Starting phenix.real_space_refine on Thu Feb 22 07:49:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vn1_21247/02_2024/6vn1_21247.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vn1_21247/02_2024/6vn1_21247.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vn1_21247/02_2024/6vn1_21247.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vn1_21247/02_2024/6vn1_21247.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vn1_21247/02_2024/6vn1_21247.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vn1_21247/02_2024/6vn1_21247.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 14058 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 99 5.16 5 C 12333 2.51 5 N 3366 2.21 5 O 3726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L ARG 41": "NH1" <-> "NH2" Residue "H ARG 50": "NH1" <-> "NH2" Residue "A GLU 343": "OE1" <-> "OE2" Residue "A GLU 376": "OE1" <-> "OE2" Residue "A GLU 378": "OE1" <-> "OE2" Residue "A GLU 546": "OE1" <-> "OE2" Residue "A GLU 586": "OE1" <-> "OE2" Residue "M ARG 41": "NH1" <-> "NH2" Residue "I ARG 50": "NH1" <-> "NH2" Residue "B GLU 343": "OE1" <-> "OE2" Residue "B GLU 376": "OE1" <-> "OE2" Residue "B GLU 378": "OE1" <-> "OE2" Residue "B GLU 546": "OE1" <-> "OE2" Residue "B GLU 586": "OE1" <-> "OE2" Residue "N ARG 41": "NH1" <-> "NH2" Residue "J ARG 50": "NH1" <-> "NH2" Residue "C TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 343": "OE1" <-> "OE2" Residue "C GLU 376": "OE1" <-> "OE2" Residue "C GLU 378": "OE1" <-> "OE2" Residue "C GLU 546": "OE1" <-> "OE2" Residue "C GLU 586": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19524 Number of models: 1 Model: "" Number of chains: 9 Chain: "L" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 832 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 957 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "A" Number of atoms: 4719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4719 Classifications: {'peptide': 584} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 559} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 832 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "I" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 957 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "B" Number of atoms: 4719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4719 Classifications: {'peptide': 584} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 559} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 832 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "J" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 957 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "C" Number of atoms: 4719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4719 Classifications: {'peptide': 584} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 559} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 9.92, per 1000 atoms: 0.51 Number of scatterers: 19524 At special positions: 0 Unit cell: (136.74, 150.52, 178.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 99 16.00 O 3726 8.00 N 3366 7.00 C 12333 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 122 " - pdb=" SG CYS A 584 " distance=2.03 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 540 " distance=2.03 Simple disulfide: pdb=" SG CYS A 213 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 369 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS A 608 " - pdb=" SG CYS A 645 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 122 " - pdb=" SG CYS B 584 " distance=2.03 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 540 " distance=2.04 Simple disulfide: pdb=" SG CYS B 213 " - pdb=" SG CYS B 277 " distance=2.03 Simple disulfide: pdb=" SG CYS B 369 " - pdb=" SG CYS B 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 608 " - pdb=" SG CYS B 645 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 122 " - pdb=" SG CYS C 584 " distance=2.03 Simple disulfide: pdb=" SG CYS C 139 " - pdb=" SG CYS C 540 " distance=2.03 Simple disulfide: pdb=" SG CYS C 213 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 369 " - pdb=" SG CYS C 417 " distance=2.03 Simple disulfide: pdb=" SG CYS C 608 " - pdb=" SG CYS C 645 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.88 Conformation dependent library (CDL) restraints added in 3.7 seconds 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4620 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 54 sheets defined 17.0% alpha, 30.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.34 Creating SS restraints... Processing helix chain 'H' and resid 26 through 30 removed outlier: 3.848A pdb=" N PHE H 29 " --> pdb=" O GLY H 26 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER H 30 " --> pdb=" O GLY H 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 26 through 30' Processing helix chain 'H' and resid 108 through 112 removed outlier: 3.632A pdb=" N PHE H 112 " --> pdb=" O PRO H 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 211 removed outlier: 5.275A pdb=" N ASP A 208 " --> pdb=" O THR A 204 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N LYS A 209 " --> pdb=" O ASP A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 233 No H-bonds generated for 'chain 'A' and resid 231 through 233' Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 363 through 367 Processing helix chain 'A' and resid 408 through 412 removed outlier: 3.538A pdb=" N ILE A 412 " --> pdb=" O LEU A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 434 removed outlier: 4.678A pdb=" N GLU A 420 " --> pdb=" O GLN A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 554 removed outlier: 4.244A pdb=" N ALA A 548 " --> pdb=" O ASN A 544 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU A 549 " --> pdb=" O ARG A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 566 removed outlier: 3.544A pdb=" N LEU A 561 " --> pdb=" O ASN A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 676 No H-bonds generated for 'chain 'A' and resid 674 through 676' Processing helix chain 'A' and resid 702 through 707 Processing helix chain 'A' and resid 713 through 722 Processing helix chain 'A' and resid 723 through 729 Processing helix chain 'I' and resid 26 through 30 removed outlier: 3.848A pdb=" N PHE I 29 " --> pdb=" O GLY I 26 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER I 30 " --> pdb=" O GLY I 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 26 through 30' Processing helix chain 'I' and resid 108 through 112 removed outlier: 3.633A pdb=" N PHE I 112 " --> pdb=" O PRO I 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 211 removed outlier: 5.275A pdb=" N ASP B 208 " --> pdb=" O THR B 204 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N LYS B 209 " --> pdb=" O ASP B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 233 No H-bonds generated for 'chain 'B' and resid 231 through 233' Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 363 through 367 Processing helix chain 'B' and resid 408 through 412 removed outlier: 3.539A pdb=" N ILE B 412 " --> pdb=" O LEU B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 434 removed outlier: 4.678A pdb=" N GLU B 420 " --> pdb=" O GLN B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 554 removed outlier: 4.244A pdb=" N ALA B 548 " --> pdb=" O ASN B 544 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU B 549 " --> pdb=" O ARG B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 566 removed outlier: 3.545A pdb=" N LEU B 561 " --> pdb=" O ASN B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 676 No H-bonds generated for 'chain 'B' and resid 674 through 676' Processing helix chain 'B' and resid 702 through 707 Processing helix chain 'B' and resid 713 through 722 Processing helix chain 'B' and resid 723 through 729 Processing helix chain 'J' and resid 26 through 30 removed outlier: 3.849A pdb=" N PHE J 29 " --> pdb=" O GLY J 26 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER J 30 " --> pdb=" O GLY J 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 26 through 30' Processing helix chain 'J' and resid 108 through 112 removed outlier: 3.631A pdb=" N PHE J 112 " --> pdb=" O PRO J 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 211 removed outlier: 5.274A pdb=" N ASP C 208 " --> pdb=" O THR C 204 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N LYS C 209 " --> pdb=" O ASP C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 233 No H-bonds generated for 'chain 'C' and resid 231 through 233' Processing helix chain 'C' and resid 312 through 316 Processing helix chain 'C' and resid 363 through 367 Processing helix chain 'C' and resid 408 through 412 removed outlier: 3.539A pdb=" N ILE C 412 " --> pdb=" O LEU C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 434 removed outlier: 4.679A pdb=" N GLU C 420 " --> pdb=" O GLN C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 554 removed outlier: 4.244A pdb=" N ALA C 548 " --> pdb=" O ASN C 544 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU C 549 " --> pdb=" O ARG C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 566 removed outlier: 3.545A pdb=" N LEU C 561 " --> pdb=" O ASN C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 674 through 676 No H-bonds generated for 'chain 'C' and resid 674 through 676' Processing helix chain 'C' and resid 702 through 707 Processing helix chain 'C' and resid 713 through 722 Processing helix chain 'C' and resid 723 through 729 Processing sheet with id=AA1, first strand: chain 'L' and resid 19 through 20 Processing sheet with id=AA2, first strand: chain 'L' and resid 23 through 24 Processing sheet with id=AA3, first strand: chain 'L' and resid 33 through 35 Processing sheet with id=AA4, first strand: chain 'L' and resid 48 through 49 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AA6, first strand: chain 'H' and resid 46 through 51 removed outlier: 3.523A pdb=" N ARG H 38 " --> pdb=" O GLU H 46 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 69 through 72 Processing sheet with id=AA8, first strand: chain 'A' and resid 573 through 574 removed outlier: 6.865A pdb=" N ILE A 130 " --> pdb=" O GLY B 677 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ILE B 679 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ARG A 132 " --> pdb=" O ILE B 679 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 398 through 403 removed outlier: 5.180A pdb=" N LYS A 373 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N LYS A 157 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASP A 379 " --> pdb=" O GLY A 151 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLY A 151 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLU A 150 " --> pdb=" O LEU A 460 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 398 through 403 removed outlier: 5.180A pdb=" N LYS A 373 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N LYS A 157 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASP A 379 " --> pdb=" O GLY A 151 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLY A 151 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLU A 150 " --> pdb=" O LEU A 460 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 186 through 197 removed outlier: 5.709A pdb=" N ILE A 188 " --> pdb=" O TRP A 180 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TRP A 180 " --> pdb=" O ILE A 188 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 241 through 242 removed outlier: 7.332A pdb=" N LYS A 166 " --> pdb=" O ASN A 360 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ASN A 360 " --> pdb=" O LYS A 166 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 212 through 214 Processing sheet with id=AB5, first strand: chain 'A' and resid 216 through 221 Processing sheet with id=AB6, first strand: chain 'A' and resid 293 through 294 Processing sheet with id=AB7, first strand: chain 'A' and resid 591 through 595 Processing sheet with id=AB8, first strand: chain 'A' and resid 607 through 609 Processing sheet with id=AB9, first strand: chain 'A' and resid 650 through 655 removed outlier: 3.660A pdb=" N ARG A 669 " --> pdb=" O TYR A 661 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N GLU A 663 " --> pdb=" O TYR A 667 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N TYR A 667 " --> pdb=" O GLU A 663 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 677 through 679 removed outlier: 3.862A pdb=" N GLY A 677 " --> pdb=" O ILE C 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 19 through 20 Processing sheet with id=AC3, first strand: chain 'M' and resid 23 through 24 Processing sheet with id=AC4, first strand: chain 'M' and resid 33 through 35 Processing sheet with id=AC5, first strand: chain 'M' and resid 48 through 49 Processing sheet with id=AC6, first strand: chain 'I' and resid 10 through 12 Processing sheet with id=AC7, first strand: chain 'I' and resid 46 through 51 removed outlier: 3.522A pdb=" N ARG I 38 " --> pdb=" O GLU I 46 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ARG I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE I 34 " --> pdb=" O ARG I 50 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 69 through 72 Processing sheet with id=AC9, first strand: chain 'B' and resid 573 through 574 removed outlier: 6.890A pdb=" N ILE B 130 " --> pdb=" O GLY C 677 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ILE C 679 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ARG B 132 " --> pdb=" O ILE C 679 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 398 through 403 removed outlier: 5.180A pdb=" N LYS B 373 " --> pdb=" O LYS B 157 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N LYS B 157 " --> pdb=" O LYS B 373 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASP B 379 " --> pdb=" O GLY B 151 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLY B 151 " --> pdb=" O ASP B 379 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLU B 150 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 398 through 403 removed outlier: 5.180A pdb=" N LYS B 373 " --> pdb=" O LYS B 157 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N LYS B 157 " --> pdb=" O LYS B 373 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASP B 379 " --> pdb=" O GLY B 151 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLY B 151 " --> pdb=" O ASP B 379 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLU B 150 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 186 through 197 removed outlier: 5.710A pdb=" N ILE B 188 " --> pdb=" O TRP B 180 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N TRP B 180 " --> pdb=" O ILE B 188 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 241 through 242 removed outlier: 7.332A pdb=" N LYS B 166 " --> pdb=" O ASN B 360 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ASN B 360 " --> pdb=" O LYS B 166 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 212 through 214 Processing sheet with id=AD6, first strand: chain 'B' and resid 216 through 221 Processing sheet with id=AD7, first strand: chain 'B' and resid 293 through 294 Processing sheet with id=AD8, first strand: chain 'B' and resid 591 through 595 Processing sheet with id=AD9, first strand: chain 'B' and resid 607 through 609 Processing sheet with id=AE1, first strand: chain 'B' and resid 650 through 655 removed outlier: 3.660A pdb=" N ARG B 669 " --> pdb=" O TYR B 661 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N GLU B 663 " --> pdb=" O TYR B 667 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N TYR B 667 " --> pdb=" O GLU B 663 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'N' and resid 19 through 20 Processing sheet with id=AE3, first strand: chain 'N' and resid 23 through 24 Processing sheet with id=AE4, first strand: chain 'N' and resid 33 through 35 Processing sheet with id=AE5, first strand: chain 'N' and resid 48 through 49 Processing sheet with id=AE6, first strand: chain 'J' and resid 10 through 12 Processing sheet with id=AE7, first strand: chain 'J' and resid 46 through 51 removed outlier: 3.523A pdb=" N ARG J 38 " --> pdb=" O GLU J 46 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ARG J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE J 34 " --> pdb=" O ARG J 50 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 69 through 72 Processing sheet with id=AE9, first strand: chain 'C' and resid 398 through 403 removed outlier: 5.180A pdb=" N LYS C 373 " --> pdb=" O LYS C 157 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N LYS C 157 " --> pdb=" O LYS C 373 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASP C 379 " --> pdb=" O GLY C 151 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLY C 151 " --> pdb=" O ASP C 379 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLU C 150 " --> pdb=" O LEU C 460 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 398 through 403 removed outlier: 5.180A pdb=" N LYS C 373 " --> pdb=" O LYS C 157 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N LYS C 157 " --> pdb=" O LYS C 373 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASP C 379 " --> pdb=" O GLY C 151 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLY C 151 " --> pdb=" O ASP C 379 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLU C 150 " --> pdb=" O LEU C 460 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 186 through 197 removed outlier: 5.710A pdb=" N ILE C 188 " --> pdb=" O TRP C 180 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N TRP C 180 " --> pdb=" O ILE C 188 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 241 through 242 removed outlier: 7.333A pdb=" N LYS C 166 " --> pdb=" O ASN C 360 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ASN C 360 " --> pdb=" O LYS C 166 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 212 through 214 Processing sheet with id=AF5, first strand: chain 'C' and resid 216 through 221 Processing sheet with id=AF6, first strand: chain 'C' and resid 293 through 294 Processing sheet with id=AF7, first strand: chain 'C' and resid 591 through 595 Processing sheet with id=AF8, first strand: chain 'C' and resid 607 through 609 Processing sheet with id=AF9, first strand: chain 'C' and resid 650 through 655 removed outlier: 3.660A pdb=" N ARG C 669 " --> pdb=" O TYR C 661 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N GLU C 663 " --> pdb=" O TYR C 667 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N TYR C 667 " --> pdb=" O GLU C 663 " (cutoff:3.500A) 683 hydrogen bonds defined for protein. 1806 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.77 Time building geometry restraints manager: 7.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6336 1.34 - 1.46: 4482 1.46 - 1.58: 9006 1.58 - 1.70: 0 1.70 - 1.82: 156 Bond restraints: 19980 Sorted by residual: bond pdb=" N GLU B 513 " pdb=" CA GLU B 513 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.23e-02 6.61e+03 5.01e+00 bond pdb=" N GLU C 513 " pdb=" CA GLU C 513 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.23e-02 6.61e+03 4.74e+00 bond pdb=" N GLU A 513 " pdb=" CA GLU A 513 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.23e-02 6.61e+03 4.66e+00 bond pdb=" N GLY B 127 " pdb=" CA GLY B 127 " ideal model delta sigma weight residual 1.449 1.469 -0.020 1.45e-02 4.76e+03 1.95e+00 bond pdb=" C LYS M 42 " pdb=" N ALA M 43 " ideal model delta sigma weight residual 1.339 1.262 0.077 5.57e-02 3.22e+02 1.91e+00 ... (remaining 19975 not shown) Histogram of bond angle deviations from ideal: 99.65 - 106.56: 546 106.56 - 113.48: 10909 113.48 - 120.39: 7197 120.39 - 127.31: 8282 127.31 - 134.23: 207 Bond angle restraints: 27141 Sorted by residual: angle pdb=" N GLU B 513 " pdb=" CA GLU B 513 " pdb=" C GLU B 513 " ideal model delta sigma weight residual 111.36 107.65 3.71 1.09e+00 8.42e-01 1.16e+01 angle pdb=" N GLU C 513 " pdb=" CA GLU C 513 " pdb=" C GLU C 513 " ideal model delta sigma weight residual 111.36 107.71 3.65 1.09e+00 8.42e-01 1.12e+01 angle pdb=" N GLU A 513 " pdb=" CA GLU A 513 " pdb=" C GLU A 513 " ideal model delta sigma weight residual 111.36 107.71 3.65 1.09e+00 8.42e-01 1.12e+01 angle pdb=" C GLY M 99 " pdb=" N GLN M 100 " pdb=" CA GLN M 100 " ideal model delta sigma weight residual 120.95 125.56 -4.61 1.78e+00 3.16e-01 6.71e+00 angle pdb=" C GLY L 99 " pdb=" N GLN L 100 " pdb=" CA GLN L 100 " ideal model delta sigma weight residual 120.95 125.55 -4.60 1.78e+00 3.16e-01 6.67e+00 ... (remaining 27136 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 10902 17.68 - 35.36: 861 35.36 - 53.04: 159 53.04 - 70.72: 24 70.72 - 88.40: 24 Dihedral angle restraints: 11970 sinusoidal: 4776 harmonic: 7194 Sorted by residual: dihedral pdb=" CB CYS C 369 " pdb=" SG CYS C 369 " pdb=" SG CYS C 417 " pdb=" CB CYS C 417 " ideal model delta sinusoidal sigma weight residual 93.00 149.03 -56.03 1 1.00e+01 1.00e-02 4.24e+01 dihedral pdb=" CB CYS A 369 " pdb=" SG CYS A 369 " pdb=" SG CYS A 417 " pdb=" CB CYS A 417 " ideal model delta sinusoidal sigma weight residual 93.00 149.02 -56.02 1 1.00e+01 1.00e-02 4.23e+01 dihedral pdb=" CB CYS B 369 " pdb=" SG CYS B 369 " pdb=" SG CYS B 417 " pdb=" CB CYS B 417 " ideal model delta sinusoidal sigma weight residual 93.00 148.98 -55.98 1 1.00e+01 1.00e-02 4.23e+01 ... (remaining 11967 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1758 0.033 - 0.067: 795 0.067 - 0.100: 327 0.100 - 0.133: 114 0.133 - 0.166: 21 Chirality restraints: 3015 Sorted by residual: chirality pdb=" CB ILE M 21 " pdb=" CA ILE M 21 " pdb=" CG1 ILE M 21 " pdb=" CG2 ILE M 21 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.17 2.00e-01 2.50e+01 6.91e-01 chirality pdb=" CB ILE N 21 " pdb=" CA ILE N 21 " pdb=" CG1 ILE N 21 " pdb=" CG2 ILE N 21 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.17 2.00e-01 2.50e+01 6.84e-01 chirality pdb=" CB ILE L 21 " pdb=" CA ILE L 21 " pdb=" CG1 ILE L 21 " pdb=" CG2 ILE L 21 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.16 2.00e-01 2.50e+01 6.57e-01 ... (remaining 3012 not shown) Planarity restraints: 3480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER M 7 " -0.042 5.00e-02 4.00e+02 6.37e-02 6.49e+00 pdb=" N PRO M 8 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO M 8 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO M 8 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER N 7 " 0.042 5.00e-02 4.00e+02 6.37e-02 6.49e+00 pdb=" N PRO N 8 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO N 8 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO N 8 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER L 7 " -0.042 5.00e-02 4.00e+02 6.34e-02 6.43e+00 pdb=" N PRO L 8 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO L 8 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO L 8 " -0.035 5.00e-02 4.00e+02 ... (remaining 3477 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 391 2.68 - 3.23: 17672 3.23 - 3.79: 29466 3.79 - 4.34: 42589 4.34 - 4.90: 72040 Nonbonded interactions: 162158 Sorted by model distance: nonbonded pdb=" OD1 ASP N 82 " pdb=" OH TYR N 86 " model vdw 2.123 2.440 nonbonded pdb=" OD1 ASP L 82 " pdb=" OH TYR L 86 " model vdw 2.123 2.440 nonbonded pdb=" OD1 ASP M 82 " pdb=" OH TYR M 86 " model vdw 2.123 2.440 nonbonded pdb=" O ILE N 21 " pdb=" NE2 GLN N 100 " model vdw 2.181 2.520 nonbonded pdb=" O ILE M 21 " pdb=" NE2 GLN M 100 " model vdw 2.182 2.520 ... (remaining 162153 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.210 Construct map_model_manager: 0.010 Extract box with map and model: 13.130 Check model and map are aligned: 0.270 Set scattering table: 0.180 Process input model: 50.160 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 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 : 0.006 0.077 19980 Z= 0.396 Angle : 0.627 6.877 27141 Z= 0.354 Chirality : 0.047 0.166 3015 Planarity : 0.004 0.064 3480 Dihedral : 13.280 88.402 7287 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -3.36 (0.15), residues: 2430 helix: -0.38 (0.29), residues: 309 sheet: -2.56 (0.18), residues: 687 loop : -2.56 (0.13), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 359 HIS 0.009 0.002 HIS A 254 PHE 0.023 0.002 PHE C 165 TYR 0.020 0.002 TYR C 682 ARG 0.003 0.000 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 307 time to evaluate : 2.244 Fit side-chains REVERT: A 120 TYR cc_start: 0.8336 (m-80) cc_final: 0.8010 (m-80) REVERT: A 236 GLN cc_start: 0.7497 (mt0) cc_final: 0.7206 (mt0) REVERT: A 270 ARG cc_start: 0.7522 (mmm-85) cc_final: 0.7309 (mmm160) REVERT: A 291 ASP cc_start: 0.8009 (p0) cc_final: 0.7403 (p0) REVERT: A 416 GLN cc_start: 0.8021 (mp10) cc_final: 0.7231 (pm20) REVERT: A 504 ARG cc_start: 0.8162 (ptt180) cc_final: 0.7962 (ptt180) REVERT: A 516 MET cc_start: 0.8284 (mtp) cc_final: 0.7987 (mtm) REVERT: A 632 ASP cc_start: 0.7613 (m-30) cc_final: 0.7394 (m-30) REVERT: A 708 ASP cc_start: 0.7926 (t70) cc_final: 0.7352 (t0) REVERT: M 53 ILE cc_start: 0.8842 (mm) cc_final: 0.8538 (mp) REVERT: B 120 TYR cc_start: 0.8361 (m-80) cc_final: 0.8154 (m-80) REVERT: B 260 TYR cc_start: 0.8707 (t80) cc_final: 0.8395 (t80) REVERT: B 270 ARG cc_start: 0.7586 (mmm-85) cc_final: 0.7340 (mmm160) REVERT: B 339 ARG cc_start: 0.7797 (mtt-85) cc_final: 0.7568 (mtp85) REVERT: B 526 GLU cc_start: 0.7421 (tt0) cc_final: 0.7200 (tm-30) REVERT: B 599 MET cc_start: 0.8896 (mtp) cc_final: 0.8615 (mtm) REVERT: B 632 ASP cc_start: 0.7577 (m-30) cc_final: 0.7274 (m-30) REVERT: B 708 ASP cc_start: 0.7850 (t70) cc_final: 0.7360 (t0) REVERT: B 716 GLU cc_start: 0.7795 (tp30) cc_final: 0.7453 (tp30) REVERT: N 53 ILE cc_start: 0.8793 (mm) cc_final: 0.8577 (mp) REVERT: J 100 ILE cc_start: 0.8767 (mt) cc_final: 0.8535 (mm) REVERT: C 291 ASP cc_start: 0.8043 (p0) cc_final: 0.7628 (p0) REVERT: C 416 GLN cc_start: 0.7822 (mp10) cc_final: 0.7226 (pm20) REVERT: C 516 MET cc_start: 0.8280 (mtp) cc_final: 0.7907 (mtp) REVERT: C 666 ARG cc_start: 0.7510 (mtp85) cc_final: 0.7277 (mtp-110) REVERT: C 708 ASP cc_start: 0.8045 (t70) cc_final: 0.7472 (t0) outliers start: 0 outliers final: 1 residues processed: 307 average time/residue: 1.3307 time to fit residues: 460.0348 Evaluate side-chains 229 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 228 time to evaluate : 2.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 696 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 0.6980 chunk 181 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 62 optimal weight: 0.0670 chunk 122 optimal weight: 0.0170 chunk 97 optimal weight: 8.9990 chunk 188 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 chunk 140 optimal weight: 0.5980 chunk 217 optimal weight: 4.9990 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN L 90 GLN A 223 ASN ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 ASN A 628 GLN M 37 GLN M 79 GLN M 90 GLN B 147 ASN B 223 ASN ** B 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 597 ASN B 628 GLN N 37 GLN N 79 GLN N 89 GLN N 90 GLN C 147 ASN C 223 ASN ** C 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 GLN C 648 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19980 Z= 0.164 Angle : 0.516 7.211 27141 Z= 0.280 Chirality : 0.044 0.203 3015 Planarity : 0.004 0.061 3480 Dihedral : 4.664 32.554 2742 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.13 % Allowed : 10.28 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -2.34 (0.16), residues: 2430 helix: 1.18 (0.31), residues: 309 sheet: -2.09 (0.18), residues: 711 loop : -1.92 (0.15), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 32 HIS 0.004 0.001 HIS C 649 PHE 0.014 0.001 PHE A 165 TYR 0.012 0.001 TYR A 430 ARG 0.003 0.000 ARG C 339 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 258 time to evaluate : 2.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 21 ILE cc_start: 0.7956 (mt) cc_final: 0.7729 (mt) REVERT: H 60 TYR cc_start: 0.7392 (m-80) cc_final: 0.7039 (m-80) REVERT: A 270 ARG cc_start: 0.7474 (mmm-85) cc_final: 0.7249 (mmm160) REVERT: A 291 ASP cc_start: 0.7946 (p0) cc_final: 0.7301 (p0) REVERT: A 416 GLN cc_start: 0.8049 (mp10) cc_final: 0.7251 (pm20) REVERT: A 516 MET cc_start: 0.8107 (mtp) cc_final: 0.7848 (mtm) REVERT: A 708 ASP cc_start: 0.7830 (t70) cc_final: 0.7271 (t0) REVERT: M 53 ILE cc_start: 0.8797 (mm) cc_final: 0.8463 (mp) REVERT: B 260 TYR cc_start: 0.8426 (t80) cc_final: 0.8155 (t80) REVERT: B 270 ARG cc_start: 0.7441 (mmm-85) cc_final: 0.7228 (mmm160) REVERT: B 339 ARG cc_start: 0.7785 (mtt-85) cc_final: 0.7547 (mtp85) REVERT: B 554 PHE cc_start: 0.8327 (OUTLIER) cc_final: 0.7912 (t80) REVERT: B 599 MET cc_start: 0.8853 (mtp) cc_final: 0.8593 (mtm) REVERT: B 632 ASP cc_start: 0.7339 (m-30) cc_final: 0.7022 (m-30) REVERT: B 708 ASP cc_start: 0.7726 (t70) cc_final: 0.7217 (t0) REVERT: B 716 GLU cc_start: 0.7757 (tp30) cc_final: 0.7429 (tp30) REVERT: N 21 ILE cc_start: 0.7744 (mt) cc_final: 0.7497 (mt) REVERT: N 47 MET cc_start: 0.7426 (mmm) cc_final: 0.7179 (tpt) REVERT: J 81 MET cc_start: 0.6985 (OUTLIER) cc_final: 0.6513 (tmm) REVERT: C 225 LYS cc_start: 0.8381 (ttmt) cc_final: 0.7972 (tppt) REVERT: C 291 ASP cc_start: 0.7969 (p0) cc_final: 0.7456 (p0) REVERT: C 416 GLN cc_start: 0.7818 (mp10) cc_final: 0.7239 (pm20) REVERT: C 513 GLU cc_start: 0.6644 (mp0) cc_final: 0.6431 (mp0) REVERT: C 516 MET cc_start: 0.8192 (mtp) cc_final: 0.7732 (mtp) REVERT: C 666 ARG cc_start: 0.7525 (mtp85) cc_final: 0.7225 (mmm-85) REVERT: C 678 MET cc_start: 0.8130 (mtm) cc_final: 0.7866 (ttm) REVERT: C 708 ASP cc_start: 0.7933 (t70) cc_final: 0.7378 (t0) REVERT: C 716 GLU cc_start: 0.7818 (tp30) cc_final: 0.7430 (tp30) outliers start: 46 outliers final: 12 residues processed: 287 average time/residue: 1.2707 time to fit residues: 412.1670 Evaluate side-chains 242 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 228 time to evaluate : 2.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 417 CYS Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain J residue 81 MET Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 417 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 181 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 218 optimal weight: 0.9980 chunk 235 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 216 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN L 79 GLN L 90 GLN A 388 ASN M 90 GLN B 543 GLN B 568 GLN N 89 GLN ** J 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 GLN C 388 ASN C 543 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 19980 Z= 0.405 Angle : 0.611 7.504 27141 Z= 0.328 Chirality : 0.047 0.192 3015 Planarity : 0.005 0.062 3480 Dihedral : 5.043 37.264 2739 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.15 % Allowed : 12.92 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -2.10 (0.16), residues: 2430 helix: 1.23 (0.31), residues: 309 sheet: -1.79 (0.18), residues: 711 loop : -1.82 (0.15), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 359 HIS 0.008 0.002 HIS A 649 PHE 0.025 0.002 PHE A 165 TYR 0.018 0.002 TYR A 652 ARG 0.006 0.000 ARG A 666 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 237 time to evaluate : 2.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 70 GLU cc_start: 0.6509 (OUTLIER) cc_final: 0.5871 (tp30) REVERT: H 60 TYR cc_start: 0.7445 (m-80) cc_final: 0.7150 (m-80) REVERT: A 147 ASN cc_start: 0.7460 (m-40) cc_final: 0.7231 (m-40) REVERT: A 236 GLN cc_start: 0.7341 (mt0) cc_final: 0.7121 (mt0) REVERT: A 322 MET cc_start: 0.8421 (mmm) cc_final: 0.8023 (mmm) REVERT: A 416 GLN cc_start: 0.8056 (mp10) cc_final: 0.7279 (pm20) REVERT: A 516 MET cc_start: 0.8248 (mtp) cc_final: 0.7998 (mtm) REVERT: A 554 PHE cc_start: 0.8383 (OUTLIER) cc_final: 0.7994 (t80) REVERT: A 582 SER cc_start: 0.8768 (t) cc_final: 0.8547 (p) REVERT: A 708 ASP cc_start: 0.7860 (t70) cc_final: 0.7309 (t0) REVERT: M 53 ILE cc_start: 0.8852 (mm) cc_final: 0.8536 (mp) REVERT: M 70 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.6344 (tm-30) REVERT: B 260 TYR cc_start: 0.8514 (t80) cc_final: 0.8113 (t80) REVERT: B 526 GLU cc_start: 0.7505 (tt0) cc_final: 0.7297 (tm-30) REVERT: B 554 PHE cc_start: 0.8374 (OUTLIER) cc_final: 0.7951 (t80) REVERT: B 583 ASN cc_start: 0.8254 (OUTLIER) cc_final: 0.7778 (m-40) REVERT: B 599 MET cc_start: 0.8887 (mtp) cc_final: 0.8545 (mtm) REVERT: B 632 ASP cc_start: 0.7441 (m-30) cc_final: 0.7116 (m-30) REVERT: B 694 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7428 (mt-10) REVERT: B 708 ASP cc_start: 0.7750 (t70) cc_final: 0.7286 (t0) REVERT: N 53 ILE cc_start: 0.8757 (mm) cc_final: 0.8447 (mp) REVERT: N 70 GLU cc_start: 0.6806 (OUTLIER) cc_final: 0.6053 (tp30) REVERT: J 81 MET cc_start: 0.6957 (OUTLIER) cc_final: 0.6593 (tmm) REVERT: C 225 LYS cc_start: 0.8389 (ttmt) cc_final: 0.7968 (tppt) REVERT: C 291 ASP cc_start: 0.8092 (p0) cc_final: 0.7388 (p0) REVERT: C 416 GLN cc_start: 0.7873 (mp10) cc_final: 0.7374 (pm20) REVERT: C 513 GLU cc_start: 0.6874 (mp0) cc_final: 0.6616 (mp0) REVERT: C 516 MET cc_start: 0.8242 (mtp) cc_final: 0.7809 (mtp) REVERT: C 554 PHE cc_start: 0.8380 (OUTLIER) cc_final: 0.8068 (t80) REVERT: C 666 ARG cc_start: 0.7543 (mtp85) cc_final: 0.7308 (mtp-110) REVERT: C 708 ASP cc_start: 0.7982 (t70) cc_final: 0.7494 (t0) outliers start: 68 outliers final: 35 residues processed: 281 average time/residue: 1.2624 time to fit residues: 402.2148 Evaluate side-chains 275 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 231 time to evaluate : 2.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 417 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 70 GLU Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 583 ASN Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain B residue 694 GLU Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 81 MET Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 417 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 568 GLN Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain C residue 700 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 0.9980 chunk 164 optimal weight: 5.9990 chunk 113 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 104 optimal weight: 0.6980 chunk 146 optimal weight: 3.9990 chunk 219 optimal weight: 1.9990 chunk 231 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 207 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN H 120 GLN A 411 GLN ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 GLN M 38 GLN M 90 GLN I 39 GLN B 411 GLN ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN N 89 GLN C 411 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19980 Z= 0.220 Angle : 0.521 6.686 27141 Z= 0.283 Chirality : 0.045 0.202 3015 Planarity : 0.004 0.060 3480 Dihedral : 4.754 33.622 2739 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.61 % Allowed : 13.19 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.68 (0.17), residues: 2430 helix: 1.59 (0.32), residues: 309 sheet: -1.52 (0.19), residues: 723 loop : -1.52 (0.15), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 359 HIS 0.005 0.001 HIS A 649 PHE 0.019 0.001 PHE B 165 TYR 0.014 0.001 TYR I 95 ARG 0.003 0.000 ARG A 569 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 239 time to evaluate : 2.302 Fit side-chains revert: symmetry clash REVERT: L 70 GLU cc_start: 0.6390 (OUTLIER) cc_final: 0.5814 (tp30) REVERT: H 60 TYR cc_start: 0.7385 (m-80) cc_final: 0.7118 (m-80) REVERT: H 120 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.7539 (pm20) REVERT: A 291 ASP cc_start: 0.8126 (p0) cc_final: 0.7763 (p0) REVERT: A 322 MET cc_start: 0.8438 (mmm) cc_final: 0.8082 (mmm) REVERT: A 416 GLN cc_start: 0.8060 (mp10) cc_final: 0.7390 (pm20) REVERT: A 516 MET cc_start: 0.8165 (mtp) cc_final: 0.7935 (mtm) REVERT: A 554 PHE cc_start: 0.8388 (OUTLIER) cc_final: 0.8028 (t80) REVERT: A 582 SER cc_start: 0.8624 (t) cc_final: 0.8384 (p) REVERT: A 708 ASP cc_start: 0.7838 (t70) cc_final: 0.7311 (t0) REVERT: M 53 ILE cc_start: 0.8806 (mm) cc_final: 0.8474 (mp) REVERT: M 70 GLU cc_start: 0.6630 (OUTLIER) cc_final: 0.6295 (tm-30) REVERT: B 260 TYR cc_start: 0.8350 (t80) cc_final: 0.8004 (t80) REVERT: B 291 ASP cc_start: 0.8146 (p0) cc_final: 0.7817 (p0) REVERT: B 416 GLN cc_start: 0.8096 (mp10) cc_final: 0.7245 (pm20) REVERT: B 513 GLU cc_start: 0.6612 (mp0) cc_final: 0.6325 (mp0) REVERT: B 554 PHE cc_start: 0.8318 (OUTLIER) cc_final: 0.7933 (t80) REVERT: B 583 ASN cc_start: 0.8017 (OUTLIER) cc_final: 0.7793 (m-40) REVERT: B 599 MET cc_start: 0.8843 (mtp) cc_final: 0.8559 (mtm) REVERT: B 708 ASP cc_start: 0.7712 (t70) cc_final: 0.7259 (t0) REVERT: N 47 MET cc_start: 0.7554 (mmm) cc_final: 0.7342 (tpt) REVERT: N 70 GLU cc_start: 0.6658 (OUTLIER) cc_final: 0.5960 (tp30) REVERT: N 82 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7824 (m-30) REVERT: J 81 MET cc_start: 0.7009 (OUTLIER) cc_final: 0.6517 (tmm) REVERT: C 139 CYS cc_start: 0.4626 (OUTLIER) cc_final: 0.4242 (t) REVERT: C 225 LYS cc_start: 0.8365 (ttmt) cc_final: 0.7961 (tppt) REVERT: C 291 ASP cc_start: 0.8047 (p0) cc_final: 0.7566 (p0) REVERT: C 416 GLN cc_start: 0.7866 (mp10) cc_final: 0.7105 (pm20) REVERT: C 513 GLU cc_start: 0.6822 (mp0) cc_final: 0.6547 (mp0) REVERT: C 516 MET cc_start: 0.8190 (mtp) cc_final: 0.7724 (mtp) REVERT: C 554 PHE cc_start: 0.8315 (OUTLIER) cc_final: 0.8028 (t80) REVERT: C 666 ARG cc_start: 0.7497 (mtp85) cc_final: 0.7262 (mtp-110) REVERT: C 678 MET cc_start: 0.8173 (mtm) cc_final: 0.7910 (ttm) REVERT: C 708 ASP cc_start: 0.7969 (t70) cc_final: 0.7488 (t0) outliers start: 78 outliers final: 36 residues processed: 291 average time/residue: 1.2227 time to fit residues: 404.1343 Evaluate side-chains 275 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 228 time to evaluate : 2.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain M residue 70 GLU Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 583 ASN Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain N residue 82 ASP Chi-restraints excluded: chain N residue 92 LYS Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 81 MET Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 128 SER Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 417 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 568 GLN Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain C residue 700 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 172 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 197 optimal weight: 0.0060 chunk 160 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 chunk 208 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 GLN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 GLN ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 GLN C 388 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 19980 Z= 0.295 Angle : 0.564 9.900 27141 Z= 0.304 Chirality : 0.046 0.233 3015 Planarity : 0.004 0.060 3480 Dihedral : 4.863 35.068 2739 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 3.80 % Allowed : 13.89 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.49 (0.17), residues: 2430 helix: 1.59 (0.32), residues: 309 sheet: -1.40 (0.19), residues: 726 loop : -1.35 (0.16), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 359 HIS 0.006 0.001 HIS A 649 PHE 0.021 0.002 PHE B 165 TYR 0.014 0.002 TYR A 652 ARG 0.003 0.000 ARG B 666 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 238 time to evaluate : 2.105 Fit side-chains revert: symmetry clash REVERT: L 70 GLU cc_start: 0.6420 (OUTLIER) cc_final: 0.5817 (tp30) REVERT: H 60 TYR cc_start: 0.7428 (m-80) cc_final: 0.7175 (m-80) REVERT: H 93 MET cc_start: 0.7839 (ttm) cc_final: 0.7619 (ttt) REVERT: A 236 GLN cc_start: 0.7318 (mt0) cc_final: 0.7096 (mt0) REVERT: A 322 MET cc_start: 0.8410 (mmm) cc_final: 0.8037 (mmm) REVERT: A 416 GLN cc_start: 0.7776 (mp10) cc_final: 0.7328 (pm20) REVERT: A 516 MET cc_start: 0.8234 (mtp) cc_final: 0.7994 (mtm) REVERT: A 554 PHE cc_start: 0.8410 (OUTLIER) cc_final: 0.8042 (t80) REVERT: A 568 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.6976 (tm-30) REVERT: A 573 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.7334 (ttp-170) REVERT: A 582 SER cc_start: 0.8617 (t) cc_final: 0.8408 (p) REVERT: A 583 ASN cc_start: 0.8066 (OUTLIER) cc_final: 0.7781 (m110) REVERT: A 708 ASP cc_start: 0.7840 (t70) cc_final: 0.7333 (t0) REVERT: M 53 ILE cc_start: 0.8833 (mm) cc_final: 0.8525 (mp) REVERT: M 70 GLU cc_start: 0.6707 (OUTLIER) cc_final: 0.6368 (tm-30) REVERT: B 260 TYR cc_start: 0.8397 (t80) cc_final: 0.8055 (t80) REVERT: B 389 PHE cc_start: 0.8393 (m-80) cc_final: 0.8125 (m-10) REVERT: B 416 GLN cc_start: 0.7937 (mp10) cc_final: 0.7474 (pm20) REVERT: B 554 PHE cc_start: 0.8333 (OUTLIER) cc_final: 0.7946 (t80) REVERT: B 583 ASN cc_start: 0.7907 (OUTLIER) cc_final: 0.7560 (m-40) REVERT: B 599 MET cc_start: 0.8864 (mtp) cc_final: 0.8596 (mtm) REVERT: B 694 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7450 (mt-10) REVERT: B 708 ASP cc_start: 0.7728 (t70) cc_final: 0.7292 (t0) REVERT: N 21 ILE cc_start: 0.7915 (mt) cc_final: 0.7689 (mt) REVERT: N 47 MET cc_start: 0.7534 (mmm) cc_final: 0.7315 (tpt) REVERT: N 70 GLU cc_start: 0.6629 (OUTLIER) cc_final: 0.5915 (tp30) REVERT: N 82 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7804 (m-30) REVERT: J 81 MET cc_start: 0.6872 (OUTLIER) cc_final: 0.6532 (tmm) REVERT: C 225 LYS cc_start: 0.8323 (ttmt) cc_final: 0.7937 (tppt) REVERT: C 291 ASP cc_start: 0.8075 (p0) cc_final: 0.7675 (p0) REVERT: C 416 GLN cc_start: 0.7781 (mp10) cc_final: 0.7072 (pm20) REVERT: C 513 GLU cc_start: 0.6911 (mp0) cc_final: 0.6598 (mp0) REVERT: C 516 MET cc_start: 0.8225 (mtp) cc_final: 0.7754 (mtp) REVERT: C 554 PHE cc_start: 0.8371 (OUTLIER) cc_final: 0.8066 (t80) REVERT: C 678 MET cc_start: 0.8169 (mtm) cc_final: 0.7906 (ttm) REVERT: C 708 ASP cc_start: 0.7981 (t70) cc_final: 0.7480 (t0) outliers start: 82 outliers final: 48 residues processed: 296 average time/residue: 1.1963 time to fit residues: 402.7262 Evaluate side-chains 290 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 229 time to evaluate : 2.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 568 GLN Chi-restraints excluded: chain A residue 573 ARG Chi-restraints excluded: chain A residue 583 ASN Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 70 GLU Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 583 ASN Chi-restraints excluded: chain B residue 618 SER Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 694 GLU Chi-restraints excluded: chain B residue 734 VAL Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain N residue 82 ASP Chi-restraints excluded: chain N residue 92 LYS Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 81 MET Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 417 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 568 GLN Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain C residue 700 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 0.9990 chunk 208 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 232 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 GLN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 GLN I 39 GLN ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 GLN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 19980 Z= 0.316 Angle : 0.582 15.550 27141 Z= 0.310 Chirality : 0.046 0.223 3015 Planarity : 0.004 0.059 3480 Dihedral : 4.976 35.634 2739 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 4.17 % Allowed : 14.07 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.39 (0.17), residues: 2430 helix: 1.57 (0.32), residues: 309 sheet: -1.30 (0.19), residues: 735 loop : -1.28 (0.16), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 539 HIS 0.006 0.001 HIS A 649 PHE 0.022 0.002 PHE B 293 TYR 0.015 0.002 TYR B 667 ARG 0.003 0.000 ARG A 569 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 236 time to evaluate : 2.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 70 GLU cc_start: 0.6400 (OUTLIER) cc_final: 0.5803 (tp30) REVERT: H 60 TYR cc_start: 0.7451 (m-80) cc_final: 0.7205 (m-80) REVERT: H 93 MET cc_start: 0.7905 (ttm) cc_final: 0.7633 (ttt) REVERT: A 236 GLN cc_start: 0.7340 (mt0) cc_final: 0.7123 (mt0) REVERT: A 322 MET cc_start: 0.8449 (mmm) cc_final: 0.8096 (mmm) REVERT: A 416 GLN cc_start: 0.8076 (mp10) cc_final: 0.7476 (pm20) REVERT: A 516 MET cc_start: 0.8242 (mtp) cc_final: 0.8004 (mtm) REVERT: A 554 PHE cc_start: 0.8380 (OUTLIER) cc_final: 0.7933 (t80) REVERT: A 568 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.6948 (tm-30) REVERT: A 573 ARG cc_start: 0.7657 (OUTLIER) cc_final: 0.7412 (ttp-170) REVERT: A 583 ASN cc_start: 0.8127 (OUTLIER) cc_final: 0.7863 (m110) REVERT: A 708 ASP cc_start: 0.7855 (t70) cc_final: 0.7358 (t0) REVERT: M 70 GLU cc_start: 0.6724 (OUTLIER) cc_final: 0.6385 (tm-30) REVERT: B 260 TYR cc_start: 0.8412 (t80) cc_final: 0.8104 (t80) REVERT: B 389 PHE cc_start: 0.8394 (m-80) cc_final: 0.8127 (m-10) REVERT: B 416 GLN cc_start: 0.7927 (mp10) cc_final: 0.7538 (pm20) REVERT: B 554 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.7947 (t80) REVERT: B 583 ASN cc_start: 0.7946 (OUTLIER) cc_final: 0.7597 (m-40) REVERT: B 599 MET cc_start: 0.8878 (mtp) cc_final: 0.8613 (mtm) REVERT: B 694 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7439 (mt-10) REVERT: B 708 ASP cc_start: 0.7781 (t70) cc_final: 0.7363 (t0) REVERT: N 47 MET cc_start: 0.7452 (mmm) cc_final: 0.7227 (tpt) REVERT: N 70 GLU cc_start: 0.6650 (OUTLIER) cc_final: 0.5912 (tp30) REVERT: N 82 ASP cc_start: 0.8092 (OUTLIER) cc_final: 0.7857 (m-30) REVERT: J 81 MET cc_start: 0.6839 (OUTLIER) cc_final: 0.6504 (tmm) REVERT: J 93 MET cc_start: 0.7552 (ttp) cc_final: 0.7295 (ttt) REVERT: C 225 LYS cc_start: 0.8334 (ttmt) cc_final: 0.7941 (tppt) REVERT: C 291 ASP cc_start: 0.8083 (p0) cc_final: 0.7380 (p0) REVERT: C 416 GLN cc_start: 0.7822 (mp10) cc_final: 0.7396 (pm20) REVERT: C 513 GLU cc_start: 0.6909 (mp0) cc_final: 0.6600 (mp0) REVERT: C 516 MET cc_start: 0.8222 (mtp) cc_final: 0.7759 (mtp) REVERT: C 554 PHE cc_start: 0.8378 (OUTLIER) cc_final: 0.8096 (t80) REVERT: C 678 MET cc_start: 0.8178 (mtm) cc_final: 0.7920 (ttm) REVERT: C 708 ASP cc_start: 0.7985 (t70) cc_final: 0.7484 (t0) outliers start: 90 outliers final: 58 residues processed: 304 average time/residue: 1.1542 time to fit residues: 400.4745 Evaluate side-chains 297 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 226 time to evaluate : 2.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 417 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 568 GLN Chi-restraints excluded: chain A residue 573 ARG Chi-restraints excluded: chain A residue 583 ASN Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 70 GLU Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 583 ASN Chi-restraints excluded: chain B residue 618 SER Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 694 GLU Chi-restraints excluded: chain B residue 734 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain N residue 82 ASP Chi-restraints excluded: chain N residue 92 LYS Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 81 MET Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 417 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 568 GLN Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 734 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 0.0970 chunk 26 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 169 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 231 optimal weight: 2.9990 chunk 144 optimal weight: 0.6980 chunk 141 optimal weight: 0.9980 chunk 106 optimal weight: 0.5980 overall best weight: 1.0780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 GLN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 GLN B 568 GLN B 583 ASN N 89 GLN C 236 GLN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 19980 Z= 0.271 Angle : 0.560 14.840 27141 Z= 0.299 Chirality : 0.045 0.230 3015 Planarity : 0.004 0.058 3480 Dihedral : 4.892 34.095 2739 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.89 % Allowed : 15.05 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.36 (0.17), residues: 2430 helix: 1.22 (0.31), residues: 327 sheet: -1.23 (0.18), residues: 750 loop : -1.22 (0.16), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 539 HIS 0.005 0.001 HIS A 649 PHE 0.020 0.001 PHE B 165 TYR 0.015 0.001 TYR B 667 ARG 0.003 0.000 ARG A 569 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 228 time to evaluate : 2.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 70 GLU cc_start: 0.6396 (OUTLIER) cc_final: 0.5807 (tp30) REVERT: H 60 TYR cc_start: 0.7420 (m-80) cc_final: 0.7202 (m-80) REVERT: H 93 MET cc_start: 0.7875 (ttm) cc_final: 0.7595 (ttt) REVERT: A 139 CYS cc_start: 0.4086 (OUTLIER) cc_final: 0.3648 (t) REVERT: A 416 GLN cc_start: 0.8032 (mp10) cc_final: 0.7462 (pm20) REVERT: A 504 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7567 (ptt90) REVERT: A 516 MET cc_start: 0.8228 (mtp) cc_final: 0.7990 (mtm) REVERT: A 554 PHE cc_start: 0.8402 (OUTLIER) cc_final: 0.8027 (t80) REVERT: A 568 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.6950 (tm-30) REVERT: A 573 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.7412 (ttp-170) REVERT: A 583 ASN cc_start: 0.8062 (OUTLIER) cc_final: 0.7691 (m110) REVERT: A 708 ASP cc_start: 0.7843 (t70) cc_final: 0.7347 (t0) REVERT: M 21 ILE cc_start: 0.7880 (mt) cc_final: 0.7576 (mt) REVERT: M 70 GLU cc_start: 0.6670 (OUTLIER) cc_final: 0.6400 (tm-30) REVERT: B 260 TYR cc_start: 0.8424 (t80) cc_final: 0.8175 (t80) REVERT: B 389 PHE cc_start: 0.8402 (m-80) cc_final: 0.8125 (m-10) REVERT: B 416 GLN cc_start: 0.7930 (mp10) cc_final: 0.7577 (pm20) REVERT: B 554 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.7941 (t80) REVERT: B 583 ASN cc_start: 0.7832 (OUTLIER) cc_final: 0.7612 (m-40) REVERT: B 599 MET cc_start: 0.8848 (mtp) cc_final: 0.8576 (mtm) REVERT: B 708 ASP cc_start: 0.7788 (t70) cc_final: 0.7372 (t0) REVERT: N 21 ILE cc_start: 0.7905 (mt) cc_final: 0.7673 (mt) REVERT: N 47 MET cc_start: 0.7491 (mmm) cc_final: 0.7264 (tpt) REVERT: N 70 GLU cc_start: 0.6605 (OUTLIER) cc_final: 0.5900 (tp30) REVERT: J 81 MET cc_start: 0.6860 (OUTLIER) cc_final: 0.6533 (tmm) REVERT: J 93 MET cc_start: 0.7519 (ttp) cc_final: 0.7307 (ttt) REVERT: C 225 LYS cc_start: 0.8321 (ttmt) cc_final: 0.7934 (tppt) REVERT: C 291 ASP cc_start: 0.8075 (p0) cc_final: 0.7705 (p0) REVERT: C 339 ARG cc_start: 0.7498 (mtp85) cc_final: 0.7145 (mtt-85) REVERT: C 416 GLN cc_start: 0.7809 (mp10) cc_final: 0.7389 (pm20) REVERT: C 513 GLU cc_start: 0.6752 (mp0) cc_final: 0.6338 (mp0) REVERT: C 516 MET cc_start: 0.8216 (mtp) cc_final: 0.7998 (mtm) REVERT: C 517 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8293 (tp) REVERT: C 554 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.7992 (t80) REVERT: C 678 MET cc_start: 0.8172 (mtm) cc_final: 0.7930 (ttm) REVERT: C 708 ASP cc_start: 0.7980 (t70) cc_final: 0.7479 (t0) outliers start: 84 outliers final: 49 residues processed: 288 average time/residue: 1.1696 time to fit residues: 384.5223 Evaluate side-chains 287 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 224 time to evaluate : 2.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 417 CYS Chi-restraints excluded: chain A residue 504 ARG Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 568 GLN Chi-restraints excluded: chain A residue 573 ARG Chi-restraints excluded: chain A residue 583 ASN Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 70 GLU Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 583 ASN Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 734 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain N residue 92 LYS Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 81 MET Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 417 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 568 GLN Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 734 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 GLN N 89 GLN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 19980 Z= 0.453 Angle : 0.667 16.319 27141 Z= 0.349 Chirality : 0.049 0.243 3015 Planarity : 0.005 0.059 3480 Dihedral : 5.310 38.915 2739 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 4.03 % Allowed : 14.91 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 (0.17), residues: 2430 helix: 1.38 (0.32), residues: 309 sheet: -1.24 (0.19), residues: 735 loop : -1.29 (0.16), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 539 HIS 0.007 0.002 HIS A 649 PHE 0.027 0.002 PHE C 165 TYR 0.020 0.002 TYR I 60 ARG 0.004 0.001 ARG B 221 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 234 time to evaluate : 2.432 Fit side-chains revert: symmetry clash REVERT: L 70 GLU cc_start: 0.6457 (OUTLIER) cc_final: 0.5798 (tp30) REVERT: H 60 TYR cc_start: 0.7481 (m-80) cc_final: 0.7264 (m-80) REVERT: A 215 SER cc_start: 0.8778 (t) cc_final: 0.8553 (t) REVERT: A 322 MET cc_start: 0.8362 (mmm) cc_final: 0.7924 (mmm) REVERT: A 416 GLN cc_start: 0.8077 (mp10) cc_final: 0.7475 (pm20) REVERT: A 504 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7570 (ptt90) REVERT: A 516 MET cc_start: 0.8283 (mtp) cc_final: 0.8057 (mtm) REVERT: A 554 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.8039 (t80) REVERT: A 573 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7419 (ttm170) REVERT: A 708 ASP cc_start: 0.7850 (t70) cc_final: 0.7352 (t0) REVERT: M 70 GLU cc_start: 0.6770 (OUTLIER) cc_final: 0.6415 (tm-30) REVERT: B 260 TYR cc_start: 0.8503 (t80) cc_final: 0.8168 (t80) REVERT: B 389 PHE cc_start: 0.8437 (m-80) cc_final: 0.8183 (m-10) REVERT: B 416 GLN cc_start: 0.8033 (mp10) cc_final: 0.7628 (pm20) REVERT: B 554 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.7948 (t80) REVERT: B 599 MET cc_start: 0.8891 (mtp) cc_final: 0.8551 (mtm) REVERT: B 666 ARG cc_start: 0.7566 (mtp-110) cc_final: 0.7337 (mtp-110) REVERT: B 694 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7489 (mt-10) REVERT: B 708 ASP cc_start: 0.7752 (t70) cc_final: 0.7353 (t0) REVERT: N 47 MET cc_start: 0.7522 (mmm) cc_final: 0.7251 (tpt) REVERT: N 70 GLU cc_start: 0.6665 (OUTLIER) cc_final: 0.6248 (tm-30) REVERT: J 81 MET cc_start: 0.6905 (OUTLIER) cc_final: 0.6548 (tmm) REVERT: C 225 LYS cc_start: 0.8350 (ttmt) cc_final: 0.7936 (tppt) REVERT: C 291 ASP cc_start: 0.8164 (p0) cc_final: 0.7723 (p0) REVERT: C 389 PHE cc_start: 0.8484 (m-80) cc_final: 0.8261 (m-10) REVERT: C 416 GLN cc_start: 0.7770 (mp10) cc_final: 0.7387 (pm20) REVERT: C 516 MET cc_start: 0.8273 (mtp) cc_final: 0.8059 (mtm) REVERT: C 554 PHE cc_start: 0.8415 (OUTLIER) cc_final: 0.8109 (t80) REVERT: C 678 MET cc_start: 0.8232 (mtm) cc_final: 0.7978 (ttm) REVERT: C 708 ASP cc_start: 0.7986 (t70) cc_final: 0.7493 (t0) outliers start: 87 outliers final: 55 residues processed: 301 average time/residue: 1.1711 time to fit residues: 402.4051 Evaluate side-chains 292 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 227 time to evaluate : 2.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 417 CYS Chi-restraints excluded: chain A residue 504 ARG Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 573 ARG Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 70 GLU Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 694 GLU Chi-restraints excluded: chain B residue 734 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 81 MET Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 417 CYS Chi-restraints excluded: chain C residue 504 ARG Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 568 GLN Chi-restraints excluded: chain C residue 618 SER Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 734 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 0.6980 chunk 221 optimal weight: 0.5980 chunk 202 optimal weight: 0.7980 chunk 215 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 93 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 194 optimal weight: 7.9990 chunk 203 optimal weight: 0.9980 chunk 214 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN M 38 GLN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 GLN I 39 GLN B 568 GLN N 89 GLN C 236 GLN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 19980 Z= 0.220 Angle : 0.559 14.424 27141 Z= 0.295 Chirality : 0.045 0.245 3015 Planarity : 0.004 0.057 3480 Dihedral : 4.878 32.505 2739 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.66 % Allowed : 15.74 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.26 (0.17), residues: 2430 helix: 1.29 (0.31), residues: 327 sheet: -1.14 (0.19), residues: 759 loop : -1.15 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 36 HIS 0.005 0.001 HIS A 649 PHE 0.018 0.001 PHE B 293 TYR 0.017 0.001 TYR B 667 ARG 0.002 0.000 ARG A 569 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 229 time to evaluate : 2.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 21 ILE cc_start: 0.7597 (mt) cc_final: 0.7294 (mt) REVERT: L 70 GLU cc_start: 0.6347 (OUTLIER) cc_final: 0.5753 (tp30) REVERT: H 60 TYR cc_start: 0.7409 (m-80) cc_final: 0.7192 (m-80) REVERT: H 93 MET cc_start: 0.7885 (ttm) cc_final: 0.7618 (ttt) REVERT: A 416 GLN cc_start: 0.8072 (mp10) cc_final: 0.7458 (pm20) REVERT: A 504 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7563 (ptt90) REVERT: A 516 MET cc_start: 0.8165 (mtp) cc_final: 0.7943 (mtm) REVERT: A 554 PHE cc_start: 0.8364 (OUTLIER) cc_final: 0.7985 (t80) REVERT: A 568 GLN cc_start: 0.7574 (OUTLIER) cc_final: 0.7103 (tm-30) REVERT: A 573 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.7368 (ttm170) REVERT: A 696 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7375 (ptm) REVERT: A 708 ASP cc_start: 0.7825 (t70) cc_final: 0.7335 (t0) REVERT: M 21 ILE cc_start: 0.7742 (mt) cc_final: 0.7439 (mt) REVERT: M 70 GLU cc_start: 0.6629 (OUTLIER) cc_final: 0.5828 (tp30) REVERT: B 291 ASP cc_start: 0.8180 (p0) cc_final: 0.7815 (p0) REVERT: B 416 GLN cc_start: 0.7870 (mp10) cc_final: 0.7659 (pm20) REVERT: B 513 GLU cc_start: 0.6617 (mp0) cc_final: 0.6283 (mp0) REVERT: B 554 PHE cc_start: 0.8312 (OUTLIER) cc_final: 0.7919 (t80) REVERT: B 582 SER cc_start: 0.8748 (t) cc_final: 0.8535 (p) REVERT: B 599 MET cc_start: 0.8806 (mtp) cc_final: 0.8546 (mtm) REVERT: B 666 ARG cc_start: 0.7551 (mtp-110) cc_final: 0.7320 (mtp-110) REVERT: B 694 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7406 (mt-10) REVERT: B 708 ASP cc_start: 0.7732 (t70) cc_final: 0.7325 (t0) REVERT: N 21 ILE cc_start: 0.7828 (mt) cc_final: 0.7581 (mt) REVERT: N 47 MET cc_start: 0.7505 (mmm) cc_final: 0.7270 (tpt) REVERT: N 70 GLU cc_start: 0.6562 (OUTLIER) cc_final: 0.5858 (tp30) REVERT: J 81 MET cc_start: 0.6626 (OUTLIER) cc_final: 0.6371 (tmm) REVERT: C 225 LYS cc_start: 0.8318 (ttmt) cc_final: 0.7928 (tppt) REVERT: C 291 ASP cc_start: 0.8023 (p0) cc_final: 0.7650 (p0) REVERT: C 339 ARG cc_start: 0.7527 (mtp85) cc_final: 0.7221 (mtt-85) REVERT: C 416 GLN cc_start: 0.7828 (mp10) cc_final: 0.7423 (pm20) REVERT: C 516 MET cc_start: 0.8214 (mtp) cc_final: 0.7750 (mtp) REVERT: C 554 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.7946 (t80) REVERT: C 670 GLU cc_start: 0.7128 (pt0) cc_final: 0.6898 (pt0) REVERT: C 678 MET cc_start: 0.8171 (mtm) cc_final: 0.7946 (ttm) REVERT: C 708 ASP cc_start: 0.7977 (t70) cc_final: 0.7479 (t0) outliers start: 79 outliers final: 49 residues processed: 292 average time/residue: 1.1904 time to fit residues: 395.3639 Evaluate side-chains 284 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 223 time to evaluate : 2.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 417 CYS Chi-restraints excluded: chain A residue 504 ARG Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 568 GLN Chi-restraints excluded: chain A residue 573 ARG Chi-restraints excluded: chain A residue 583 ASN Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 70 GLU Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 568 GLN Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 694 GLU Chi-restraints excluded: chain B residue 734 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 81 MET Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 417 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 568 GLN Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 734 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 158 optimal weight: 0.7980 chunk 239 optimal weight: 0.6980 chunk 220 optimal weight: 0.5980 chunk 190 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 GLN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 GLN B 568 GLN N 89 GLN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19980 Z= 0.215 Angle : 0.558 14.527 27141 Z= 0.292 Chirality : 0.045 0.244 3015 Planarity : 0.004 0.057 3480 Dihedral : 4.805 32.815 2739 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.96 % Allowed : 16.48 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.14 (0.17), residues: 2430 helix: 1.38 (0.32), residues: 327 sheet: -1.11 (0.18), residues: 774 loop : -1.04 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 539 HIS 0.005 0.001 HIS B 724 PHE 0.017 0.001 PHE A 165 TYR 0.019 0.001 TYR J 95 ARG 0.002 0.000 ARG A 569 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 234 time to evaluate : 2.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 21 ILE cc_start: 0.7665 (mt) cc_final: 0.7375 (mt) REVERT: L 70 GLU cc_start: 0.6316 (OUTLIER) cc_final: 0.5751 (tp30) REVERT: H 60 TYR cc_start: 0.7457 (m-80) cc_final: 0.7232 (m-80) REVERT: H 93 MET cc_start: 0.7899 (ttm) cc_final: 0.7627 (ttt) REVERT: A 416 GLN cc_start: 0.8076 (mp10) cc_final: 0.7460 (pm20) REVERT: A 516 MET cc_start: 0.8215 (mtp) cc_final: 0.7987 (mtm) REVERT: A 554 PHE cc_start: 0.8348 (OUTLIER) cc_final: 0.7961 (t80) REVERT: A 708 ASP cc_start: 0.7803 (t70) cc_final: 0.7319 (t0) REVERT: M 70 GLU cc_start: 0.6678 (OUTLIER) cc_final: 0.5933 (tp30) REVERT: B 416 GLN cc_start: 0.7846 (mp10) cc_final: 0.7508 (pm20) REVERT: B 554 PHE cc_start: 0.8320 (OUTLIER) cc_final: 0.7938 (t80) REVERT: B 599 MET cc_start: 0.8801 (mtp) cc_final: 0.8540 (mtm) REVERT: B 666 ARG cc_start: 0.7538 (mtp-110) cc_final: 0.7309 (mtp-110) REVERT: B 694 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7384 (mt-10) REVERT: B 708 ASP cc_start: 0.7700 (t70) cc_final: 0.7303 (t0) REVERT: N 21 ILE cc_start: 0.7893 (mt) cc_final: 0.7634 (mt) REVERT: N 47 MET cc_start: 0.7503 (mmm) cc_final: 0.7263 (tpt) REVERT: N 70 GLU cc_start: 0.6577 (OUTLIER) cc_final: 0.5942 (tp30) REVERT: J 81 MET cc_start: 0.6706 (OUTLIER) cc_final: 0.6439 (tmm) REVERT: C 204 THR cc_start: 0.8917 (p) cc_final: 0.8430 (p) REVERT: C 225 LYS cc_start: 0.8311 (ttmt) cc_final: 0.7926 (tppt) REVERT: C 291 ASP cc_start: 0.8049 (p0) cc_final: 0.7534 (p0) REVERT: C 339 ARG cc_start: 0.7594 (mtp85) cc_final: 0.7295 (mtt-85) REVERT: C 416 GLN cc_start: 0.7796 (mp10) cc_final: 0.7409 (pm20) REVERT: C 513 GLU cc_start: 0.6870 (mp0) cc_final: 0.6592 (mp0) REVERT: C 516 MET cc_start: 0.8223 (mtp) cc_final: 0.7733 (mtp) REVERT: C 554 PHE cc_start: 0.8290 (OUTLIER) cc_final: 0.7960 (t80) REVERT: C 678 MET cc_start: 0.8172 (mtm) cc_final: 0.7935 (ttm) REVERT: C 708 ASP cc_start: 0.7944 (t70) cc_final: 0.7487 (t0) outliers start: 64 outliers final: 41 residues processed: 284 average time/residue: 1.2037 time to fit residues: 389.2516 Evaluate side-chains 275 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 226 time to evaluate : 2.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 417 CYS Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain M residue 70 GLU Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 670 GLU Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 694 GLU Chi-restraints excluded: chain B residue 734 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 81 MET Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 417 CYS Chi-restraints excluded: chain C residue 504 ARG Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 568 GLN Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain C residue 734 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 4.9990 chunk 202 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 175 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 190 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 195 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 35 optimal weight: 0.0470 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 GLN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 GLN I 39 GLN B 568 GLN N 89 GLN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.183960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.146615 restraints weight = 20787.621| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 1.90 r_work: 0.3524 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19980 Z= 0.212 Angle : 0.560 18.069 27141 Z= 0.291 Chirality : 0.045 0.244 3015 Planarity : 0.004 0.057 3480 Dihedral : 4.785 32.659 2739 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.01 % Allowed : 16.62 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.08 (0.17), residues: 2430 helix: 1.42 (0.32), residues: 327 sheet: -1.06 (0.19), residues: 774 loop : -1.00 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 36 HIS 0.005 0.001 HIS B 724 PHE 0.017 0.001 PHE A 165 TYR 0.021 0.001 TYR I 95 ARG 0.002 0.000 ARG A 569 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7114.87 seconds wall clock time: 127 minutes 58.04 seconds (7678.04 seconds total)