Starting phenix.real_space_refine (version: 1.21rc1) on Fri Jul 14 05:03:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c0m_30267/07_2023/7c0m_30267.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c0m_30267/07_2023/7c0m_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_30267/07_2023/7c0m_30267.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c0m_30267/07_2023/7c0m_30267.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c0m_30267/07_2023/7c0m_30267.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c0m_30267/07_2023/7c0m_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 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. Process input model Symmetric amino acids flipped Residue "A GLU 94": "OE1" <-> "OE2" Residue "C ARG 35": "NH1" <-> "NH2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D GLU 71": "OE1" <-> "OE2" Residue "D GLU 105": "OE1" <-> "OE2" Residue "E ASP 81": "OD1" <-> "OD2" Residue "G ARG 71": "NH1" <-> "NH2" Residue "G ASP 90": "OD1" <-> "OD2" Residue "H GLU 71": "OE1" <-> "OE2" Residue "H GLU 76": "OE1" <-> "OE2" Residue "H TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 170": "OE1" <-> "OE2" Residue "K ASP 177": "OD1" <-> "OD2" Residue "K ASP 178": "OD1" <-> "OD2" Residue "K ASP 191": "OD1" <-> "OD2" Residue "K ARG 196": "NH1" <-> "NH2" Residue "K ASP 200": "OD1" <-> "OD2" Residue "K ARG 204": "NH1" <-> "NH2" Residue "K TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 216": "OE1" <-> "OE2" Residue "K GLU 240": "OE1" <-> "OE2" Residue "K GLU 267": "OE1" <-> "OE2" Residue "K GLU 269": "OE1" <-> "OE2" Residue "K GLU 286": "OE1" <-> "OE2" Residue "K ASP 290": "OD1" <-> "OD2" Residue "K ASP 293": "OD1" <-> "OD2" Residue "K ASP 319": "OD1" <-> "OD2" Residue "K ARG 339": "NH1" <-> "NH2" Residue "K GLU 366": "OE1" <-> "OE2" Residue "K PHE 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 372": "OE1" <-> "OE2" Residue "K GLU 373": "OE1" <-> "OE2" Residue "K GLU 398": "OE1" <-> "OE2" Residue "K ASP 408": "OD1" <-> "OD2" Residue "K GLU 418": "OE1" <-> "OE2" Residue "K GLU 422": "OE1" <-> "OE2" Residue "K ASP 431": "OD1" <-> "OD2" Residue "K PHE 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 452": "OD1" <-> "OD2" Residue "K ASP 459": "OD1" <-> "OD2" Residue "K ASP 465": "OD1" <-> "OD2" Residue "K GLU 481": "OE1" <-> "OE2" Residue "K GLU 502": "OE1" <-> "OE2" Residue "K PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 509": "OE1" <-> "OE2" Residue "K GLU 511": "OE1" <-> "OE2" Residue "K ASP 520": "OD1" <-> "OD2" Residue "K GLU 521": "OE1" <-> "OE2" Residue "a GLU 94": "OE1" <-> "OE2" Residue "c ARG 35": "NH1" <-> "NH2" Residue "c GLU 91": "OE1" <-> "OE2" Residue "c GLU 92": "OE1" <-> "OE2" Residue "d GLU 35": "OE1" <-> "OE2" Residue "d GLU 71": "OE1" <-> "OE2" Residue "d GLU 105": "OE1" <-> "OE2" Residue "e ASP 81": "OD1" <-> "OD2" Residue "g ARG 71": "NH1" <-> "NH2" Residue "g ASP 90": "OD1" <-> "OD2" Residue "h GLU 71": "OE1" <-> "OE2" Residue "h GLU 76": "OE1" <-> "OE2" Residue "h TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 170": "OE1" <-> "OE2" Residue "k ASP 177": "OD1" <-> "OD2" Residue "k ASP 178": "OD1" <-> "OD2" Residue "k ASP 191": "OD1" <-> "OD2" Residue "k ARG 196": "NH1" <-> "NH2" Residue "k ASP 200": "OD1" <-> "OD2" Residue "k ARG 204": "NH1" <-> "NH2" Residue "k TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 216": "OE1" <-> "OE2" Residue "k GLU 240": "OE1" <-> "OE2" Residue "k GLU 267": "OE1" <-> "OE2" Residue "k GLU 269": "OE1" <-> "OE2" Residue "k GLU 286": "OE1" <-> "OE2" Residue "k ASP 290": "OD1" <-> "OD2" Residue "k ASP 293": "OD1" <-> "OD2" Residue "k ASP 319": "OD1" <-> "OD2" Residue "k ARG 339": "NH1" <-> "NH2" Residue "k GLU 366": "OE1" <-> "OE2" Residue "k PHE 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 372": "OE1" <-> "OE2" Residue "k GLU 373": "OE1" <-> "OE2" Residue "k GLU 398": "OE1" <-> "OE2" Residue "k ASP 408": "OD1" <-> "OD2" Residue "k GLU 418": "OE1" <-> "OE2" Residue "k GLU 422": "OE1" <-> "OE2" Residue "k ASP 431": "OD1" <-> "OD2" Residue "k PHE 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 452": "OD1" <-> "OD2" Residue "k ASP 459": "OD1" <-> "OD2" Residue "k ASP 465": "OD1" <-> "OD2" Residue "k GLU 481": "OE1" <-> "OE2" Residue "k GLU 502": "OE1" <-> "OE2" Residue "k PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 509": "OE1" <-> "OE2" Residue "k GLU 511": "OE1" <-> "OE2" Residue "k ASP 520": "OD1" <-> "OD2" Residue "k GLU 521": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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: 16.21, per 1000 atoms: 0.54 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: 15.59 Conformation dependent library (CDL) restraints added in 3.7 seconds Dynamic metal 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: 11.99 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: 15.76 Time building geometry restraints manager: 16.48 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 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: 0.800 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: 0.030 Extract box with map and model: 6.310 Check model and map are aligned: 0.460 Set scattering table: 0.270 Process input model: 98.110 Find NCS groups from input model: 1.590 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.970 ------------------------------------------------------------------------------- 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 : 13.32 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 : 2.511 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: 0.4533 time to fit residues: 103.0583 Evaluate side-chains 60 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 2.510 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2551 time to fit residues: 4.5064 ------------------------------------------------------------------------------- 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: 10.0000 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 a 39 HIS ** 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: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5797 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.077 31542 Z= 0.266 Angle : 0.648 9.009 45028 Z= 0.373 Chirality : 0.037 0.227 5070 Planarity : 0.005 0.046 3698 Dihedral : 30.835 177.763 8294 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % 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: 0.40 (0.17), residues: 2204 helix: 1.14 (0.13), residues: 1394 sheet: -0.67 (0.46), residues: 106 loop : -1.32 (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 77 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 62 time to evaluate : 2.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 73 average time/residue: 0.4010 time to fit residues: 50.2750 Evaluate side-chains 56 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 50 time to evaluate : 2.622 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2659 time to fit residues: 6.0624 ------------------------------------------------------------------------------- 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: 6.9990 chunk 76 optimal weight: 10.0000 chunk 204 optimal weight: 0.9980 chunk 166 optimal weight: 20.0000 chunk 67 optimal weight: 1.9990 chunk 245 optimal weight: 5.9990 chunk 265 optimal weight: 50.0000 chunk 218 optimal weight: 30.0000 chunk 243 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 197 optimal weight: 6.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- 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** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5824 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 31542 Z= 0.219 Angle : 0.599 11.146 45028 Z= 0.348 Chirality : 0.035 0.349 5070 Planarity : 0.004 0.051 3698 Dihedral : 30.765 178.375 8294 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % 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: 1.37 (0.18), residues: 2204 helix: 1.94 (0.14), residues: 1388 sheet: -0.23 (0.48), residues: 106 loop : -1.02 (0.24), residues: 710 *********************** 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: 13 poor density : 55 time to evaluate : 2.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 66 average time/residue: 0.3970 time to fit residues: 46.0977 Evaluate side-chains 58 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 49 time to evaluate : 2.737 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2626 time to fit residues: 7.6301 ------------------------------------------------------------------------------- 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: 4.9990 chunk 184 optimal weight: 9.9990 chunk 127 optimal weight: 40.0000 chunk 27 optimal weight: 6.9990 chunk 117 optimal weight: 10.0000 chunk 164 optimal weight: 0.0370 chunk 246 optimal weight: 7.9990 chunk 260 optimal weight: 20.0000 chunk 128 optimal weight: 10.0000 chunk 233 optimal weight: 40.0000 chunk 70 optimal weight: 9.9990 overall best weight: 6.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** d 63 ASN d 82 HIS ** g 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 38 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5906 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 31542 Z= 0.254 Angle : 0.607 10.781 45028 Z= 0.351 Chirality : 0.035 0.314 5070 Planarity : 0.004 0.059 3698 Dihedral : 30.756 174.798 8294 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer Outliers : 0.62 % 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: 1.66 (0.18), residues: 2204 helix: 2.20 (0.14), residues: 1360 sheet: -0.44 (0.50), residues: 114 loop : -0.78 (0.24), residues: 730 *********************** 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 64 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 52 time to evaluate : 2.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 62 average time/residue: 0.4096 time to fit residues: 43.9167 Evaluate side-chains 53 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 2.373 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2616 time to fit residues: 6.0401 ------------------------------------------------------------------------------- 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: 20.0000 chunk 3 optimal weight: 5.9990 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 0.9990 chunk 222 optimal weight: 30.0000 chunk 180 optimal weight: 6.9990 chunk 0 optimal weight: 40.0000 chunk 133 optimal weight: 20.0000 chunk 234 optimal weight: 20.0000 chunk 65 optimal weight: 0.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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** ** d 63 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: 0.5893 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 31542 Z= 0.214 Angle : 0.583 12.356 45028 Z= 0.338 Chirality : 0.034 0.341 5070 Planarity : 0.004 0.070 3698 Dihedral : 30.769 174.074 8294 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 0.62 % 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: 1.87 (0.18), residues: 2204 helix: 2.35 (0.14), residues: 1362 sheet: -0.31 (0.52), residues: 114 loop : -0.67 (0.24), residues: 728 *********************** 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 59 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 47 time to evaluate : 2.441 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 58 average time/residue: 0.3939 time to fit residues: 40.6594 Evaluate side-chains 51 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 2.431 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2658 time to fit residues: 5.6400 ------------------------------------------------------------------------------- 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: 30.0000 chunk 51 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 261 optimal weight: 2.9990 chunk 216 optimal weight: 20.0000 chunk 120 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 86 optimal weight: 20.0000 chunk 137 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 ** 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: 0.5928 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 31542 Z= 0.227 Angle : 0.583 11.883 45028 Z= 0.338 Chirality : 0.034 0.341 5070 Planarity : 0.004 0.068 3698 Dihedral : 30.721 172.877 8294 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer Outliers : 0.36 % 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: 1.90 (0.18), residues: 2204 helix: 2.36 (0.14), residues: 1372 sheet: -0.53 (0.52), residues: 112 loop : -0.63 (0.25), residues: 720 *********************** 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 51 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 2.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 51 average time/residue: 0.4148 time to fit residues: 37.4728 Evaluate side-chains 46 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 2.507 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2554 time to fit residues: 4.5873 ------------------------------------------------------------------------------- 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: 1.9990 chunk 148 optimal weight: 7.9990 chunk 190 optimal weight: 30.0000 chunk 147 optimal weight: 20.0000 chunk 219 optimal weight: 30.0000 chunk 145 optimal weight: 9.9990 chunk 260 optimal weight: 30.0000 chunk 162 optimal weight: 20.0000 chunk 158 optimal weight: 6.9990 chunk 120 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 ** 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** ** H 49 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5983 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 31542 Z= 0.273 Angle : 0.616 12.790 45028 Z= 0.354 Chirality : 0.035 0.327 5070 Planarity : 0.004 0.071 3698 Dihedral : 30.903 172.686 8294 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer Outliers : 0.57 % 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: 1.71 (0.18), residues: 2204 helix: 2.17 (0.14), residues: 1372 sheet: -0.41 (0.52), residues: 104 loop : -0.67 (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 59 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 48 time to evaluate : 2.845 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 59 average time/residue: 0.4066 time to fit residues: 43.6137 Evaluate side-chains 47 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 43 time to evaluate : 2.934 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2587 time to fit residues: 5.0512 ------------------------------------------------------------------------------- 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: 10.0000 chunk 103 optimal weight: 1.9990 chunk 155 optimal weight: 7.9990 chunk 78 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 165 optimal weight: 5.9990 chunk 177 optimal weight: 20.0000 chunk 128 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 204 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 24 GLN ** 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: 0.5951 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 31542 Z= 0.219 Angle : 0.582 13.660 45028 Z= 0.337 Chirality : 0.035 0.325 5070 Planarity : 0.004 0.069 3698 Dihedral : 30.833 172.601 8294 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % 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: 1.93 (0.18), residues: 2204 helix: 2.39 (0.14), residues: 1362 sheet: -0.58 (0.50), residues: 104 loop : -0.58 (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 : 2.524 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 45 average time/residue: 0.4452 time to fit residues: 35.1192 Evaluate side-chains 42 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 2.646 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1628 ------------------------------------------------------------------------------- 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: 40.0000 chunk 249 optimal weight: 10.0000 chunk 227 optimal weight: 20.0000 chunk 242 optimal weight: 40.0000 chunk 145 optimal weight: 8.9990 chunk 105 optimal weight: 0.9980 chunk 190 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 219 optimal weight: 30.0000 chunk 229 optimal weight: 20.0000 chunk 241 optimal weight: 30.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- 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** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 76 GLN ** g 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6028 moved from start: 0.5019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 31542 Z= 0.302 Angle : 0.641 16.914 45028 Z= 0.364 Chirality : 0.037 0.314 5070 Planarity : 0.004 0.071 3698 Dihedral : 31.033 171.476 8294 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % 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: 1.60 (0.18), residues: 2204 helix: 2.11 (0.14), residues: 1360 sheet: -0.96 (0.49), residues: 108 loop : -0.62 (0.24), residues: 736 *********************** 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 44 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 2.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 44 average time/residue: 0.4250 time to fit residues: 33.5659 Evaluate side-chains 44 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 2.635 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3357 time to fit residues: 3.8203 ------------------------------------------------------------------------------- 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: 9.9990 chunk 256 optimal weight: 50.0000 chunk 156 optimal weight: 6.9990 chunk 121 optimal weight: 9.9990 chunk 178 optimal weight: 30.0000 chunk 268 optimal weight: 30.0000 chunk 247 optimal weight: 0.9990 chunk 214 optimal weight: 20.0000 chunk 22 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 131 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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** ** 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5987 moved from start: 0.5130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 31542 Z= 0.233 Angle : 0.601 13.885 45028 Z= 0.344 Chirality : 0.035 0.312 5070 Planarity : 0.004 0.077 3698 Dihedral : 31.022 172.147 8294 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % 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: 1.78 (0.18), residues: 2204 helix: 2.26 (0.14), residues: 1360 sheet: -0.77 (0.49), residues: 104 loop : -0.59 (0.24), residues: 740 ********************** 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 : 2.564 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.4169 time to fit residues: 34.7312 Evaluate side-chains 44 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 2.579 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0581 ------------------------------------------------------------------------------- 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: 9.9990 chunk 228 optimal weight: 30.0000 chunk 65 optimal weight: 2.9990 chunk 197 optimal weight: 30.0000 chunk 31 optimal weight: 5.9990 chunk 59 optimal weight: 20.0000 chunk 214 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 chunk 220 optimal weight: 50.0000 chunk 27 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.066884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.048036 restraints weight = 603905.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.045830 restraints weight = 389718.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.045001 restraints weight = 333602.179| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3340 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3341 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.5269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 31542 Z= 0.251 Angle : 0.606 11.752 45028 Z= 0.348 Chirality : 0.035 0.320 5070 Planarity : 0.004 0.078 3698 Dihedral : 30.997 171.226 8294 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % 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: 1.75 (0.18), residues: 2204 helix: 2.22 (0.14), residues: 1362 sheet: -0.85 (0.49), residues: 104 loop : -0.57 (0.24), residues: 738 =============================================================================== Job complete usr+sys time: 3616.25 seconds wall clock time: 68 minutes 30.35 seconds (4110.35 seconds total)