdb=" O ASP A 278 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 601 through 603 removed outlier: 6.545A pdb=" N GLU A 759 " --> pdb=" O LEU A 602 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 629 through 633 removed outlier: 7.401A pdb=" N VAL A 673 " --> pdb=" O VAL A 630 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ILE A 632 " --> pdb=" O VAL A 673 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU A 675 " --> pdb=" O ILE A 632 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N VAL A 713 " --> pdb=" O ILE A 674 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU A 676 " --> pdb=" O VAL A 713 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE A 715 " --> pdb=" O LEU A 676 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 698 through 700 Processing sheet with id= E, first strand: chain 'A' and resid 793 through 795 removed outlier: 5.931A pdb=" N ILE A 844 " --> pdb=" O HIS A 794 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 165 through 167 Processing sheet with id= G, first strand: chain 'B' and resid 311 through 314 removed outlier: 7.905A pdb=" N THR B 314 " --> pdb=" O PRO B 202 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N LEU B 204 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N GLN B 334 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE B 205 " --> pdb=" O GLN B 334 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N VAL B 336 " --> pdb=" O ILE B 205 " (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: 3.764A pdb=" N ASP B 677 " --> pdb=" O ILE B 632 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL B 713 " --> pdb=" O SER B 672 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 793 through 795 removed outlier: 5.836A pdb=" N ILE B 844 " --> pdb=" O HIS B 794 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 165 through 167 removed outlier: 4.936A pdb=" N ASP C 278 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N VAL C 311 " --> pdb=" O ILE C 277 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 202 through 205 removed outlier: 5.843A pdb=" N GLN C 334 " --> pdb=" O VAL C 203 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE C 205 " --> pdb=" O GLN C 334 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N VAL C 336 " --> pdb=" O ILE C 205 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'C' and resid 599 through 604 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 843 through 845 removed outlier: 3.512A pdb=" N ARG C 845 " --> pdb=" O VAL C 856 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 165 through 167 removed outlier: 4.482A pdb=" N ASP D 278 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA D 313 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N GLN D 334 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE D 205 " --> pdb=" O GLN D 334 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N VAL D 336 " --> pdb=" O ILE D 205 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 759 through 762 removed outlier: 3.550A pdb=" N GLU D 759 " --> pdb=" O SER D 600 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU D 602 " --> pdb=" O GLU D 759 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL D 714 " --> pdb=" O PHE D 601 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N PHE D 603 " --> pdb=" O VAL D 714 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N MET D 716 " --> pdb=" O PHE D 603 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 698 through 700 removed outlier: 3.869A pdb=" N LEU D 699 " --> pdb=" O VAL D 707 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 792 through 795 removed outlier: 3.770A pdb=" N HIS D 858 " --> pdb=" O VAL D 843 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG D 845 " --> pdb=" O VAL D 856 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 165 through 167 removed outlier: 5.223A pdb=" N ASP E 278 " --> pdb=" O LEU E 240 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA E 313 " --> pdb=" O ILE E 277 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 759 through 761 removed outlier: 3.583A pdb=" N GLU E 759 " --> pdb=" O SER E 600 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLY E 599 " --> pdb=" O THR E 712 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N SER E 672 " --> pdb=" O VAL E 713 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ILE E 715 " --> pdb=" O SER E 672 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ILE E 674 " --> pdb=" O ILE E 715 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N THR E 717 " --> pdb=" O ILE E 674 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N LEU E 676 " --> pdb=" O THR E 717 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL E 630 " --> pdb=" O LEU E 675 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASP E 677 " --> pdb=" O VAL E 630 " (cutoff:3.500A) removed outlier: 6.751A 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 removed outlier: 3.816A pdb=" N LEU E 699 " --> pdb=" O VAL E 707 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 792 through 795 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 203 through 206 removed outlier: 6.896A pdb=" N GLY F 312 " --> pdb=" O LEU F 204 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N GLY F 206 " --> pdb=" O GLY F 312 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N THR F 314 " --> pdb=" O GLY F 206 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'F' and resid 760 through 762 removed outlier: 7.957A pdb=" N VAL F 761 " --> pdb=" O SER F 600 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU F 602 " --> pdb=" O VAL F 761 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N VAL F 714 " --> pdb=" O PHE F 601 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N PHE F 603 " --> pdb=" O VAL F 714 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N MET F 716 " --> pdb=" O PHE F 603 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE F 715 " --> pdb=" O ILE F 674 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU F 676 " --> pdb=" O ILE F 715 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 698 through 700 Processing sheet with id= AA, first strand: chain 'F' and resid 793 through 795 removed outlier: 5.894A pdb=" N ILE F 844 " --> pdb=" O HIS F 794 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG F 845 " --> pdb=" O VAL F 856 " (cutoff:3.500A) 1177 hydrogen bonds defined for protein. 3414 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: 9.46 Time building geometry restraints manager: 11.13 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: 10204 1.36 - 1.51: 8221 1.51 - 1.65: 10651 1.65 - 1.80: 156 1.80 - 1.95: 37 Bond restraints: 29269 Sorted by residual: bond pdb=" O1B AGS D1003 " pdb=" PB AGS D1003 " ideal model delta sigma weight residual 1.481 1.556 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" CB PHE C 687 " pdb=" CG PHE C 687 " ideal model delta sigma weight residual 1.502 1.443 0.059 2.30e-02 1.89e+03 6.65e+00 bond pdb=" CB GLN D 692 " pdb=" CG GLN D 692 " ideal model delta sigma weight residual 1.520 1.444 0.076 3.00e-02 1.11e+03 6.48e+00 bond pdb=" CG GLN C 385 " pdb=" CD GLN C 385 " ideal model delta sigma weight residual 1.516 1.453 0.063 2.50e-02 1.60e+03 6.35e+00 bond pdb=" CB GLU D 613 " pdb=" CG GLU D 613 " ideal model delta sigma weight residual 1.520 1.446 0.074 3.00e-02 1.11e+03 6.11e+00 ... (remaining 29264 not shown) Histogram of bond angle deviations from ideal: 95.33 - 103.60: 377 103.60 - 111.87: 13933 111.87 - 120.14: 13612 120.14 - 128.41: 11444 128.41 - 136.69: 189 Bond angle restraints: 39555 Sorted by residual: angle pdb=" C HIS C 641 " pdb=" N SER C 642 " pdb=" CA SER C 642 " ideal model delta sigma weight residual 121.54 131.23 -9.69 1.91e+00 2.74e-01 2.57e+01 angle pdb=" C GLY E 610 " pdb=" N LYS E 611 " pdb=" CA LYS E 611 " ideal model delta sigma weight residual 120.88 112.88 8.00 1.62e+00 3.81e-01 2.44e+01 angle pdb=" C ARG B 645 " pdb=" N LEU B 646 " pdb=" CA LEU B 646 " ideal model delta sigma weight residual 121.66 113.49 8.17 1.76e+00 3.23e-01 2.15e+01 angle pdb=" C PHE B 749 " pdb=" N ARG B 750 " pdb=" CA ARG B 750 " ideal model delta sigma weight residual 120.97 134.06 -13.09 2.84e+00 1.24e-01 2.13e+01 angle pdb=" C MET D 293 " pdb=" N ASP D 294 " pdb=" CA ASP D 294 " ideal model delta sigma weight residual 122.44 116.97 5.47 1.19e+00 7.06e-01 2.11e+01 ... (remaining 39550 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.80: 17588 24.80 - 49.61: 401 49.61 - 74.41: 41 74.41 - 99.21: 11 99.21 - 124.02: 2 Dihedral angle restraints: 18043 sinusoidal: 7634 harmonic: 10409 Sorted by residual: dihedral pdb=" O1B ADP F1001 " pdb=" O3A ADP F1001 " pdb=" PB ADP F1001 " pdb=" PA ADP F1001 " ideal model delta sinusoidal sigma weight residual 300.00 175.98 124.02 1 2.00e+01 2.50e-03 3.74e+01 dihedral pdb=" CA TYR C 653 " pdb=" C TYR C 653 " pdb=" N VAL C 654 " pdb=" CA VAL C 654 " ideal model delta harmonic sigma weight residual -180.00 -149.92 -30.08 0 5.00e+00 4.00e-02 3.62e+01 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 180.00 149.98 30.02 0 5.00e+00 4.00e-02 3.61e+01 ... (remaining 18040 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3210 0.060 - 0.120: 1048 0.120 - 0.179: 189 0.179 - 0.239: 22 0.239 - 0.299: 4 Chirality restraints: 4473 Sorted by residual: chirality pdb=" PB AGS D1003 " pdb=" O2B AGS D1003 " pdb=" O3A AGS D1003 " pdb=" O3B AGS D1003 " both_signs ideal model delta sigma weight residual True 3.18 3.48 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" PB AGS D1001 " pdb=" O2B AGS D1001 " pdb=" O3A AGS D1001 " pdb=" O3B AGS D1001 " both_signs ideal model delta sigma weight residual True 3.18 2.91 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CB ILE E 571 " pdb=" CA ILE E 571 " pdb=" CG1 ILE E 571 " pdb=" CG2 ILE E 571 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 4470 not shown) Planarity restraints: 5164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 543 " -0.037 2.00e-02 2.50e+03 3.14e-02 2.46e+01 pdb=" CG TRP E 543 " 0.080 2.00e-02 2.50e+03 pdb=" CD1 TRP E 543 " -0.042 2.00e-02 2.50e+03 pdb=" CD2 TRP E 543 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP E 543 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP E 543 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 543 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 543 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 543 " -0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP E 543 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 367 " 0.048 5.00e-02 4.00e+02 7.15e-02 8.19e+00 pdb=" N PRO C 368 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO C 368 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 368 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS D 683 " 0.045 5.00e-02 4.00e+02 6.73e-02 7.25e+00 pdb=" N PRO D 684 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO D 684 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 684 " 0.037 5.00e-02 4.00e+02 ... (remaining 5161 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5716 2.77 - 3.30: 27604 3.30 - 3.83: 48808 3.83 - 4.37: 56802 4.37 - 4.90: 94833 Nonbonded interactions: 233763 Sorted by model distance: nonbonded pdb=" O GLN D 195 " pdb=" OG SER E 399 " model vdw 2.235 2.440 nonbonded pdb=" OH TYR B 656 " pdb=" OE1 GLU C 658 " model vdw 2.239 2.440 nonbonded pdb=" O1B AGS D1003 " pdb=" O2A AGS D1003 " model vdw 2.248 2.440 nonbonded pdb=" OH TYR A 656 " pdb=" OE1 GLU B 658 " model vdw 2.250 2.440 nonbonded pdb=" OD1 ASP B 677 " pdb=" OG1 THR B 717 " model vdw 2.252 2.440 ... (remaining 233758 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 159 through 858) selection = (chain 'B' and (resid 159 through 287 or resid 293 through 543 or resid 553 thro \ ugh 858)) selection = (chain 'C' and (resid 159 through 287 or resid 293 through 408 or resid 527 thro \ ugh 543 or resid 553 through 858)) selection = (chain 'D' and (resid 159 through 408 or resid 527 through 543 or resid 553 thro \ ugh 858)) selection = (chain 'E' and (resid 159 through 408 or resid 527 through 543 or resid 553 thro \ ugh 858)) selection = (chain 'F' and resid 159 through 858) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.640 Check model and map are aligned: 0.440 Set scattering table: 0.280 Process input model: 69.740 Find NCS groups from input model: 2.070 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 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 : 0.009 0.100 29269 Z= 0.595 Angle : 1.074 15.878 39555 Z= 0.572 Chirality : 0.058 0.299 4473 Planarity : 0.008 0.072 5164 Dihedral : 11.032 124.017 11327 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 0.10 % Allowed : 1.06 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.77 (0.11), residues: 3578 helix: -2.25 (0.09), residues: 1888 sheet: -2.85 (0.25), residues: 356 loop : -2.50 (0.15), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.006 TRP E 543 HIS 0.014 0.002 HIS F 747 PHE 0.037 0.004 PHE D 763 TYR 0.030 0.003 TYR B 322 ARG 0.019 0.001 ARG C 332 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 612 time to evaluate : 3.122 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 LEU cc_start: 0.8506 (mt) cc_final: 0.8232 (tp) REVERT: A 293 MET cc_start: 0.0194 (tpt) cc_final: -0.0891 (mmt) REVERT: A 723 ASP cc_start: 0.9453 (m-30) cc_final: 0.9215 (p0) REVERT: B 293 MET cc_start: 0.4802 (mmt) cc_final: 0.4521 (mmt) REVERT: B 602 LEU cc_start: 0.7729 (tp) cc_final: 0.6921 (tp) REVERT: E 350 LEU cc_start: 0.8124 (mt) cc_final: 0.7910 (tp) REVERT: F 403 MET cc_start: 0.9102 (mtp) cc_final: 0.8203 (tpt) REVERT: F 661 TYR cc_start: 0.7678 (t80) cc_final: 0.7448 (t80) outliers start: 3 outliers final: 0 residues processed: 615 average time/residue: 0.4698 time to fit residues: 430.6485 Evaluate side-chains 335 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 335 time to evaluate : 3.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 303 optimal weight: 9.9990 chunk 272 optimal weight: 7.9990 chunk 150 optimal weight: 20.0000 chunk 92 optimal weight: 4.9990 chunk 183 optimal weight: 0.9980 chunk 145 optimal weight: 5.9990 chunk 281 optimal weight: 0.9990 chunk 108 optimal weight: 8.9990 chunk 171 optimal weight: 9.9990 chunk 209 optimal weight: 1.9990 chunk 326 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN A 281 HIS ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 HIS A 726 GLN A 770 HIS ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 823 GLN A 849 ASN A 858 HIS B 192 GLN B 195 GLN B 641 HIS ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 806 ASN ** B 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 GLN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 858 HIS C 297 ASN C 421 GLN ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 849 ASN D 192 GLN D 195 GLN D 421 GLN D 641 HIS ** D 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 ASN D 794 HIS D 822 GLN D 849 ASN D 858 HIS E 174 GLN E 297 ASN E 321 GLN E 361 HIS E 421 GLN E 567 HIS E 641 HIS E 692 GLN E 822 GLN ** E 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 858 HIS F 281 HIS F 309 HIS F 321 GLN F 620 ASN F 688 ASN ** F 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 857 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 29269 Z= 0.250 Angle : 0.702 12.004 39555 Z= 0.356 Chirality : 0.045 0.250 4473 Planarity : 0.006 0.094 5164 Dihedral : 9.588 115.364 4193 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.10 % Allowed : 2.29 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % 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: -2.16 (0.13), residues: 3578 helix: -0.76 (0.11), residues: 1910 sheet: -2.46 (0.24), residues: 391 loop : -1.94 (0.17), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 543 HIS 0.011 0.001 HIS C 794 PHE 0.036 0.003 PHE F 637 TYR 0.023 0.002 TYR B 322 ARG 0.018 0.001 ARG F 645 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 389 time to evaluate : 3.317 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 LEU cc_start: 0.8597 (mt) cc_final: 0.8194 (tp) REVERT: A 293 MET cc_start: 0.0881 (tpt) cc_final: -0.0056 (tpp) REVERT: A 403 MET cc_start: 0.8053 (mtt) cc_final: 0.7687 (mtt) REVERT: B 280 LEU cc_start: 0.7818 (tt) cc_final: 0.7547 (tt) REVERT: B 298 MET cc_start: 0.6986 (ttt) cc_final: 0.6712 (ttt) REVERT: B 544 THR cc_start: 0.8599 (OUTLIER) cc_final: 0.7482 (p) REVERT: B 629 MET cc_start: 0.6450 (ppp) cc_final: 0.5519 (ppp) REVERT: C 629 MET cc_start: 0.6551 (ppp) cc_final: 0.5288 (ppp) REVERT: D 745 VAL cc_start: 0.8739 (t) cc_final: 0.8512 (p) REVERT: E 321 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8180 (pp30) REVERT: E 737 MET cc_start: 0.5762 (mmt) cc_final: 0.5240 (mmm) REVERT: F 629 MET cc_start: 0.6057 (mmm) cc_final: 0.5276 (mmm) REVERT: F 661 TYR cc_start: 0.7616 (t80) cc_final: 0.7392 (t80) REVERT: F 737 MET cc_start: 0.7910 (mtt) cc_final: 0.6676 (mmm) outliers start: 3 outliers final: 1 residues processed: 392 average time/residue: 0.4370 time to fit residues: 262.2660 Evaluate side-chains 291 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 288 time to evaluate : 3.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 181 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 271 optimal weight: 1.9990 chunk 221 optimal weight: 0.6980 chunk 89 optimal weight: 7.9990 chunk 326 optimal weight: 8.9990 chunk 352 optimal weight: 9.9990 chunk 290 optimal weight: 10.0000 chunk 323 optimal weight: 5.9990 chunk 111 optimal weight: 20.0000 chunk 262 optimal weight: 10.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 567 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 GLN ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 GLN ** B 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 849 ASN ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 GLN ** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 GLN D 567 HIS ** D 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 747 HIS ** E 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 806 ASN E 824 GLN ** E 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 GLN F 620 ASN F 726 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 29269 Z= 0.251 Angle : 0.665 12.281 39555 Z= 0.338 Chirality : 0.043 0.233 4473 Planarity : 0.005 0.060 5164 Dihedral : 9.190 118.683 4193 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.07 % Allowed : 2.73 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % 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: -1.40 (0.14), residues: 3578 helix: -0.09 (0.11), residues: 1924 sheet: -2.20 (0.24), residues: 401 loop : -1.64 (0.17), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 543 HIS 0.010 0.001 HIS B 281 PHE 0.022 0.002 PHE B 687 TYR 0.020 0.002 TYR A 251 ARG 0.017 0.001 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 335 time to evaluate : 3.546 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 LEU cc_start: 0.8776 (mt) cc_final: 0.8441 (tp) REVERT: A 293 MET cc_start: 0.0752 (tpt) cc_final: 0.0104 (tpp) REVERT: A 403 MET cc_start: 0.7985 (mtt) cc_final: 0.7588 (mtt) REVERT: A 851 ASP cc_start: 0.9239 (m-30) cc_final: 0.9032 (m-30) REVERT: B 277 ILE cc_start: 0.8374 (tt) cc_final: 0.7807 (mp) REVERT: B 298 MET cc_start: 0.7160 (ttt) cc_final: 0.6752 (ttt) REVERT: B 629 MET cc_start: 0.6639 (ppp) cc_final: 0.5694 (ppp) REVERT: C 281 HIS cc_start: 0.5812 (p-80) cc_final: 0.4295 (p-80) REVERT: C 552 MET cc_start: 0.7702 (ppp) cc_final: 0.7490 (ppp) REVERT: C 676 LEU cc_start: 0.7561 (mm) cc_final: 0.7321 (mm) REVERT: D 281 HIS cc_start: 0.6966 (p-80) cc_final: 0.6654 (p-80) REVERT: D 745 VAL cc_start: 0.8983 (t) cc_final: 0.8778 (p) REVERT: E 350 LEU cc_start: 0.8089 (tp) cc_final: 0.7827 (tp) REVERT: E 737 MET cc_start: 0.5834 (mmt) cc_final: 0.5504 (mmp) REVERT: F 602 LEU cc_start: 0.8679 (pt) cc_final: 0.8471 (pt) REVERT: F 629 MET cc_start: 0.6104 (mmm) cc_final: 0.5838 (tpp) REVERT: F 661 TYR cc_start: 0.7777 (t80) cc_final: 0.7507 (t80) REVERT: F 737 MET cc_start: 0.7802 (mtt) cc_final: 0.6761 (mmm) outliers start: 2 outliers final: 1 residues processed: 337 average time/residue: 0.4231 time to fit residues: 224.2789 Evaluate side-chains 258 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 257 time to evaluate : 3.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 322 optimal weight: 20.0000 chunk 245 optimal weight: 6.9990 chunk 169 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 219 optimal weight: 10.0000 chunk 327 optimal weight: 1.9990 chunk 347 optimal weight: 0.5980 chunk 171 optimal weight: 6.9990 chunk 310 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 567 HIS A 574 ASN A 794 HIS ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 ASN ** D 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 806 ASN ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 321 GLN E 334 GLN ** E 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 GLN F 620 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 29269 Z= 0.243 Angle : 0.646 12.109 39555 Z= 0.327 Chirality : 0.043 0.232 4473 Planarity : 0.005 0.054 5164 Dihedral : 8.964 120.318 4193 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 21.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.07 % Allowed : 2.89 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % 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: -1.00 (0.14), residues: 3578 helix: 0.25 (0.12), residues: 1938 sheet: -2.03 (0.23), residues: 428 loop : -1.48 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 543 HIS 0.008 0.001 HIS C 281 PHE 0.024 0.002 PHE C 333 TYR 0.015 0.001 TYR B 357 ARG 0.007 0.001 ARG B 171 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 291 time to evaluate : 3.686 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: A 194 LEU cc_start: 0.8831 (mt) cc_final: 0.8587 (tp) REVERT: A 293 MET cc_start: 0.0963 (tpt) cc_final: 0.0270 (tpt) REVERT: A 403 MET cc_start: 0.7980 (mtt) cc_final: 0.7600 (mtt) REVERT: A 595 ASN cc_start: 0.8542 (t0) cc_final: 0.8331 (t0) REVERT: B 242 MET cc_start: 0.8149 (mpp) cc_final: 0.5561 (mpp) REVERT: B 298 MET cc_start: 0.7364 (ttt) cc_final: 0.7010 (ttt) REVERT: B 629 MET cc_start: 0.6922 (ppp) cc_final: 0.6283 (ppp) REVERT: D 737 MET cc_start: 0.6896 (mtt) cc_final: 0.6603 (mtt) REVERT: D 745 VAL cc_start: 0.9109 (t) cc_final: 0.8898 (p) REVERT: E 321 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.8441 (pp30) REVERT: E 350 LEU cc_start: 0.8152 (tp) cc_final: 0.7898 (tp) REVERT: F 403 MET cc_start: 0.8726 (mtt) cc_final: 0.8346 (tmm) REVERT: F 602 LEU cc_start: 0.8496 (pt) cc_final: 0.8275 (pt) REVERT: F 661 TYR cc_start: 0.7822 (t80) cc_final: 0.7543 (t80) REVERT: F 737 MET cc_start: 0.7882 (mtt) cc_final: 0.7124 (mmm) outliers start: 2 outliers final: 1 residues processed: 293 average time/residue: 0.4049 time to fit residues: 188.2586 Evaluate side-chains 241 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 239 time to evaluate : 3.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 289 optimal weight: 6.9990 chunk 196 optimal weight: 9.9990 chunk 5 optimal weight: 20.0000 chunk 258 optimal weight: 0.9990 chunk 143 optimal weight: 0.5980 chunk 296 optimal weight: 8.9990 chunk 239 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 177 optimal weight: 20.0000 chunk 311 optimal weight: 8.9990 chunk 87 optimal weight: 9.9990 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 ASN ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 HIS B 747 HIS B 794 HIS ** B 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 321 GLN ** E 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 692 GLN ** E 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 GLN F 567 HIS ** F 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 620 ASN F 849 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.5482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 29269 Z= 0.293 Angle : 0.692 9.681 39555 Z= 0.349 Chirality : 0.043 0.181 4473 Planarity : 0.005 0.120 5164 Dihedral : 8.849 122.966 4193 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 24.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 0.03 % Allowed : 2.03 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % 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: -0.82 (0.14), residues: 3578 helix: 0.32 (0.12), residues: 1937 sheet: -1.79 (0.24), residues: 425 loop : -1.31 (0.18), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 543 HIS 0.015 0.002 HIS C 281 PHE 0.017 0.002 PHE C 729 TYR 0.018 0.002 TYR B 357 ARG 0.014 0.001 ARG A 384 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 270 time to evaluate : 3.318 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 194 LEU cc_start: 0.8980 (mt) cc_final: 0.8650 (tp) REVERT: A 293 MET cc_start: 0.0851 (tpt) cc_final: -0.1237 (mmp) REVERT: A 595 ASN cc_start: 0.8744 (t0) cc_final: 0.8510 (t0) REVERT: B 280 LEU cc_start: 0.8603 (mp) cc_final: 0.8203 (mp) REVERT: B 562 MET cc_start: 0.7846 (ptt) cc_final: 0.7581 (ptt) REVERT: B 629 MET cc_start: 0.7335 (ppp) cc_final: 0.6587 (ppp) REVERT: C 629 MET cc_start: 0.7530 (ppp) cc_final: 0.6860 (ppp) REVERT: E 350 LEU cc_start: 0.8274 (tp) cc_final: 0.7929 (tp) REVERT: E 675 LEU cc_start: 0.8105 (tt) cc_final: 0.7485 (tt) REVERT: E 737 MET cc_start: 0.6563 (mmp) cc_final: 0.6057 (mmm) REVERT: F 403 MET cc_start: 0.8733 (mtt) cc_final: 0.8386 (tmm) REVERT: F 602 LEU cc_start: 0.8402 (pt) cc_final: 0.8162 (pt) REVERT: F 603 PHE cc_start: 0.8349 (m-10) cc_final: 0.7959 (m-10) REVERT: F 629 MET cc_start: 0.6678 (tpp) cc_final: 0.5980 (tmm) REVERT: F 661 TYR cc_start: 0.7918 (t80) cc_final: 0.7564 (t80) REVERT: F 737 MET cc_start: 0.8096 (mtt) cc_final: 0.7366 (mmm) outliers start: 1 outliers final: 1 residues processed: 271 average time/residue: 0.4157 time to fit residues: 178.9578 Evaluate side-chains 210 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 209 time to evaluate : 2.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 116 optimal weight: 7.9990 chunk 312 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 203 optimal weight: 20.0000 chunk 85 optimal weight: 20.0000 chunk 347 optimal weight: 2.9990 chunk 288 optimal weight: 2.9990 chunk 160 optimal weight: 0.6980 chunk 28 optimal weight: 8.9990 chunk 114 optimal weight: 20.0000 chunk 182 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 HIS ** A 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 HIS ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS ** B 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 GLN D 688 ASN ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 321 GLN ** E 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 GLN F 620 ASN ** F 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 770 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.5718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29269 Z= 0.185 Angle : 0.595 9.612 39555 Z= 0.299 Chirality : 0.042 0.169 4473 Planarity : 0.005 0.091 5164 Dihedral : 8.594 121.165 4193 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 20.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.03 % Allowed : 1.50 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % 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: -0.49 (0.14), residues: 3578 helix: 0.64 (0.12), residues: 1923 sheet: -1.64 (0.24), residues: 436 loop : -1.25 (0.18), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 543 HIS 0.005 0.001 HIS F 747 PHE 0.032 0.002 PHE B 603 TYR 0.018 0.001 TYR C 380 ARG 0.009 0.000 ARG C 418 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 268 time to evaluate : 3.135 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: A 194 LEU cc_start: 0.8980 (mt) cc_final: 0.8690 (tp) REVERT: A 293 MET cc_start: 0.0712 (tpt) cc_final: -0.1336 (mmp) REVERT: B 293 MET cc_start: 0.6331 (tpp) cc_final: 0.5795 (tpp) REVERT: B 629 MET cc_start: 0.7163 (ppp) cc_final: 0.6534 (ppp) REVERT: C 242 MET cc_start: 0.8212 (ppp) cc_final: 0.7864 (ppp) REVERT: C 629 MET cc_start: 0.7574 (ppp) cc_final: 0.6937 (ppp) REVERT: E 299 LEU cc_start: 0.8916 (mt) cc_final: 0.8213 (mt) REVERT: E 321 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8388 (pp30) REVERT: E 350 LEU cc_start: 0.8194 (tp) cc_final: 0.7840 (tp) REVERT: F 403 MET cc_start: 0.8781 (mtt) cc_final: 0.8525 (tmm) REVERT: F 603 PHE cc_start: 0.8052 (m-10) cc_final: 0.7817 (m-10) REVERT: F 629 MET cc_start: 0.6651 (tpp) cc_final: 0.6426 (tpp) REVERT: F 737 MET cc_start: 0.8163 (mtt) cc_final: 0.7401 (mmm) outliers start: 1 outliers final: 0 residues processed: 269 average time/residue: 0.3937 time to fit residues: 171.0910 Evaluate side-chains 202 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 201 time to evaluate : 3.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 334 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 chunk 253 optimal weight: 0.8980 chunk 196 optimal weight: 1.9990 chunk 292 optimal weight: 9.9990 chunk 193 optimal weight: 8.9990 chunk 346 optimal weight: 8.9990 chunk 216 optimal weight: 2.9990 chunk 210 optimal weight: 7.9990 chunk 159 optimal weight: 9.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 GLN D 688 ASN E 321 GLN ** E 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 GLN F 620 ASN ** F 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.5982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 29269 Z= 0.192 Angle : 0.605 12.453 39555 Z= 0.303 Chirality : 0.042 0.165 4473 Planarity : 0.004 0.077 5164 Dihedral : 8.475 120.642 4193 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 20.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.03 % Allowed : 1.10 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % 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: -0.31 (0.14), residues: 3578 helix: 0.77 (0.12), residues: 1919 sheet: -1.58 (0.24), residues: 439 loop : -1.10 (0.19), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 543 HIS 0.006 0.001 HIS B 281 PHE 0.030 0.002 PHE B 687 TYR 0.017 0.001 TYR A 322 ARG 0.007 0.000 ARG C 418 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 254 time to evaluate : 3.684 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 194 LEU cc_start: 0.8912 (mt) cc_final: 0.8696 (tp) REVERT: A 293 MET cc_start: 0.0488 (tpt) cc_final: -0.1306 (mmp) REVERT: A 595 ASN cc_start: 0.8654 (t0) cc_final: 0.8427 (t0) REVERT: B 293 MET cc_start: 0.6375 (tpp) cc_final: 0.5876 (tpp) REVERT: B 562 MET cc_start: 0.7819 (ptt) cc_final: 0.7519 (ptt) REVERT: B 629 MET cc_start: 0.7275 (ppp) cc_final: 0.6178 (ppp) REVERT: C 242 MET cc_start: 0.8060 (ppp) cc_final: 0.7745 (ppp) REVERT: C 280 LEU cc_start: 0.8237 (tp) cc_final: 0.8015 (tt) REVERT: C 552 MET cc_start: 0.8223 (ppp) cc_final: 0.7978 (ppp) REVERT: C 629 MET cc_start: 0.7618 (ppp) cc_final: 0.6977 (ppp) REVERT: E 299 LEU cc_start: 0.8892 (mt) cc_final: 0.8554 (mt) REVERT: E 321 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8389 (pp30) REVERT: E 350 LEU cc_start: 0.8208 (tp) cc_final: 0.7865 (tp) REVERT: E 737 MET cc_start: 0.6230 (mmm) cc_final: 0.5971 (mmm) REVERT: F 603 PHE cc_start: 0.8011 (m-10) cc_final: 0.7787 (m-10) REVERT: F 629 MET cc_start: 0.6535 (tpp) cc_final: 0.6265 (tpp) REVERT: F 737 MET cc_start: 0.8221 (mtt) cc_final: 0.7469 (mmm) outliers start: 1 outliers final: 0 residues processed: 255 average time/residue: 0.4266 time to fit residues: 174.9177 Evaluate side-chains 206 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 205 time to evaluate : 2.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 214 optimal weight: 0.0770 chunk 138 optimal weight: 7.9990 chunk 206 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 chunk 219 optimal weight: 8.9990 chunk 235 optimal weight: 6.9990 chunk 171 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 271 optimal weight: 5.9990 chunk 314 optimal weight: 8.9990 overall best weight: 1.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 822 GLN D 174 GLN ** E 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 GLN F 620 ASN ** F 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.6209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29269 Z= 0.169 Angle : 0.586 9.517 39555 Z= 0.292 Chirality : 0.042 0.193 4473 Planarity : 0.004 0.073 5164 Dihedral : 8.356 119.520 4193 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 18.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % 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: -0.03 (0.15), residues: 3578 helix: 0.97 (0.12), residues: 1912 sheet: -1.38 (0.25), residues: 438 loop : -0.98 (0.19), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 543 HIS 0.005 0.001 HIS C 683 PHE 0.022 0.002 PHE B 603 TYR 0.019 0.001 TYR C 322 ARG 0.005 0.000 ARG C 418 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 3.428 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: A 194 LEU cc_start: 0.8923 (mt) cc_final: 0.8703 (tp) REVERT: A 293 MET cc_start: 0.0435 (tpt) cc_final: -0.1128 (mmp) REVERT: A 595 ASN cc_start: 0.8639 (t0) cc_final: 0.8418 (t0) REVERT: A 638 MET cc_start: 0.8203 (mmm) cc_final: 0.7946 (mmm) REVERT: B 280 LEU cc_start: 0.8458 (mp) cc_final: 0.8063 (mp) REVERT: B 293 MET cc_start: 0.6259 (tpp) cc_final: 0.5860 (tpp) REVERT: B 562 MET cc_start: 0.7970 (ptt) cc_final: 0.7435 (ptt) REVERT: B 629 MET cc_start: 0.7341 (ppp) cc_final: 0.5943 (ppp) REVERT: C 242 MET cc_start: 0.7957 (ppp) cc_final: 0.7753 (ppp) REVERT: C 552 MET cc_start: 0.8032 (ppp) cc_final: 0.7679 (ppp) REVERT: C 629 MET cc_start: 0.7308 (ppp) cc_final: 0.6829 (ppp) REVERT: E 350 LEU cc_start: 0.8180 (tp) cc_final: 0.7895 (tp) REVERT: F 629 MET cc_start: 0.6474 (tpp) cc_final: 0.6193 (tpp) REVERT: F 737 MET cc_start: 0.8308 (mtt) cc_final: 0.7642 (mmm) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.4227 time to fit residues: 180.8087 Evaluate side-chains 208 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 3.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 331 optimal weight: 0.0470 chunk 302 optimal weight: 0.7980 chunk 322 optimal weight: 6.9990 chunk 194 optimal weight: 7.9990 chunk 140 optimal weight: 10.0000 chunk 253 optimal weight: 6.9990 chunk 98 optimal weight: 0.0030 chunk 291 optimal weight: 20.0000 chunk 304 optimal weight: 9.9990 chunk 321 optimal weight: 0.0370 chunk 211 optimal weight: 8.9990 overall best weight: 1.5768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 GLN ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 321 GLN E 454 GLN ** E 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 GLN F 620 ASN ** F 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.6423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 29269 Z= 0.157 Angle : 0.571 9.473 39555 Z= 0.283 Chirality : 0.042 0.170 4473 Planarity : 0.004 0.063 5164 Dihedral : 8.194 118.554 4193 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.03 % Allowed : 0.40 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.15), residues: 3578 helix: 1.03 (0.12), residues: 1932 sheet: -1.23 (0.26), residues: 413 loop : -0.88 (0.19), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 543 HIS 0.006 0.001 HIS A 281 PHE 0.025 0.002 PHE C 255 TYR 0.013 0.001 TYR C 322 ARG 0.008 0.000 ARG B 586 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 270 time to evaluate : 3.487 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: A 194 LEU cc_start: 0.8971 (mt) cc_final: 0.8753 (tp) REVERT: A 293 MET cc_start: 0.0484 (tpt) cc_final: -0.1084 (mmp) REVERT: B 194 LEU cc_start: 0.8725 (pp) cc_final: 0.8417 (mt) REVERT: B 280 LEU cc_start: 0.8428 (mp) cc_final: 0.8102 (mp) REVERT: B 293 MET cc_start: 0.6095 (tpp) cc_final: 0.5756 (tpp) REVERT: B 562 MET cc_start: 0.7904 (ptt) cc_final: 0.7373 (ptt) REVERT: B 629 MET cc_start: 0.7332 (ppp) cc_final: 0.5991 (ppp) REVERT: C 242 MET cc_start: 0.7897 (ppp) cc_final: 0.7643 (ppp) REVERT: C 552 MET cc_start: 0.8078 (ppp) cc_final: 0.7677 (ppp) REVERT: C 629 MET cc_start: 0.7457 (ppp) cc_final: 0.6989 (ppp) REVERT: E 321 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.7935 (pp30) REVERT: E 350 LEU cc_start: 0.8159 (tp) cc_final: 0.7883 (tp) REVERT: E 447 GLU cc_start: 0.8527 (pm20) cc_final: 0.8301 (pm20) REVERT: E 737 MET cc_start: 0.6103 (mmm) cc_final: 0.5738 (mmm) REVERT: F 293 MET cc_start: 0.3291 (mmt) cc_final: 0.2403 (tpp) REVERT: F 622 MET cc_start: 0.8204 (tpp) cc_final: 0.7811 (tpp) REVERT: F 629 MET cc_start: 0.6435 (tpp) cc_final: 0.6178 (tpp) REVERT: F 737 MET cc_start: 0.8386 (mtt) cc_final: 0.7700 (mmm) outliers start: 1 outliers final: 0 residues processed: 271 average time/residue: 0.4087 time to fit residues: 176.2013 Evaluate side-chains 204 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 203 time to evaluate : 3.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 340 optimal weight: 7.9990 chunk 208 optimal weight: 4.9990 chunk 161 optimal weight: 9.9990 chunk 237 optimal weight: 7.9990 chunk 357 optimal weight: 50.0000 chunk 329 optimal weight: 20.0000 chunk 284 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 219 optimal weight: 0.0470 chunk 174 optimal weight: 0.8980 chunk 226 optimal weight: 3.9990 overall best weight: 3.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 GLN ** E 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 620 ASN ** F 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 806 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.6833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29269 Z= 0.213 Angle : 0.617 9.809 39555 Z= 0.308 Chirality : 0.042 0.171 4473 Planarity : 0.004 0.060 5164 Dihedral : 8.238 119.141 4193 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 21.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % 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: 0.19 (0.15), residues: 3578 helix: 1.05 (0.12), residues: 1927 sheet: -1.23 (0.25), residues: 446 loop : -0.71 (0.19), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 543 HIS 0.009 0.001 HIS E 641 PHE 0.030 0.002 PHE A 601 TYR 0.038 0.001 TYR E 322 ARG 0.004 0.000 ARG D 188 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7156 Ramachandran restraints generated. 3578 Oldfield, 0 Emsley, 3578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 3.663 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: A 194 LEU cc_start: 0.9041 (mt) cc_final: 0.8775 (tp) REVERT: A 293 MET cc_start: 0.0953 (tpt) cc_final: -0.0682 (mmt) REVERT: A 320 ARG cc_start: 0.9224 (ptp-170) cc_final: 0.8867 (mtm-85) REVERT: A 595 ASN cc_start: 0.8762 (t0) cc_final: 0.8544 (t0) REVERT: B 629 MET cc_start: 0.7586 (ppp) cc_final: 0.6365 (ppp) REVERT: C 552 MET cc_start: 0.8171 (ppp) cc_final: 0.7798 (ppp) REVERT: C 629 MET cc_start: 0.7543 (ppp) cc_final: 0.7019 (ppp) REVERT: E 350 LEU cc_start: 0.8283 (tp) cc_final: 0.8017 (tp) REVERT: E 447 GLU cc_start: 0.8347 (pm20) cc_final: 0.8076 (pm20) REVERT: E 737 MET cc_start: 0.6410 (mmm) cc_final: 0.6077 (mmm) REVERT: F 297 ASN cc_start: 0.7742 (t0) cc_final: 0.6979 (t0) REVERT: F 622 MET cc_start: 0.8237 (tpp) cc_final: 0.8008 (tpp) REVERT: F 629 MET cc_start: 0.6643 (tpp) cc_final: 0.6152 (tpp) REVERT: F 737 MET cc_start: 0.8451 (mtt) cc_final: 0.7819 (mmm) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.4336 time to fit residues: 170.8216 Evaluate side-chains 191 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 3.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 303 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 262 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 chunk 79 optimal weight: 9.9990 chunk 285 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 chunk 292 optimal weight: 0.8980 chunk 36 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 250 optimal weight: 20.0000 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 GLN D 427 GLN ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 620 ASN ** F 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.050301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.039476 restraints weight = 278719.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.039957 restraints weight = 226317.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.040338 restraints weight = 194241.824| |-----------------------------------------------------------------------------| r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.7115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29269 Z= 0.184 Angle : 0.587 9.369 39555 Z= 0.293 Chirality : 0.042 0.189 4473 Planarity : 0.004 0.062 5164 Dihedral : 8.172 117.599 4193 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 19.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % 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: 0.21 (0.15), residues: 3578 helix: 1.02 (0.12), residues: 1953 sheet: -1.17 (0.25), residues: 426 loop : -0.67 (0.19), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 543 HIS 0.009 0.001 HIS E 641 PHE 0.023 0.002 PHE B 687 TYR 0.012 0.001 TYR E 322 ARG 0.005 0.000 ARG B 586 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5212.09 seconds wall clock time: 95 minutes 36.40 seconds (5736.40 seconds total)