Starting phenix.real_space_refine (version: 1.21rc1) on Sat Jul 15 19:03:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vn1_21247/07_2023/6vn1_21247.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vn1_21247/07_2023/6vn1_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_21247/07_2023/6vn1_21247.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vn1_21247/07_2023/6vn1_21247.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vn1_21247/07_2023/6vn1_21247.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vn1_21247/07_2023/6vn1_21247.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-5013/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: 9.68, per 1000 atoms: 0.50 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: 6.69 Conformation dependent library (CDL) restraints added in 2.6 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: 1.43 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: 7.49 Time building geometry restraints manager: 7.24 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: 3.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.010 Extract box with map and model: 14.120 Check model and map are aligned: 0.290 Set scattering table: 0.160 Process input model: 47.540 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.420 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 2.477 Fit side-chains outliers start: 0 outliers final: 1 residues processed: 307 average time/residue: 1.3502 time to fit residues: 467.0524 Evaluate side-chains 226 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 225 time to evaluate : 2.192 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 1.2738 time to fit residues: 4.4506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 0.9990 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: 1.9990 chunk 114 optimal weight: 4.9990 chunk 140 optimal weight: 0.5980 chunk 217 optimal weight: 4.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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 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 597 ASN C 628 GLN C 648 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1230 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= 0.171 Angle : 0.524 6.918 27141 Z= 0.285 Chirality : 0.044 0.195 3015 Planarity : 0.004 0.061 3480 Dihedral : 4.667 32.898 2739 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer Outliers : 2.18 % 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: 1.17 (0.31), residues: 309 sheet: -2.11 (0.18), residues: 717 loop : -1.90 (0.15), residues: 1404 *********************** 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 301 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 254 time to evaluate : 2.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 14 residues processed: 283 average time/residue: 1.2959 time to fit residues: 414.4690 Evaluate side-chains 238 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 224 time to evaluate : 2.162 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 9 residues processed: 5 average time/residue: 0.8672 time to fit residues: 8.0725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 181 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 218 optimal weight: 2.9990 chunk 235 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 216 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 388 ASN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 GLN B 543 GLN B 568 GLN B 648 ASN N 89 GLN ** J 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 GLN C 388 ASN C 543 GLN C 648 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.073 19980 Z= 0.489 Angle : 0.670 11.059 27141 Z= 0.356 Chirality : 0.049 0.231 3015 Planarity : 0.005 0.063 3480 Dihedral : 5.291 38.849 2739 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer Outliers : 3.10 % 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: -2.14 (0.16), residues: 2430 helix: 1.11 (0.31), residues: 309 sheet: -1.76 (0.18), residues: 711 loop : -1.86 (0.15), residues: 1410 *********************** 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 303 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 236 time to evaluate : 2.203 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 38 residues processed: 281 average time/residue: 1.2439 time to fit residues: 397.8554 Evaluate side-chains 260 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 222 time to evaluate : 2.147 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 31 residues processed: 7 average time/residue: 0.5191 time to fit residues: 7.7675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 1.9990 chunk 164 optimal weight: 6.9990 chunk 113 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 219 optimal weight: 0.5980 chunk 231 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 207 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN A 411 GLN ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 GLN M 38 GLN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 GLN I 39 GLN B 411 GLN B 568 GLN B 648 ASN N 37 GLN N 89 GLN C 236 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 19980 Z= 0.224 Angle : 0.533 9.177 27141 Z= 0.289 Chirality : 0.044 0.214 3015 Planarity : 0.004 0.060 3480 Dihedral : 4.838 33.589 2739 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer Outliers : 3.56 % 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: -1.68 (0.17), residues: 2430 helix: 1.54 (0.31), residues: 309 sheet: -1.52 (0.19), residues: 726 loop : -1.51 (0.15), residues: 1395 *********************** 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 302 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 225 time to evaluate : 2.303 Fit side-chains revert: symmetry clash outliers start: 77 outliers final: 39 residues processed: 280 average time/residue: 1.2112 time to fit residues: 386.6097 Evaluate side-chains 256 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 217 time to evaluate : 2.066 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 34 residues processed: 5 average time/residue: 0.9223 time to fit residues: 8.3272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 0.2980 chunk 131 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 172 optimal weight: 0.9990 chunk 95 optimal weight: 0.0020 chunk 197 optimal weight: 3.9990 chunk 160 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 0.7980 chunk 208 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN A 388 ASN ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 GLN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 GLN N 89 GLN C 388 ASN C 411 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 19980 Z= 0.190 Angle : 0.516 11.632 27141 Z= 0.279 Chirality : 0.044 0.214 3015 Planarity : 0.004 0.060 3480 Dihedral : 4.636 32.523 2739 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer Outliers : 3.38 % 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: -1.48 (0.17), residues: 2430 helix: 1.34 (0.31), residues: 327 sheet: -1.34 (0.19), residues: 738 loop : -1.34 (0.16), residues: 1365 *********************** 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 312 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 239 time to evaluate : 2.148 Fit side-chains outliers start: 73 outliers final: 39 residues processed: 295 average time/residue: 1.1824 time to fit residues: 400.5152 Evaluate side-chains 270 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 231 time to evaluate : 2.180 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 32 residues processed: 7 average time/residue: 0.3720 time to fit residues: 6.8097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 1.9990 chunk 208 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 136 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 232 optimal weight: 0.8980 chunk 192 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 19 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 GLN N 89 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 19980 Z= 0.275 Angle : 0.566 12.027 27141 Z= 0.301 Chirality : 0.046 0.244 3015 Planarity : 0.004 0.058 3480 Dihedral : 4.821 34.892 2739 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer Outliers : 3.10 % 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: -1.29 (0.17), residues: 2430 helix: 1.63 (0.32), residues: 309 sheet: -1.21 (0.19), residues: 720 loop : -1.22 (0.16), residues: 1401 *********************** 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 304 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 237 time to evaluate : 2.430 Fit side-chains outliers start: 67 outliers final: 45 residues processed: 287 average time/residue: 1.1971 time to fit residues: 394.5006 Evaluate side-chains 269 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 224 time to evaluate : 2.229 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 39 residues processed: 6 average time/residue: 0.8271 time to fit residues: 8.9032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 0.0870 chunk 26 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 169 optimal weight: 0.7980 chunk 131 optimal weight: 0.3980 chunk 195 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 231 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 chunk 106 optimal weight: 0.5980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN L 90 GLN H 39 GLN A 388 ASN ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 583 ASN 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** N 89 GLN C 388 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 19980 Z= 0.174 Angle : 0.513 9.102 27141 Z= 0.277 Chirality : 0.044 0.220 3015 Planarity : 0.004 0.058 3480 Dihedral : 4.541 31.633 2739 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer Outliers : 2.73 % 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: -1.19 (0.17), residues: 2430 helix: 1.39 (0.31), residues: 327 sheet: -1.16 (0.19), residues: 750 loop : -1.08 (0.17), residues: 1353 *********************** 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 293 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 234 time to evaluate : 2.216 Fit side-chains outliers start: 59 outliers final: 45 residues processed: 282 average time/residue: 1.1585 time to fit residues: 374.3147 Evaluate side-chains 273 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 228 time to evaluate : 2.146 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 40 residues processed: 6 average time/residue: 1.1361 time to fit residues: 10.6696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 0.5980 chunk 92 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 44 optimal weight: 0.1980 chunk 147 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 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 38 GLN H 39 GLN A 583 ASN M 38 GLN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 GLN N 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.093 19980 Z= 0.407 Angle : 0.633 12.678 27141 Z= 0.335 Chirality : 0.048 0.236 3015 Planarity : 0.005 0.059 3480 Dihedral : 5.061 37.711 2739 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer Outliers : 2.92 % 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: -1.27 (0.17), residues: 2430 helix: 1.45 (0.31), residues: 309 sheet: -1.20 (0.19), residues: 747 loop : -1.15 (0.16), residues: 1374 *********************** 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 288 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 225 time to evaluate : 2.236 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 42 residues processed: 277 average time/residue: 1.2197 time to fit residues: 388.2428 Evaluate side-chains 263 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 221 time to evaluate : 2.267 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 40 residues processed: 2 average time/residue: 0.3004 time to fit residues: 4.0878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 0.9980 chunk 221 optimal weight: 0.9980 chunk 202 optimal weight: 0.7980 chunk 215 optimal weight: 0.9980 chunk 129 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 chunk 169 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 194 optimal weight: 6.9990 chunk 203 optimal weight: 0.8980 chunk 214 optimal weight: 2.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN ** A 543 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 N 89 GLN C 236 GLN C 388 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 19980 Z= 0.246 Angle : 0.558 14.388 27141 Z= 0.299 Chirality : 0.045 0.255 3015 Planarity : 0.004 0.058 3480 Dihedral : 4.856 33.634 2739 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer Outliers : 2.87 % 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: -1.23 (0.17), residues: 2430 helix: 1.19 (0.31), residues: 327 sheet: -1.11 (0.19), residues: 753 loop : -1.11 (0.17), residues: 1350 *********************** 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 291 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 229 time to evaluate : 2.217 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 44 residues processed: 281 average time/residue: 1.1965 time to fit residues: 385.4339 Evaluate side-chains 268 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 224 time to evaluate : 2.211 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 40 residues processed: 4 average time/residue: 0.5755 time to fit residues: 6.0011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 139 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 158 optimal weight: 1.9990 chunk 239 optimal weight: 2.9990 chunk 220 optimal weight: 0.5980 chunk 190 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 M 38 GLN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 GLN N 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 19980 Z= 0.274 Angle : 0.586 15.411 27141 Z= 0.309 Chirality : 0.046 0.264 3015 Planarity : 0.004 0.057 3480 Dihedral : 4.909 34.387 2739 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer Outliers : 2.55 % 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: -1.21 (0.17), residues: 2430 helix: 1.19 (0.31), residues: 327 sheet: -1.13 (0.18), residues: 783 loop : -1.06 (0.17), residues: 1320 ********************** 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 287 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 232 time to evaluate : 2.357 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 46 residues processed: 279 average time/residue: 1.2538 time to fit residues: 404.7130 Evaluate side-chains 273 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 227 time to evaluate : 2.199 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 41 residues processed: 5 average time/residue: 0.6887 time to fit residues: 7.3014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 3.9990 chunk 202 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 175 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 190 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 195 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 568 GLN M 38 GLN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 GLN I 39 GLN C 388 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.183084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.145458 restraints weight = 20832.514| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 1.85 r_work: 0.3505 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 19980 Z= 0.225 Angle : 0.565 15.141 27141 Z= 0.296 Chirality : 0.045 0.251 3015 Planarity : 0.004 0.057 3480 Dihedral : 4.796 32.942 2739 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer Outliers : 2.55 % 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: -1.11 (0.17), residues: 2430 helix: 1.30 (0.31), residues: 327 sheet: -1.09 (0.19), residues: 744 loop : -1.00 (0.17), residues: 1359 =============================================================================== Job complete usr+sys time: 6880.37 seconds wall clock time: 123 minutes 50.75 seconds (7430.75 seconds total)