Starting phenix.real_space_refine (version: dev) on Mon May 16 04:33:30 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c0m_30267/05_2022/7c0m_30267.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c0m_30267/05_2022/7c0m_30267.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c0m_30267/05_2022/7c0m_30267.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c0m_30267/05_2022/7c0m_30267.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c0m_30267/05_2022/7c0m_30267.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c0m_30267/05_2022/7c0m_30267.pdb" } resolution = 3.9 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= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "K PHE 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 29816 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 796 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 618 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 810 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 3013 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 366, 3004 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 12, 'TRANS': 353} Conformer: "B" Number of residues, atoms: 364, 2988 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 12, 'TRANS': 351} Chain breaks: 2 bond proxies already assigned to first conformer: 3037 Chain: "a" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "b" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "c" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 796 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "d" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "e" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "f" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 618 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "g" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 810 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "h" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "i" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "j" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "k" Number of atoms: 3013 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 366, 3004 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 12, 'TRANS': 353} Conformer: "B" Number of residues, atoms: 364, 2988 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 12, 'TRANS': 351} Chain breaks: 2 bond proxies already assigned to first conformer: 3037 Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13813 SG CYS K 396 74.336 42.987 112.768 1.00224.74 S ATOM 13819 SG CYS K 397 71.623 44.934 115.606 1.00228.17 S ATOM 13887 SG CYS K 404 74.626 45.271 115.000 1.00229.83 S ATOM 28720 SG CYS k 396 140.692 95.752 81.168 1.00224.74 S ATOM 28726 SG CYS k 397 141.323 94.576 76.994 1.00228.17 S ATOM 28794 SG CYS k 404 140.924 92.968 79.593 1.00229.83 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ALEU K 387 " occ=0.50 ... (6 atoms not shown) pdb=" CD2ALEU K 387 " occ=0.50 residue: pdb=" N AGLU K 401 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU K 401 " occ=0.50 residue: pdb=" N ALEU k 387 " occ=0.50 ... (6 atoms not shown) pdb=" CD2ALEU k 387 " occ=0.50 residue: pdb=" N AGLU k 401 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU k 401 " occ=0.50 Time building chain proxies: 19.82, per 1000 atoms: 0.66 Number of scatterers: 29816 At special positions: 0 Unit cell: (163.8, 172.2, 150.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 58 16.00 P 576 15.00 O 6678 8.00 N 5506 7.00 C 16996 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.35 Conformation dependent library (CDL) restraints added in 3.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN K 601 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 397 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 396 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 404 " pdb="ZN ZN K 601 " - pdb=" NE2 HIS K 390 " pdb=" ZN k 601 " pdb="ZN ZN k 601 " - pdb=" SG CYS k 397 " pdb="ZN ZN k 601 " - pdb=" SG CYS k 396 " pdb="ZN ZN k 601 " - pdb=" SG CYS k 404 " pdb="ZN ZN k 601 " - pdb=" NE2 HIS k 390 " Number of angles added : 6 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4208 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 28 sheets defined 64.0% alpha, 7.7% beta 282 base pairs and 500 stacking pairs defined. Time for finding SS restraints: 12.88 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.218A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.806A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.647A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 18 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.592A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 95 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 124 Processing helix chain 'E' and resid 44 through 56 removed outlier: 4.026A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.805A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.409A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 39 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.617A pdb=" N ASN H 67 " --> pdb=" O ASN H 63 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.774A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 123 Processing helix chain 'K' and resid 161 through 175 removed outlier: 4.239A pdb=" N LEU K 165 " --> pdb=" O GLY K 161 " (cutoff:3.500A) Processing helix chain 'K' and resid 179 through 198 Processing helix chain 'K' and resid 199 through 204 removed outlier: 6.165A pdb=" N ALA K 202 " --> pdb=" O CYS K 199 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG K 204 " --> pdb=" O SER K 201 " (cutoff:3.500A) Processing helix chain 'K' and resid 262 through 264 No H-bonds generated for 'chain 'K' and resid 262 through 264' Processing helix chain 'K' and resid 272 through 289 Processing helix chain 'K' and resid 345 through 354 Processing helix chain 'K' and resid 379 through 389 Processing helix chain 'K' and resid 405 through 424 Processing helix chain 'K' and resid 425 through 428 removed outlier: 3.749A pdb=" N LYS K 428 " --> pdb=" O LYS K 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 425 through 428' Processing helix chain 'K' and resid 434 through 449 removed outlier: 3.957A pdb=" N VAL K 438 " --> pdb=" O SER K 434 " (cutoff:3.500A) Processing helix chain 'K' and resid 451 through 458 removed outlier: 3.695A pdb=" N ASP K 456 " --> pdb=" O SER K 453 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ARG K 457 " --> pdb=" O GLN K 454 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N LYS K 458 " --> pdb=" O TRP K 455 " (cutoff:3.500A) Processing helix chain 'K' and resid 459 through 478 removed outlier: 3.748A pdb=" N ASP K 465 " --> pdb=" O GLY K 461 " (cutoff:3.500A) Processing helix chain 'K' and resid 497 through 514 Processing helix chain 'K' and resid 517 through 522 removed outlier: 4.274A pdb=" N PHE K 522 " --> pdb=" O VAL K 518 " (cutoff:3.500A) Processing helix chain 'a' and resid 44 through 57 Processing helix chain 'a' and resid 63 through 77 removed outlier: 4.218A pdb=" N ASP a 77 " --> pdb=" O GLU a 73 " (cutoff:3.500A) Processing helix chain 'a' and resid 85 through 114 removed outlier: 3.807A pdb=" N ASP a 106 " --> pdb=" O GLY a 102 " (cutoff:3.500A) Processing helix chain 'a' and resid 120 through 132 Processing helix chain 'b' and resid 25 through 29 Processing helix chain 'b' and resid 30 through 42 Processing helix chain 'b' and resid 49 through 76 removed outlier: 3.646A pdb=" N GLU b 53 " --> pdb=" O LEU b 49 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ASP b 68 " --> pdb=" O ASN b 64 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 94 Processing helix chain 'c' and resid 18 through 22 Processing helix chain 'c' and resid 26 through 36 Processing helix chain 'c' and resid 46 through 73 removed outlier: 3.592A pdb=" N TYR c 50 " --> pdb=" O GLY c 46 " (cutoff:3.500A) Processing helix chain 'c' and resid 79 through 90 Processing helix chain 'c' and resid 90 through 95 Processing helix chain 'd' and resid 37 through 49 Processing helix chain 'd' and resid 55 through 84 Processing helix chain 'd' and resid 90 through 102 Processing helix chain 'd' and resid 103 through 124 Processing helix chain 'e' and resid 44 through 56 removed outlier: 4.027A pdb=" N LEU e 48 " --> pdb=" O GLY e 44 " (cutoff:3.500A) Processing helix chain 'e' and resid 63 through 76 removed outlier: 3.806A pdb=" N PHE e 67 " --> pdb=" O ARG e 63 " (cutoff:3.500A) Processing helix chain 'e' and resid 85 through 114 Processing helix chain 'e' and resid 120 through 132 Processing helix chain 'f' and resid 25 through 29 Processing helix chain 'f' and resid 30 through 42 Processing helix chain 'f' and resid 49 through 76 Processing helix chain 'f' and resid 82 through 94 Processing helix chain 'g' and resid 16 through 21 Processing helix chain 'g' and resid 26 through 36 Processing helix chain 'g' and resid 45 through 73 removed outlier: 4.410A pdb=" N VAL g 49 " --> pdb=" O ALA g 45 " (cutoff:3.500A) Processing helix chain 'g' and resid 79 through 89 Processing helix chain 'g' and resid 90 through 97 Processing helix chain 'h' and resid 39 through 49 Processing helix chain 'h' and resid 55 through 84 removed outlier: 3.617A pdb=" N ASN h 67 " --> pdb=" O ASN h 63 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN h 84 " --> pdb=" O LEU h 80 " (cutoff:3.500A) Processing helix chain 'h' and resid 90 through 102 removed outlier: 3.774A pdb=" N ILE h 94 " --> pdb=" O THR h 90 " (cutoff:3.500A) Processing helix chain 'h' and resid 103 through 123 Processing helix chain 'k' and resid 161 through 175 removed outlier: 4.240A pdb=" N LEU k 165 " --> pdb=" O GLY k 161 " (cutoff:3.500A) Processing helix chain 'k' and resid 179 through 198 Processing helix chain 'k' and resid 199 through 204 removed outlier: 6.164A pdb=" N ALA k 202 " --> pdb=" O CYS k 199 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG k 204 " --> pdb=" O SER k 201 " (cutoff:3.500A) Processing helix chain 'k' and resid 262 through 264 No H-bonds generated for 'chain 'k' and resid 262 through 264' Processing helix chain 'k' and resid 272 through 289 Processing helix chain 'k' and resid 345 through 354 Processing helix chain 'k' and resid 379 through 389 Processing helix chain 'k' and resid 405 through 424 Processing helix chain 'k' and resid 425 through 428 removed outlier: 3.749A pdb=" N LYS k 428 " --> pdb=" O LYS k 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 425 through 428' Processing helix chain 'k' and resid 434 through 449 removed outlier: 3.957A pdb=" N VAL k 438 " --> pdb=" O SER k 434 " (cutoff:3.500A) Processing helix chain 'k' and resid 451 through 458 removed outlier: 3.695A pdb=" N ASP k 456 " --> pdb=" O SER k 453 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ARG k 457 " --> pdb=" O GLN k 454 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N LYS k 458 " --> pdb=" O TRP k 455 " (cutoff:3.500A) Processing helix chain 'k' and resid 459 through 478 removed outlier: 3.748A pdb=" N ASP k 465 " --> pdb=" O GLY k 461 " (cutoff:3.500A) Processing helix chain 'k' and resid 497 through 514 Processing helix chain 'k' and resid 517 through 522 removed outlier: 4.274A pdb=" N PHE k 522 " --> pdb=" O VAL k 518 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.989A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.601A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.790A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.484A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 206 through 208 removed outlier: 6.608A pdb=" N PHE K 226 " --> pdb=" O ASP K 319 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N THR K 321 " --> pdb=" O PHE K 226 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL K 228 " --> pdb=" O THR K 321 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ALA K 323 " --> pdb=" O VAL K 228 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N PHE K 230 " --> pdb=" O ALA K 323 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLU K 325 " --> pdb=" O PHE K 230 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU K 232 " --> pdb=" O GLU K 325 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N LEU K 322 " --> pdb=" O PRO K 361 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 206 through 208 removed outlier: 6.608A pdb=" N PHE K 226 " --> pdb=" O ASP K 319 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N THR K 321 " --> pdb=" O PHE K 226 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL K 228 " --> pdb=" O THR K 321 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ALA K 323 " --> pdb=" O VAL K 228 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N PHE K 230 " --> pdb=" O ALA K 323 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLU K 325 " --> pdb=" O PHE K 230 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU K 232 " --> pdb=" O GLU K 325 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 266 through 267 Processing sheet with id=AB5, first strand: chain 'K' and resid 364 through 365 removed outlier: 4.071A pdb=" N ALA K 364 " --> pdb=" O GLN K 371 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'a' and resid 83 through 84 removed outlier: 6.989A pdb=" N ARG a 83 " --> pdb=" O VAL b 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'a' and resid 118 through 119 Processing sheet with id=AB8, first strand: chain 'b' and resid 97 through 98 Processing sheet with id=AB9, first strand: chain 'c' and resid 42 through 43 removed outlier: 7.601A pdb=" N ARG c 42 " --> pdb=" O ILE d 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'c' and resid 77 through 78 Processing sheet with id=AC2, first strand: chain 'c' and resid 100 through 102 Processing sheet with id=AC3, first strand: chain 'e' and resid 83 through 84 removed outlier: 6.791A pdb=" N ARG e 83 " --> pdb=" O VAL f 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'e' and resid 118 through 119 Processing sheet with id=AC5, first strand: chain 'g' and resid 42 through 43 removed outlier: 7.484A pdb=" N ARG g 42 " --> pdb=" O ILE h 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'g' and resid 77 through 78 Processing sheet with id=AC7, first strand: chain 'k' and resid 206 through 208 removed outlier: 6.608A pdb=" N PHE k 226 " --> pdb=" O ASP k 319 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N THR k 321 " --> pdb=" O PHE k 226 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL k 228 " --> pdb=" O THR k 321 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ALA k 323 " --> pdb=" O VAL k 228 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N PHE k 230 " --> pdb=" O ALA k 323 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLU k 325 " --> pdb=" O PHE k 230 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU k 232 " --> pdb=" O GLU k 325 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N LEU k 322 " --> pdb=" O PRO k 361 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'k' and resid 206 through 208 removed outlier: 6.608A pdb=" N PHE k 226 " --> pdb=" O ASP k 319 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N THR k 321 " --> pdb=" O PHE k 226 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL k 228 " --> pdb=" O THR k 321 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ALA k 323 " --> pdb=" O VAL k 228 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N PHE k 230 " --> pdb=" O ALA k 323 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLU k 325 " --> pdb=" O PHE k 230 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU k 232 " --> pdb=" O GLU k 325 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'k' and resid 266 through 267 Processing sheet with id=AD1, first strand: chain 'k' and resid 364 through 365 removed outlier: 4.071A pdb=" N ALA k 364 " --> pdb=" O GLN k 371 " (cutoff:3.500A) 1090 hydrogen bonds defined for protein. 3186 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 724 hydrogen bonds 1448 hydrogen bond angles 0 basepair planarities 282 basepair parallelities 500 stacking parallelities Total time for adding SS restraints: 15.90 Time building geometry restraints manager: 16.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5715 1.33 - 1.45: 9947 1.45 - 1.57: 14640 1.57 - 1.69: 1152 1.69 - 1.81: 88 Bond restraints: 31542 Sorted by residual: bond pdb=" C HIS D 49 " pdb=" N PRO D 50 " ideal model delta sigma weight residual 1.336 1.301 0.035 1.08e-02 8.57e+03 1.04e+01 bond pdb=" C ARG h 86 " pdb=" N SER h 87 " ideal model delta sigma weight residual 1.332 1.287 0.045 1.40e-02 5.10e+03 1.03e+01 bond pdb=" C ARG H 86 " pdb=" N SER H 87 " ideal model delta sigma weight residual 1.332 1.288 0.044 1.40e-02 5.10e+03 1.01e+01 bond pdb=" C HIS d 49 " pdb=" N PRO d 50 " ideal model delta sigma weight residual 1.336 1.302 0.034 1.08e-02 8.57e+03 1.00e+01 bond pdb=" CB ASN d 63 " pdb=" CG ASN d 63 " ideal model delta sigma weight residual 1.516 1.461 0.055 2.50e-02 1.60e+03 4.82e+00 ... (remaining 31537 not shown) Histogram of bond angle deviations from ideal: 97.87 - 105.09: 2636 105.09 - 112.32: 17381 112.32 - 119.54: 10222 119.54 - 126.77: 13114 126.77 - 133.99: 1675 Bond angle restraints: 45028 Sorted by residual: angle pdb=" O3' DA j 5 " pdb=" C3' DA j 5 " pdb=" C2' DA j 5 " ideal model delta sigma weight residual 111.50 102.64 8.86 1.50e+00 4.44e-01 3.49e+01 angle pdb=" O3' DA J 5 " pdb=" C3' DA J 5 " pdb=" C2' DA J 5 " ideal model delta sigma weight residual 111.50 102.65 8.85 1.50e+00 4.44e-01 3.48e+01 angle pdb=" O3' DA I 48 " pdb=" C3' DA I 48 " pdb=" C2' DA I 48 " ideal model delta sigma weight residual 111.50 103.19 8.31 1.50e+00 4.44e-01 3.07e+01 angle pdb=" O3' DA i 48 " pdb=" C3' DA i 48 " pdb=" C2' DA i 48 " ideal model delta sigma weight residual 111.50 103.22 8.28 1.50e+00 4.44e-01 3.05e+01 angle pdb=" N GLU K 233 " pdb=" CA GLU K 233 " pdb=" C GLU K 233 " ideal model delta sigma weight residual 111.11 117.41 -6.30 1.20e+00 6.94e-01 2.76e+01 ... (remaining 45023 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.02: 13840 34.02 - 68.03: 3127 68.03 - 102.05: 83 102.05 - 136.07: 0 136.07 - 170.08: 4 Dihedral angle restraints: 17054 sinusoidal: 10544 harmonic: 6510 Sorted by residual: dihedral pdb=" CA PRO D 103 " pdb=" C PRO D 103 " pdb=" N GLY D 104 " pdb=" CA GLY D 104 " ideal model delta harmonic sigma weight residual -180.00 -158.02 -21.98 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA PRO d 103 " pdb=" C PRO d 103 " pdb=" N GLY d 104 " pdb=" CA GLY d 104 " ideal model delta harmonic sigma weight residual 180.00 -158.08 -21.92 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA ASN k 389 " pdb=" C ASN k 389 " pdb=" N HIS k 390 " pdb=" CA HIS k 390 " ideal model delta harmonic sigma weight residual -180.00 -159.01 -20.99 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 17051 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3813 0.054 - 0.108: 1128 0.108 - 0.162: 104 0.162 - 0.215: 14 0.215 - 0.269: 11 Chirality restraints: 5070 Sorted by residual: chirality pdb=" CA LYS K 428 " pdb=" N LYS K 428 " pdb=" C LYS K 428 " pdb=" CB LYS K 428 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA LYS k 428 " pdb=" N LYS k 428 " pdb=" C LYS k 428 " pdb=" CB LYS k 428 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA ARG C 71 " pdb=" N ARG C 71 " pdb=" C ARG C 71 " pdb=" CB ARG C 71 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 5067 not shown) Planarity restraints: 3698 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA j 5 " 0.002 2.00e-02 2.50e+03 3.09e-02 2.63e+01 pdb=" N9 DA j 5 " -0.020 2.00e-02 2.50e+03 pdb=" C8 DA j 5 " 0.071 2.00e-02 2.50e+03 pdb=" N7 DA j 5 " -0.064 2.00e-02 2.50e+03 pdb=" C5 DA j 5 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA j 5 " 0.023 2.00e-02 2.50e+03 pdb=" N6 DA j 5 " -0.000 2.00e-02 2.50e+03 pdb=" N1 DA j 5 " 0.012 2.00e-02 2.50e+03 pdb=" C2 DA j 5 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DA j 5 " -0.000 2.00e-02 2.50e+03 pdb=" C4 DA j 5 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA J 5 " 0.002 2.00e-02 2.50e+03 3.09e-02 2.63e+01 pdb=" N9 DA J 5 " -0.020 2.00e-02 2.50e+03 pdb=" C8 DA J 5 " 0.072 2.00e-02 2.50e+03 pdb=" N7 DA J 5 " -0.063 2.00e-02 2.50e+03 pdb=" C5 DA J 5 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA J 5 " 0.022 2.00e-02 2.50e+03 pdb=" N6 DA J 5 " -0.000 2.00e-02 2.50e+03 pdb=" N1 DA J 5 " 0.012 2.00e-02 2.50e+03 pdb=" C2 DA J 5 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DA J 5 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DA J 5 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 16 " -0.002 2.00e-02 2.50e+03 1.99e-02 8.87e+00 pdb=" N1 DC I 16 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DC I 16 " -0.033 2.00e-02 2.50e+03 pdb=" O2 DC I 16 " 0.034 2.00e-02 2.50e+03 pdb=" N3 DC I 16 " -0.012 2.00e-02 2.50e+03 pdb=" C4 DC I 16 " -0.024 2.00e-02 2.50e+03 pdb=" N4 DC I 16 " 0.020 2.00e-02 2.50e+03 pdb=" C5 DC I 16 " 0.011 2.00e-02 2.50e+03 pdb=" C6 DC I 16 " 0.009 2.00e-02 2.50e+03 ... (remaining 3695 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 3532 2.73 - 3.27: 28511 3.27 - 3.82: 57214 3.82 - 4.36: 68318 4.36 - 4.90: 99719 Nonbonded interactions: 257294 Sorted by model distance: nonbonded pdb=" O GLU E 133 " pdb=" NE ARG E 134 " model vdw 2.189 2.520 nonbonded pdb=" O GLU e 133 " pdb=" NE ARG e 134 " model vdw 2.189 2.520 nonbonded pdb=" NH2 ARG E 63 " pdb=" O3' DA J 59 " model vdw 2.204 2.520 nonbonded pdb=" NH2 ARG e 63 " pdb=" O3' DA j 59 " model vdw 2.206 2.520 nonbonded pdb=" OH TYR H 40 " pdb=" OP1 DG I 121 " model vdw 2.231 2.440 ... (remaining 257289 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 39 through 134) selection = (chain 'E' and resid 39 through 134) selection = (chain 'a' and resid 39 through 134) selection = (chain 'e' and resid 39 through 134) } ncs_group { reference = (chain 'B' and resid 25 through 102) selection = chain 'F' selection = (chain 'b' and resid 25 through 102) selection = chain 'f' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 118) selection = chain 'c' selection = (chain 'g' and resid 16 through 118) } ncs_group { reference = (chain 'D' and resid 32 through 124) selection = chain 'H' selection = (chain 'd' and resid 32 through 124) selection = chain 'h' } ncs_group { reference = chain 'I' selection = chain 'i' } ncs_group { reference = chain 'J' selection = chain 'j' } ncs_group { reference = (chain 'K' and (resid 157 through 386 or resid 388 through 400 or resid 402 thro \ ugh 412 or resid 414 through 522 or resid 601)) selection = (chain 'k' and (resid 157 through 386 or resid 388 through 400 or resid 402 thro \ ugh 412 or resid 414 through 522 or resid 601)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 576 5.49 5 S 58 5.16 5 C 16996 2.51 5 N 5506 2.21 5 O 6678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.330 Check model and map are aligned: 0.510 Convert atoms to be neutral: 0.300 Process input model: 102.800 Find NCS groups from input model: 1.790 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5662 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.079 31542 Z= 0.691 Angle : 0.834 8.858 45028 Z= 0.492 Chirality : 0.049 0.269 5070 Planarity : 0.005 0.049 3698 Dihedral : 27.429 170.083 12846 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.85 (0.16), residues: 2204 helix: -0.68 (0.12), residues: 1374 sheet: -1.23 (0.45), residues: 106 loop : -2.12 (0.23), residues: 724 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 133 time to evaluate : 3.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 3 residues processed: 145 average time/residue: 0.4432 time to fit residues: 100.2218 Evaluate side-chains 60 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 2.539 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2443 time to fit residues: 4.4002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 227 optimal weight: 10.0000 chunk 204 optimal weight: 6.9990 chunk 113 optimal weight: 0.4980 chunk 69 optimal weight: 6.9990 chunk 138 optimal weight: 9.9990 chunk 109 optimal weight: 10.0000 chunk 211 optimal weight: 20.0000 chunk 81 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 157 optimal weight: 8.9990 chunk 245 optimal weight: 9.9990 overall best weight: 5.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 108 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN K 192 HIS K 210 ASN K 264 GLN K 289 ASN K 429 HIS K 437 HIS K 466 ASN ** K 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 513 ASN K 514 ASN ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 47 GLN ** d 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 39 HIS e 68 GLN e 108 ASN ** g 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 210 ASN k 264 GLN k 289 ASN k 466 ASN k 482 ASN k 514 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5809 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.095 31542 Z= 0.269 Angle : 0.656 9.160 45028 Z= 0.376 Chirality : 0.037 0.218 5070 Planarity : 0.005 0.065 3698 Dihedral : 30.834 178.060 8294 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.18), residues: 2204 helix: 1.17 (0.13), residues: 1394 sheet: -0.64 (0.46), residues: 106 loop : -1.31 (0.24), residues: 704 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 63 time to evaluate : 2.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 73 average time/residue: 0.3962 time to fit residues: 50.2950 Evaluate side-chains 56 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 49 time to evaluate : 2.822 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2512 time to fit residues: 6.6424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 136 optimal weight: 20.0000 chunk 76 optimal weight: 10.0000 chunk 204 optimal weight: 0.1980 chunk 166 optimal weight: 20.0000 chunk 67 optimal weight: 3.9990 chunk 245 optimal weight: 5.9990 chunk 265 optimal weight: 20.0000 chunk 218 optimal weight: 30.0000 chunk 243 optimal weight: 6.9990 chunk 83 optimal weight: 20.0000 chunk 197 optimal weight: 7.9990 overall best weight: 5.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 39 HIS ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 47 GLN ** d 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 482 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5848 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.116 31542 Z= 0.233 Angle : 0.613 12.649 45028 Z= 0.353 Chirality : 0.035 0.293 5070 Planarity : 0.004 0.050 3698 Dihedral : 30.808 178.091 8294 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.33 (0.18), residues: 2204 helix: 1.90 (0.14), residues: 1392 sheet: -0.61 (0.49), residues: 114 loop : -0.96 (0.24), residues: 698 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 54 time to evaluate : 2.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 4 residues processed: 65 average time/residue: 0.4074 time to fit residues: 47.1464 Evaluate side-chains 52 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 2.890 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2530 time to fit residues: 5.4851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 242 optimal weight: 10.0000 chunk 184 optimal weight: 9.9990 chunk 127 optimal weight: 40.0000 chunk 27 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 164 optimal weight: 10.0000 chunk 246 optimal weight: 2.9990 chunk 260 optimal weight: 10.0000 chunk 128 optimal weight: 10.0000 chunk 233 optimal weight: 40.0000 chunk 70 optimal weight: 10.0000 overall best weight: 6.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 68 GLN ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5941 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.075 31542 Z= 0.274 Angle : 0.620 10.100 45028 Z= 0.358 Chirality : 0.036 0.322 5070 Planarity : 0.005 0.087 3698 Dihedral : 30.850 174.123 8294 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.18), residues: 2204 helix: 2.04 (0.14), residues: 1364 sheet: -0.45 (0.50), residues: 114 loop : -0.82 (0.24), residues: 726 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 50 time to evaluate : 2.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 61 average time/residue: 0.3956 time to fit residues: 42.0106 Evaluate side-chains 51 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 2.715 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2449 time to fit residues: 5.5766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 217 optimal weight: 20.0000 chunk 148 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 0.3980 chunk 222 optimal weight: 30.0000 chunk 180 optimal weight: 1.9990 chunk 0 optimal weight: 40.0000 chunk 133 optimal weight: 0.8980 chunk 234 optimal weight: 40.0000 chunk 65 optimal weight: 4.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5851 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 31542 Z= 0.167 Angle : 0.561 10.400 45028 Z= 0.328 Chirality : 0.034 0.304 5070 Planarity : 0.004 0.068 3698 Dihedral : 30.692 174.958 8294 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.99 (0.18), residues: 2204 helix: 2.46 (0.14), residues: 1356 sheet: -0.34 (0.51), residues: 114 loop : -0.63 (0.24), residues: 734 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 2.798 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 54 average time/residue: 0.3836 time to fit residues: 37.4720 Evaluate side-chains 45 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 44 time to evaluate : 2.834 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2538 time to fit residues: 3.8502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 87 optimal weight: 10.0000 chunk 235 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 chunk 153 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 chunk 261 optimal weight: 10.0000 chunk 216 optimal weight: 20.0000 chunk 120 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 86 optimal weight: 20.0000 chunk 137 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 HIS ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5937 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 31542 Z= 0.244 Angle : 0.589 13.909 45028 Z= 0.341 Chirality : 0.035 0.285 5070 Planarity : 0.004 0.068 3698 Dihedral : 30.695 172.764 8294 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.91 (0.18), residues: 2204 helix: 2.36 (0.14), residues: 1362 sheet: -0.56 (0.51), residues: 112 loop : -0.56 (0.24), residues: 730 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 46 time to evaluate : 2.853 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 56 average time/residue: 0.3839 time to fit residues: 38.5837 Evaluate side-chains 51 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 2.729 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2546 time to fit residues: 6.7135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 251 optimal weight: 50.0000 chunk 29 optimal weight: 0.8980 chunk 148 optimal weight: 10.0000 chunk 190 optimal weight: 20.0000 chunk 147 optimal weight: 9.9990 chunk 219 optimal weight: 30.0000 chunk 145 optimal weight: 6.9990 chunk 260 optimal weight: 30.0000 chunk 162 optimal weight: 40.0000 chunk 158 optimal weight: 8.9990 chunk 120 optimal weight: 7.9990 overall best weight: 6.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5976 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.064 31542 Z= 0.265 Angle : 0.611 16.088 45028 Z= 0.352 Chirality : 0.035 0.271 5070 Planarity : 0.005 0.115 3698 Dihedral : 30.901 173.362 8294 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.74 (0.18), residues: 2204 helix: 2.20 (0.14), residues: 1372 sheet: -0.45 (0.51), residues: 104 loop : -0.65 (0.24), residues: 728 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 49 time to evaluate : 2.596 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 58 average time/residue: 0.3773 time to fit residues: 39.5570 Evaluate side-chains 46 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 44 time to evaluate : 2.958 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2435 time to fit residues: 4.3746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 160 optimal weight: 9.9990 chunk 103 optimal weight: 0.0060 chunk 155 optimal weight: 7.9990 chunk 78 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 165 optimal weight: 5.9990 chunk 177 optimal weight: 20.0000 chunk 128 optimal weight: 50.0000 chunk 24 optimal weight: 2.9990 chunk 204 optimal weight: 5.9990 overall best weight: 2.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5910 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.088 31542 Z= 0.180 Angle : 0.564 12.737 45028 Z= 0.328 Chirality : 0.034 0.272 5070 Planarity : 0.004 0.088 3698 Dihedral : 30.679 173.199 8294 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.09 (0.18), residues: 2204 helix: 2.51 (0.14), residues: 1362 sheet: -0.46 (0.50), residues: 104 loop : -0.52 (0.24), residues: 738 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 43 time to evaluate : 2.958 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 45 average time/residue: 0.3726 time to fit residues: 31.7377 Evaluate side-chains 42 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 2.910 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 236 optimal weight: 50.0000 chunk 249 optimal weight: 6.9990 chunk 227 optimal weight: 20.0000 chunk 242 optimal weight: 40.0000 chunk 145 optimal weight: 20.0000 chunk 105 optimal weight: 8.9990 chunk 190 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 chunk 219 optimal weight: 40.0000 chunk 229 optimal weight: 20.0000 chunk 241 optimal weight: 20.0000 overall best weight: 13.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 73 ASN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 82 HIS e 76 GLN ** g 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 38 ASN ** g 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 49 HIS ** k 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6107 moved from start: 0.5153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.084 31542 Z= 0.452 Angle : 0.745 17.169 45028 Z= 0.420 Chirality : 0.042 0.356 5070 Planarity : 0.006 0.072 3698 Dihedral : 31.345 169.931 8294 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 21.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.01 (0.18), residues: 2204 helix: 1.57 (0.13), residues: 1366 sheet: -0.89 (0.49), residues: 108 loop : -0.76 (0.24), residues: 730 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 2.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 47 average time/residue: 0.3933 time to fit residues: 33.4212 Evaluate side-chains 45 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 42 time to evaluate : 2.756 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2783 time to fit residues: 4.7375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 159 optimal weight: 20.0000 chunk 256 optimal weight: 8.9990 chunk 156 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 chunk 178 optimal weight: 40.0000 chunk 268 optimal weight: 6.9990 chunk 247 optimal weight: 2.9990 chunk 214 optimal weight: 20.0000 chunk 22 optimal weight: 6.9990 chunk 165 optimal weight: 5.9990 chunk 131 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6015 moved from start: 0.5155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.074 31542 Z= 0.251 Angle : 0.628 18.975 45028 Z= 0.357 Chirality : 0.036 0.287 5070 Planarity : 0.004 0.074 3698 Dihedral : 31.251 171.162 8294 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.46 (0.18), residues: 2204 helix: 1.99 (0.14), residues: 1360 sheet: -0.96 (0.49), residues: 108 loop : -0.67 (0.24), residues: 736 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 2.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.3953 time to fit residues: 33.0954 Evaluate side-chains 44 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 2.863 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 170 optimal weight: 3.9990 chunk 228 optimal weight: 30.0000 chunk 65 optimal weight: 0.8980 chunk 197 optimal weight: 30.0000 chunk 31 optimal weight: 0.9990 chunk 59 optimal weight: 8.9990 chunk 214 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 chunk 220 optimal weight: 50.0000 chunk 27 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN ** g 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.082648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.051701 restraints weight = 552515.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.051144 restraints weight = 304963.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.050311 restraints weight = 218343.816| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4395 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4395 r_free = 0.4395 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4399 r_free = 0.4399 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.4399 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.5230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 31542 Z= 0.179 Angle : 0.585 18.471 45028 Z= 0.335 Chirality : 0.034 0.320 5070 Planarity : 0.004 0.067 3698 Dihedral : 30.765 172.813 8294 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.01 (0.18), residues: 2204 helix: 2.46 (0.14), residues: 1360 sheet: -0.73 (0.50), residues: 104 loop : -0.53 (0.24), residues: 740 =============================================================================== Job complete usr+sys time: 3504.37 seconds wall clock time: 66 minutes 27.70 seconds (3987.70 seconds total)