Starting phenix.real_space_refine on Wed Sep 25 15:06:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8by8_16324/09_2024/8by8_16324.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8by8_16324/09_2024/8by8_16324.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8by8_16324/09_2024/8by8_16324.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8by8_16324/09_2024/8by8_16324.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8by8_16324/09_2024/8by8_16324.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8by8_16324/09_2024/8by8_16324.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 19435 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 86 5.16 5 C 12259 2.51 5 N 3487 2.21 5 O 3728 1.98 5 H 19223 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 38783 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 19385 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1284, 19245 Classifications: {'peptide': 1284} Link IDs: {'PCIS': 1, 'PTRANS': 76, 'TRANS': 1206} Conformer: "B" Number of residues, atoms: 1284, 19245 Classifications: {'peptide': 1284} Link IDs: {'PCIS': 1, 'PTRANS': 76, 'TRANS': 1206} bond proxies already assigned to first conformer: 19312 Chain: "B" Number of atoms: 19398 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1284, 19249 Classifications: {'peptide': 1284} Link IDs: {'PCIS': 1, 'PTRANS': 76, 'TRANS': 1206} Conformer: "B" Number of residues, atoms: 1284, 19249 Classifications: {'peptide': 1284} Link IDs: {'PCIS': 1, 'PTRANS': 76, 'TRANS': 1206} bond proxies already assigned to first conformer: 19307 Residues with excluded nonbonded symmetry interactions: 13 residue: pdb=" N AARG A 28 " occ=0.50 ... (46 atoms not shown) pdb="HH22BARG A 28 " occ=0.50 residue: pdb=" N AARG A 63 " occ=0.63 ... (46 atoms not shown) pdb="HH22BARG A 63 " occ=0.37 residue: pdb=" N AARG A 277 " occ=0.42 ... (46 atoms not shown) pdb="HH22BARG A 277 " occ=0.58 residue: pdb=" N AARG A 315 " occ=0.49 ... (46 atoms not shown) pdb="HH22BARG A 315 " occ=0.51 residue: pdb=" N ATYR A 538 " occ=0.81 ... (40 atoms not shown) pdb=" HH BTYR A 538 " occ=0.19 residue: pdb=" N AASP A1224 " occ=0.49 ... (22 atoms not shown) pdb=" HB3BASP A1224 " occ=0.51 residue: pdb=" N AARG B 28 " occ=0.51 ... (46 atoms not shown) pdb="HH22BARG B 28 " occ=0.49 residue: pdb=" N AARG B 277 " occ=0.59 ... (46 atoms not shown) pdb="HH22BARG B 277 " occ=0.41 residue: pdb=" N ATYR B 538 " occ=0.74 ... (40 atoms not shown) pdb=" HH BTYR B 538 " occ=0.26 residue: pdb=" N AARG B 569 " occ=0.22 ... (46 atoms not shown) pdb="HH22BARG B 569 " occ=0.78 residue: pdb=" N AARG B 768 " occ=0.53 ... (46 atoms not shown) pdb="HH22BARG B 768 " occ=0.47 residue: pdb=" N AGLN B 981 " occ=0.23 ... (32 atoms not shown) pdb="HE22BGLN B 981 " occ=0.77 residue: pdb=" N AGLU B1250 " occ=0.50 ... (28 atoms not shown) pdb=" HG3BGLU B1250 " occ=0.50 Time building chain proxies: 23.55, per 1000 atoms: 0.61 Number of scatterers: 38783 At special positions: 0 Unit cell: (201.72, 95.12, 129.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 86 16.00 O 3728 8.00 N 3487 7.00 C 12259 6.00 H 19223 1.00 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 - 3.00 Amino acid : True - 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: 7.21 Conformation dependent library (CDL) restraints added in 4.2 seconds 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4816 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 17 sheets defined 47.4% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.65 Creating SS restraints... Processing helix chain 'A' and resid 19 through 29 Processing helix chain 'A' and resid 32 through 51 Proline residue: A 43 - end of helix Processing helix chain 'A' and resid 54 through 59 removed outlier: 3.753A pdb=" N GLU A 59 " --> pdb=" O SER A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 68 No H-bonds generated for 'chain 'A' and resid 66 through 68' Processing helix chain 'A' and resid 69 through 77 removed outlier: 4.172A pdb=" N ARG A 73 " --> pdb=" O GLU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 102 Processing helix chain 'A' and resid 120 through 131 removed outlier: 4.119A pdb=" N THR A 124 " --> pdb=" O THR A 120 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 163 Proline residue: A 139 - end of helix Processing helix chain 'A' and resid 184 through 200 removed outlier: 3.754A pdb=" N ASP A 190 " --> pdb=" O GLN A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 256 through 264 Processing helix chain 'A' and resid 294 through 309 Processing helix chain 'A' and resid 315 through 327 Processing helix chain 'A' and resid 341 through 343 No H-bonds generated for 'chain 'A' and resid 341 through 343' Processing helix chain 'A' and resid 344 through 351 Processing helix chain 'A' and resid 398 through 408 Processing helix chain 'A' and resid 453 through 457 Processing helix chain 'A' and resid 467 through 485 Processing helix chain 'A' and resid 491 through 495 removed outlier: 3.676A pdb=" N GLN A 495 " --> pdb=" O SER A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 514 Processing helix chain 'A' and resid 515 through 518 removed outlier: 3.568A pdb=" N ASN A 518 " --> pdb=" O SER A 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 515 through 518' Processing helix chain 'A' and resid 522 through 528 Processing helix chain 'A' and resid 530 through 540 removed outlier: 3.882A pdb=" N VAL A 536 " --> pdb=" O ILE A 532 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS A 540 " --> pdb=" O VAL A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 553 No H-bonds generated for 'chain 'A' and resid 551 through 553' Processing helix chain 'A' and resid 554 through 570 Processing helix chain 'A' and resid 585 through 595 removed outlier: 3.941A pdb=" N THR A 589 " --> pdb=" O ASN A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 634 Processing helix chain 'A' and resid 660 through 676 removed outlier: 3.827A pdb=" N GLN A 664 " --> pdb=" O HIS A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 708 Processing helix chain 'A' and resid 726 through 730 removed outlier: 3.594A pdb=" N SER A 729 " --> pdb=" O ALA A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 753 Processing helix chain 'A' and resid 771 through 776 Processing helix chain 'A' and resid 838 through 856 Processing helix chain 'A' and resid 862 through 873 Processing helix chain 'A' and resid 888 through 906 removed outlier: 3.540A pdb=" N ILE A 892 " --> pdb=" O ASP A 888 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY A 906 " --> pdb=" O ARG A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 941 Processing helix chain 'A' and resid 941 through 958 Processing helix chain 'A' and resid 964 through 968 Processing helix chain 'A' and resid 972 through 976 Processing helix chain 'A' and resid 977 through 999 Processing helix chain 'A' and resid 1011 through 1021 removed outlier: 4.341A pdb=" N ALA A1015 " --> pdb=" O LEU A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1043 Processing helix chain 'A' and resid 1056 through 1064 Processing helix chain 'A' and resid 1089 through 1102 removed outlier: 3.613A pdb=" N LYS A1102 " --> pdb=" O ALA A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1122 removed outlier: 3.670A pdb=" N VAL A1120 " --> pdb=" O THR A1117 " (cutoff:3.500A) Proline residue: A1122 - end of helix Processing helix chain 'A' and resid 1123 through 1134 removed outlier: 3.786A pdb=" N CYS A1134 " --> pdb=" O VAL A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1154 through 1158 removed outlier: 3.598A pdb=" N ASP A1157 " --> pdb=" O SER A1154 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1169 removed outlier: 4.038A pdb=" N CYS A1167 " --> pdb=" O PHE A1163 " (cutoff:3.500A) Processing helix chain 'A' and resid 1173 through 1183 Processing helix chain 'A' and resid 1200 through 1210 Processing helix chain 'A' and resid 1224 through 1240 Processing helix chain 'A' and resid 1244 through 1249 removed outlier: 3.596A pdb=" N TYR A1248 " --> pdb=" O GLU A1244 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS A1249 " --> pdb=" O TRP A1245 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1244 through 1249' Processing helix chain 'A' and resid 1252 through 1256 Processing helix chain 'A' and resid 1278 through 1282 removed outlier: 3.675A pdb=" N LEU A1281 " --> pdb=" O ASP A1278 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 29 Processing helix chain 'B' and resid 32 through 51 Proline residue: B 43 - end of helix Processing helix chain 'B' and resid 54 through 59 Processing helix chain 'B' and resid 66 through 68 No H-bonds generated for 'chain 'B' and resid 66 through 68' Processing helix chain 'B' and resid 69 through 77 removed outlier: 4.274A pdb=" N ARG B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 102 Processing helix chain 'B' and resid 120 through 130 removed outlier: 4.245A pdb=" N THR B 124 " --> pdb=" O THR B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 163 Proline residue: B 139 - end of helix Processing helix chain 'B' and resid 184 through 199 Processing helix chain 'B' and resid 223 through 233 removed outlier: 3.848A pdb=" N THR B 233 " --> pdb=" O ALA B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 264 Processing helix chain 'B' and resid 294 through 308 Processing helix chain 'B' and resid 312 through 314 No H-bonds generated for 'chain 'B' and resid 312 through 314' Processing helix chain 'B' and resid 315 through 327 Processing helix chain 'B' and resid 341 through 343 No H-bonds generated for 'chain 'B' and resid 341 through 343' Processing helix chain 'B' and resid 344 through 351 Processing helix chain 'B' and resid 398 through 408 Processing helix chain 'B' and resid 422 through 427 Processing helix chain 'B' and resid 453 through 457 Processing helix chain 'B' and resid 467 through 485 Processing helix chain 'B' and resid 491 through 495 removed outlier: 3.879A pdb=" N GLN B 495 " --> pdb=" O SER B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 514 Processing helix chain 'B' and resid 515 through 518 removed outlier: 3.614A pdb=" N ASN B 518 " --> pdb=" O SER B 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 515 through 518' Processing helix chain 'B' and resid 522 through 528 Processing helix chain 'B' and resid 530 through 540 removed outlier: 3.863A pdb=" N VAL B 536 " --> pdb=" O ILE B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 570 Processing helix chain 'B' and resid 585 through 595 removed outlier: 3.960A pdb=" N THR B 589 " --> pdb=" O ASN B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 635 Processing helix chain 'B' and resid 660 through 676 removed outlier: 3.586A pdb=" N GLN B 664 " --> pdb=" O HIS B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 708 Processing helix chain 'B' and resid 727 through 732 Processing helix chain 'B' and resid 737 through 753 Processing helix chain 'B' and resid 772 through 775 Processing helix chain 'B' and resid 838 through 856 Processing helix chain 'B' and resid 862 through 874 removed outlier: 3.553A pdb=" N GLN B 866 " --> pdb=" O ALA B 862 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG B 874 " --> pdb=" O THR B 870 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 906 removed outlier: 3.516A pdb=" N GLY B 906 " --> pdb=" O ARG B 902 " (cutoff:3.500A) Processing helix chain 'B' and resid 934 through 941 removed outlier: 3.614A pdb=" N TYR B 938 " --> pdb=" O GLY B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 958 Processing helix chain 'B' and resid 964 through 968 Processing helix chain 'B' and resid 977 through 999 removed outlier: 3.523A pdb=" N LEU B 999 " --> pdb=" O LEU B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1011 through 1021 removed outlier: 4.220A pdb=" N ALA B1015 " --> pdb=" O LEU B1011 " (cutoff:3.500A) Processing helix chain 'B' and resid 1024 through 1043 Processing helix chain 'B' and resid 1056 through 1064 Processing helix chain 'B' and resid 1089 through 1102 Processing helix chain 'B' and resid 1117 through 1122 Proline residue: B1122 - end of helix Processing helix chain 'B' and resid 1123 through 1133 Processing helix chain 'B' and resid 1154 through 1158 Processing helix chain 'B' and resid 1161 through 1166 Processing helix chain 'B' and resid 1173 through 1183 Processing helix chain 'B' and resid 1200 through 1210 removed outlier: 3.739A pdb=" N PHE B1204 " --> pdb=" O VAL B1200 " (cutoff:3.500A) Processing helix chain 'B' and resid 1224 through 1240 Processing helix chain 'B' and resid 1244 through 1250 Processing helix chain 'B' and resid 1252 through 1256 Processing helix chain 'B' and resid 1278 through 1282 removed outlier: 3.680A pdb=" N LEU B1281 " --> pdb=" O ASP B1278 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 113 through 116 removed outlier: 6.990A pdb=" N MET A 7 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 208 through 211 removed outlier: 5.381A pdb=" N LEU A 209 " --> pdb=" O SER A 221 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N SER A 221 " --> pdb=" O LEU A 209 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 280 through 281 Processing sheet with id=AA4, first strand: chain 'A' and resid 546 through 549 removed outlier: 8.929A pdb=" N TYR A 547 " --> pdb=" O VAL A 499 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL A 501 " --> pdb=" O TYR A 547 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ILE A 549 " --> pdb=" O VAL A 501 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TYR A 503 " --> pdb=" O ILE A 549 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N GLY A 500 " --> pdb=" O ILE A 576 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N GLY A 578 " --> pdb=" O GLY A 500 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N TRP A 502 " --> pdb=" O GLY A 578 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N THR A 580 " --> pdb=" O TRP A 502 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLY A 504 " --> pdb=" O THR A 580 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL A 620 " --> pdb=" O GLY A 391 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLY A 391 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR A 622 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ALA A 389 " --> pdb=" O THR A 622 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE A 624 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA A 640 " --> pdb=" O ILE A 386 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL A 811 " --> pdb=" O LEU A 643 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ILE A 645 " --> pdb=" O CYS A 809 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N CYS A 809 " --> pdb=" O ILE A 645 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N THR A 647 " --> pdb=" O ASN A 807 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ASN A 807 " --> pdb=" O THR A 647 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N LEU A 797 " --> pdb=" O SER A 683 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N CYS A 685 " --> pdb=" O LEU A 797 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ASN A 799 " --> pdb=" O CYS A 685 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N SER A 683 " --> pdb=" O TYR A 723 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N GLY A 725 " --> pdb=" O SER A 683 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N CYS A 685 " --> pdb=" O GLY A 725 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU A 722 " --> pdb=" O HIS A 778 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA6, first strand: chain 'A' and resid 754 through 755 Processing sheet with id=AA7, first strand: chain 'A' and resid 830 through 836 Processing sheet with id=AA8, first strand: chain 'A' and resid 1150 through 1152 removed outlier: 8.166A pdb=" N ILE A1144 " --> pdb=" O LYS A1004 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL A1006 " --> pdb=" O ILE A1144 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N PHE A 919 " --> pdb=" O LYS A1004 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N VAL A1006 " --> pdb=" O PHE A 919 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU A 921 " --> pdb=" O VAL A1006 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL A 920 " --> pdb=" O LEU A1193 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ILE A1195 " --> pdb=" O VAL A 920 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA A 922 " --> pdb=" O ILE A1195 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1106 through 1108 removed outlier: 7.673A pdb=" N ARG A1082 " --> pdb=" O ARG A1077 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ARG A1077 " --> pdb=" O ARG A1082 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL A1084 " --> pdb=" O SER A1075 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 289 through 290 removed outlier: 3.544A pdb=" N ILE B 280 " --> pdb=" O SER B 290 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N ILE B 281 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE B 115 " --> pdb=" O ILE B 281 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N MET B 7 " --> pdb=" O LEU B 333 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 208 through 211 removed outlier: 5.440A pdb=" N LEU B 209 " --> pdb=" O SER B 221 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N SER B 221 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N THR B 177 " --> pdb=" O LEU B 243 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 546 through 549 removed outlier: 8.886A pdb=" N TYR B 547 " --> pdb=" O VAL B 499 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL B 501 " --> pdb=" O TYR B 547 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ILE B 549 " --> pdb=" O VAL B 501 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N TYR B 503 " --> pdb=" O ILE B 549 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N GLY B 500 " --> pdb=" O ILE B 576 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N GLY B 578 " --> pdb=" O GLY B 500 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N TRP B 502 " --> pdb=" O GLY B 578 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N THR B 580 " --> pdb=" O TRP B 502 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLY B 504 " --> pdb=" O THR B 580 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL B 620 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLY B 391 " --> pdb=" O VAL B 620 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR B 622 " --> pdb=" O ALA B 389 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA B 389 " --> pdb=" O THR B 622 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE B 624 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA B 640 " --> pdb=" O ILE B 386 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER B 641 " --> pdb=" O GLU B 813 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL B 811 " --> pdb=" O LEU B 643 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ILE B 645 " --> pdb=" O CYS B 809 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N CYS B 809 " --> pdb=" O ILE B 645 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N THR B 647 " --> pdb=" O ASN B 807 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN B 807 " --> pdb=" O THR B 647 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N LEU B 797 " --> pdb=" O SER B 683 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N CYS B 685 " --> pdb=" O LEU B 797 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ASN B 799 " --> pdb=" O CYS B 685 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N SER B 683 " --> pdb=" O TYR B 723 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N GLY B 725 " --> pdb=" O SER B 683 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N CYS B 685 " --> pdb=" O GLY B 725 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU B 722 " --> pdb=" O HIS B 778 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 414 through 415 Processing sheet with id=AB5, first strand: chain 'B' and resid 754 through 755 Processing sheet with id=AB6, first strand: chain 'B' and resid 830 through 836 Processing sheet with id=AB7, first strand: chain 'B' and resid 1150 through 1152 removed outlier: 8.306A pdb=" N ILE B1144 " --> pdb=" O LYS B1004 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL B1006 " --> pdb=" O ILE B1144 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N PHE B 919 " --> pdb=" O LYS B1004 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N VAL B1006 " --> pdb=" O PHE B 919 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU B 921 " --> pdb=" O VAL B1006 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N SER B 918 " --> pdb=" O ILE B1191 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N LEU B1193 " --> pdb=" O SER B 918 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL B 920 " --> pdb=" O LEU B1193 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE B1195 " --> pdb=" O VAL B 920 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ALA B 922 " --> pdb=" O ILE B1195 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1106 through 1108 removed outlier: 6.601A pdb=" N VAL B1084 " --> pdb=" O SER B1075 " (cutoff:3.500A) 907 hydrogen bonds defined for protein. 2577 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.13 Time building geometry restraints manager: 8.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 19183 1.03 - 1.23: 47 1.23 - 1.42: 8290 1.42 - 1.62: 11577 1.62 - 1.81: 132 Bond restraints: 39229 Sorted by residual: bond pdb=" N VAL A 206 " pdb=" CA VAL A 206 " ideal model delta sigma weight residual 1.468 1.459 0.009 1.05e-02 9.07e+03 7.87e-01 bond pdb=" CG PRO A 237 " pdb=" CD PRO A 237 " ideal model delta sigma weight residual 1.512 1.490 0.022 2.70e-02 1.37e+03 6.48e-01 bond pdb=" C ASP A 681 " pdb=" N ILE A 682 " ideal model delta sigma weight residual 1.334 1.324 0.010 1.24e-02 6.50e+03 6.40e-01 bond pdb=" CA ILE A 368 " pdb=" CB ILE A 368 " ideal model delta sigma weight residual 1.537 1.546 -0.009 1.29e-02 6.01e+03 4.94e-01 bond pdb=" CA SER B 546 " pdb=" C SER B 546 " ideal model delta sigma weight residual 1.522 1.529 -0.007 1.08e-02 8.57e+03 4.46e-01 ... (remaining 39224 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.05: 66181 1.05 - 2.10: 4376 2.10 - 3.15: 220 3.15 - 4.20: 91 4.20 - 5.25: 11 Bond angle restraints: 70879 Sorted by residual: angle pdb=" CA GLY A 442 " pdb=" C GLY A 442 " pdb=" N CYS A 443 " ideal model delta sigma weight residual 114.58 117.04 -2.46 8.60e-01 1.35e+00 8.16e+00 angle pdb=" C SER A 367 " pdb=" N ILE A 368 " pdb=" CA ILE A 368 " ideal model delta sigma weight residual 122.13 127.38 -5.25 1.85e+00 2.92e-01 8.06e+00 angle pdb=" NE BARG B 28 " pdb=" CZ BARG B 28 " pdb=" NH2BARG B 28 " ideal model delta sigma weight residual 119.20 121.71 -2.51 9.00e-01 1.23e+00 7.77e+00 angle pdb=" NE BARG A 28 " pdb=" CZ BARG A 28 " pdb=" NH2BARG A 28 " ideal model delta sigma weight residual 119.20 121.65 -2.45 9.00e-01 1.23e+00 7.43e+00 angle pdb=" NE BARG A 315 " pdb=" CZ BARG A 315 " pdb=" NH2BARG A 315 " ideal model delta sigma weight residual 119.20 121.58 -2.38 9.00e-01 1.23e+00 6.98e+00 ... (remaining 70874 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 18093 35.98 - 71.97: 539 71.97 - 107.95: 31 107.95 - 143.93: 0 143.93 - 179.91: 3 Dihedral angle restraints: 18666 sinusoidal: 10140 harmonic: 8526 Sorted by residual: dihedral pdb=" CD BARG A 28 " pdb=" NE BARG A 28 " pdb=" CZ BARG A 28 " pdb=" NH1BARG A 28 " ideal model delta sinusoidal sigma weight residual 0.00 -179.91 179.91 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CD BARG A 315 " pdb=" NE BARG A 315 " pdb=" CZ BARG A 315 " pdb=" NH1BARG A 315 " ideal model delta sinusoidal sigma weight residual 0.00 -179.77 179.77 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CD BARG B 28 " pdb=" NE BARG B 28 " pdb=" CZ BARG B 28 " pdb=" NH1BARG B 28 " ideal model delta sinusoidal sigma weight residual 0.00 -178.46 178.46 1 1.00e+01 1.00e-02 1.92e+02 ... (remaining 18663 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1965 0.029 - 0.058: 755 0.058 - 0.087: 200 0.087 - 0.116: 143 0.116 - 0.145: 41 Chirality restraints: 3104 Sorted by residual: chirality pdb=" CA VAL B 487 " pdb=" N VAL B 487 " pdb=" C VAL B 487 " pdb=" CB VAL B 487 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" CA ILE B 278 " pdb=" N ILE B 278 " pdb=" C ILE B 278 " pdb=" CB ILE B 278 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" CB ILE A 368 " pdb=" CA ILE A 368 " pdb=" CG1 ILE A 368 " pdb=" CG2 ILE A 368 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.17e-01 ... (remaining 3101 not shown) Planarity restraints: 6017 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 788 " -0.028 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO B 789 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 789 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 789 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 536 " -0.007 2.00e-02 2.50e+03 1.31e-02 1.73e+00 pdb=" C VAL B 536 " 0.023 2.00e-02 2.50e+03 pdb=" O VAL B 536 " -0.009 2.00e-02 2.50e+03 pdb=" N ASN B 537 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 107 " 0.020 5.00e-02 4.00e+02 3.03e-02 1.47e+00 pdb=" N PRO A 108 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 108 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 108 " 0.017 5.00e-02 4.00e+02 ... (remaining 6014 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 1376 2.15 - 2.76: 73942 2.76 - 3.38: 109570 3.38 - 3.99: 143966 3.99 - 4.60: 228916 Nonbonded interactions: 557770 Sorted by model distance: nonbonded pdb="HH21 ARG B 616 " pdb=" OE2 GLU B 735 " model vdw 1.541 2.450 nonbonded pdb=" O VAL B 883 " pdb="HE22 GLN B 899 " model vdw 1.546 2.450 nonbonded pdb=" O SER A 841 " pdb="HD21 ASN A 845 " model vdw 1.574 2.450 nonbonded pdb=" O SER B 841 " pdb="HD21 ASN B 845 " model vdw 1.579 2.450 nonbonded pdb=" O VAL A 883 " pdb="HE22 GLN A 899 " model vdw 1.603 2.450 ... (remaining 557765 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 27 or resid 29 through 62 or resid 64 through 27 \ 6 or resid 278 through 314 or resid 316 through 354 or (resid 355 and (name N or \ name CA or name C or name O )) or resid 356 through 537 or resid 539 through 56 \ 8 or resid 570 through 767 or resid 769 through 980 or resid 982 through 1043 or \ resid 1045 through 1223 or resid 1225 through 1249 or resid 1251 through 1288)) \ selection = (chain 'B' and (resid 5 through 27 or resid 29 through 62 or resid 64 through 27 \ 6 or resid 278 through 314 or resid 316 through 363 or (resid 364 and (name N or \ name CA or name C or name O or name CB or name OG1 or name CG2)) or (resid 365 \ and (name N or name CA or name C or name O or name CB or name OG or name HA or n \ ame HB2 or name HB3 or name HG )) or resid 366 through 537 or resid 539 through \ 568 or resid 570 through 767 or resid 769 through 980 or resid 982 through 1043 \ or resid 1045 through 1223 or resid 1225 through 1249 or resid 1251 through 1288 \ )) } 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.250 Construct map_model_manager: 0.500 Extract box with map and model: 1.070 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 75.350 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.130 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:8.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1857 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 : 0.002 0.037 20006 Z= 0.168 Angle : 0.501 5.253 27279 Z= 0.283 Chirality : 0.039 0.145 3104 Planarity : 0.004 0.043 3593 Dihedral : 13.679 179.913 7265 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.51 % Favored : 96.37 % Rotamer: Outliers : 2.50 % Allowed : 7.73 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: 0.08 (0.17), residues: 2606 helix: 1.25 (0.17), residues: 1078 sheet: 0.09 (0.33), residues: 246 loop : -1.00 (0.17), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1226 HIS 0.003 0.001 HIS A 688 PHE 0.008 0.001 PHE A1252 TYR 0.009 0.001 TYR A 547 ARG 0.002 0.000 ARG B1282 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 186 time to evaluate : 2.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 562 MET cc_start: 0.4682 (mmt) cc_final: 0.4470 (mmt) REVERT: A 1051 LEU cc_start: 0.0865 (mt) cc_final: 0.0611 (mt) REVERT: A 1202 THR cc_start: 0.1525 (t) cc_final: 0.1258 (t) REVERT: B 1260 GLU cc_start: 0.7009 (tt0) cc_final: 0.6806 (tm-30) outliers start: 49 outliers final: 23 residues processed: 233 average time/residue: 1.9933 time to fit residues: 538.7616 Evaluate side-chains 158 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 135 time to evaluate : 2.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 508 ASN Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 673 THR Chi-restraints excluded: chain B residue 697 SER Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 809 CYS Chi-restraints excluded: chain B residue 853 ILE Chi-restraints excluded: chain B residue 871 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.7980 chunk 149 optimal weight: 5.9990 chunk 232 optimal weight: 10.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 953 GLN ** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 GLN B 395 GLN B1083 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1876 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 20006 Z= 0.366 Angle : 0.598 7.335 27279 Z= 0.317 Chirality : 0.044 0.215 3104 Planarity : 0.005 0.082 3593 Dihedral : 8.138 179.891 2832 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.69 % Favored : 94.23 % Rotamer: Outliers : 2.26 % Allowed : 12.73 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: -0.50 (0.16), residues: 2606 helix: 0.75 (0.15), residues: 1126 sheet: -0.30 (0.31), residues: 254 loop : -1.38 (0.17), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1226 HIS 0.006 0.001 HIS A 985 PHE 0.014 0.002 PHE A 944 TYR 0.017 0.002 TYR B1018 ARG 0.010 0.001 ARG B 712 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 145 time to evaluate : 2.146 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 30 residues processed: 184 average time/residue: 1.9603 time to fit residues: 420.7512 Evaluate side-chains 166 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 136 time to evaluate : 2.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1215 THR Chi-restraints excluded: chain A residue 1250 GLU Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain B residue 508 ASN Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 809 CYS Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 853 ILE Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 1108 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 129 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 193 optimal weight: 0.9990 chunk 158 optimal weight: 0.3980 chunk 64 optimal weight: 6.9990 chunk 232 optimal weight: 10.0000 chunk 251 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 230 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 186 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1871 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 20006 Z= 0.226 Angle : 0.540 7.227 27279 Z= 0.280 Chirality : 0.041 0.181 3104 Planarity : 0.004 0.070 3593 Dihedral : 7.815 179.809 2823 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.45 % Favored : 95.48 % Rotamer: Outliers : 2.11 % Allowed : 13.88 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: -0.18 (0.16), residues: 2606 helix: 1.10 (0.16), residues: 1114 sheet: -0.31 (0.32), residues: 254 loop : -1.23 (0.17), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1226 HIS 0.004 0.001 HIS A 688 PHE 0.009 0.001 PHE B1115 TYR 0.070 0.002 TYR B1108 ARG 0.011 0.000 ARG B 712 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 140 time to evaluate : 2.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 562 MET cc_start: 0.4592 (mmt) cc_final: 0.4372 (mtt) outliers start: 40 outliers final: 27 residues processed: 174 average time/residue: 1.8164 time to fit residues: 371.9510 Evaluate side-chains 156 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 129 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 952 ASP Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1215 THR Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 508 ASN Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 809 CYS Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 853 ILE Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 1106 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 230 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 156 optimal weight: 7.9990 chunk 233 optimal weight: 3.9990 chunk 247 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 221 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 104 GLN ** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1891 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.114 20006 Z= 0.389 Angle : 0.597 6.875 27279 Z= 0.314 Chirality : 0.044 0.189 3104 Planarity : 0.005 0.074 3593 Dihedral : 7.900 179.457 2822 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.36 % Favored : 93.56 % Rotamer: Outliers : 2.55 % Allowed : 14.51 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: -0.75 (0.16), residues: 2606 helix: 0.57 (0.15), residues: 1126 sheet: -0.61 (0.31), residues: 256 loop : -1.50 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1226 HIS 0.005 0.001 HIS B 540 PHE 0.015 0.002 PHE B 944 TYR 0.033 0.002 TYR B1108 ARG 0.016 0.001 ARG B 712 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 130 time to evaluate : 2.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 36 residues processed: 171 average time/residue: 1.9472 time to fit residues: 389.1407 Evaluate side-chains 165 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 129 time to evaluate : 2.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1215 THR Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1250 GLU Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 266 CYS Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 508 ASN Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 809 CYS Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 853 ILE Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 952 ASP Chi-restraints excluded: chain B residue 1085 LEU Chi-restraints excluded: chain B residue 1106 CYS Chi-restraints excluded: chain B residue 1222 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 206 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 184 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 211 optimal weight: 0.7980 chunk 171 optimal weight: 0.4980 chunk 0 optimal weight: 4.9990 chunk 126 optimal weight: 0.7980 chunk 222 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN ** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 GLN B 57 GLN ** B 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1875 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 20006 Z= 0.174 Angle : 0.521 7.250 27279 Z= 0.268 Chirality : 0.041 0.172 3104 Planarity : 0.004 0.069 3593 Dihedral : 7.715 179.755 2822 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.51 % Favored : 96.41 % Rotamer: Outliers : 1.92 % Allowed : 15.61 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: -0.09 (0.16), residues: 2606 helix: 1.25 (0.16), residues: 1112 sheet: -0.33 (0.32), residues: 250 loop : -1.23 (0.17), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B1226 HIS 0.004 0.001 HIS A 688 PHE 0.009 0.001 PHE B1252 TYR 0.014 0.001 TYR A1275 ARG 0.011 0.000 ARG B 712 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 136 time to evaluate : 2.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 26 residues processed: 164 average time/residue: 2.0037 time to fit residues: 388.3596 Evaluate side-chains 158 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 132 time to evaluate : 2.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 952 ASP Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1215 THR Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 809 CYS Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 1085 LEU Chi-restraints excluded: chain B residue 1106 CYS Chi-restraints excluded: chain B residue 1222 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 83 optimal weight: 0.9990 chunk 222 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 247 optimal weight: 0.9980 chunk 205 optimal weight: 5.9990 chunk 114 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1881 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 20006 Z= 0.217 Angle : 0.526 7.503 27279 Z= 0.270 Chirality : 0.041 0.172 3104 Planarity : 0.004 0.080 3593 Dihedral : 7.621 179.982 2816 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.56 % Favored : 95.36 % Rotamer: Outliers : 1.92 % Allowed : 15.80 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: -0.10 (0.16), residues: 2606 helix: 1.25 (0.16), residues: 1116 sheet: -0.45 (0.31), residues: 254 loop : -1.23 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1226 HIS 0.004 0.001 HIS B 100 PHE 0.012 0.001 PHE A1115 TYR 0.018 0.001 TYR B 614 ARG 0.019 0.000 ARG B 712 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 138 time to evaluate : 2.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 29 residues processed: 168 average time/residue: 1.9151 time to fit residues: 376.2250 Evaluate side-chains 159 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 130 time to evaluate : 2.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1157 ASP Chi-restraints excluded: chain A residue 1215 THR Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 809 CYS Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 952 ASP Chi-restraints excluded: chain B residue 1085 LEU Chi-restraints excluded: chain B residue 1106 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 238 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 208 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 246 optimal weight: 3.9990 chunk 154 optimal weight: 0.7980 chunk 150 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN ** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 GLN ** B 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1881 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 20006 Z= 0.199 Angle : 0.522 8.267 27279 Z= 0.268 Chirality : 0.041 0.167 3104 Planarity : 0.004 0.064 3593 Dihedral : 7.574 179.841 2815 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.37 % Favored : 95.55 % Rotamer: Outliers : 1.87 % Allowed : 15.80 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: -0.04 (0.16), residues: 2606 helix: 1.33 (0.16), residues: 1116 sheet: -0.25 (0.32), residues: 238 loop : -1.26 (0.17), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1226 HIS 0.004 0.001 HIS B 100 PHE 0.013 0.001 PHE A1115 TYR 0.015 0.001 TYR B1275 ARG 0.010 0.000 ARG B 712 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 132 time to evaluate : 2.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 29 residues processed: 163 average time/residue: 1.9849 time to fit residues: 378.2577 Evaluate side-chains 158 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 129 time to evaluate : 2.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 952 ASP Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1157 ASP Chi-restraints excluded: chain A residue 1215 THR Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 809 CYS Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 1085 LEU Chi-restraints excluded: chain B residue 1106 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 152 optimal weight: 0.0980 chunk 98 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 156 optimal weight: 0.5980 chunk 168 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1880 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 20006 Z= 0.195 Angle : 0.517 8.297 27279 Z= 0.264 Chirality : 0.041 0.162 3104 Planarity : 0.004 0.062 3593 Dihedral : 7.530 179.705 2815 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.06 % Favored : 95.87 % Rotamer: Outliers : 1.83 % Allowed : 15.90 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.16), residues: 2606 helix: 1.42 (0.16), residues: 1114 sheet: -0.26 (0.32), residues: 238 loop : -1.25 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1226 HIS 0.004 0.001 HIS B 100 PHE 0.016 0.001 PHE A1115 TYR 0.020 0.001 TYR B 614 ARG 0.010 0.000 ARG B1082 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 134 time to evaluate : 2.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 29 residues processed: 163 average time/residue: 1.8300 time to fit residues: 350.5092 Evaluate side-chains 157 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 128 time to evaluate : 2.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1215 THR Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 809 CYS Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 1085 LEU Chi-restraints excluded: chain B residue 1106 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 224 optimal weight: 1.9990 chunk 236 optimal weight: 0.9980 chunk 215 optimal weight: 0.8980 chunk 229 optimal weight: 3.9990 chunk 138 optimal weight: 0.2980 chunk 100 optimal weight: 3.9990 chunk 180 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 217 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN ** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 GLN ** B 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1884 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 20006 Z= 0.207 Angle : 0.522 8.271 27279 Z= 0.266 Chirality : 0.041 0.157 3104 Planarity : 0.005 0.115 3593 Dihedral : 7.501 179.648 2815 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.52 % Favored : 95.40 % Rotamer: Outliers : 1.78 % Allowed : 16.19 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: -0.00 (0.16), residues: 2606 helix: 1.38 (0.16), residues: 1114 sheet: -0.37 (0.32), residues: 242 loop : -1.24 (0.17), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1226 HIS 0.004 0.001 HIS B 100 PHE 0.018 0.001 PHE A1115 TYR 0.010 0.001 TYR A1162 ARG 0.022 0.001 ARG B 712 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 131 time to evaluate : 2.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 30 residues processed: 161 average time/residue: 1.9792 time to fit residues: 371.8261 Evaluate side-chains 156 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 126 time to evaluate : 2.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 952 ASP Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1215 THR Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 809 CYS Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 1085 LEU Chi-restraints excluded: chain B residue 1106 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 243 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 169 optimal weight: 0.8980 chunk 255 optimal weight: 1.9990 chunk 234 optimal weight: 0.0370 chunk 203 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 156 optimal weight: 7.9990 chunk 124 optimal weight: 0.3980 chunk 161 optimal weight: 1.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 891 GLN ** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1880 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.081 20006 Z= 0.166 Angle : 0.514 8.543 27279 Z= 0.261 Chirality : 0.040 0.163 3104 Planarity : 0.004 0.060 3593 Dihedral : 7.439 179.798 2815 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.86 % Favored : 96.06 % Rotamer: Outliers : 1.39 % Allowed : 16.71 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: 0.16 (0.17), residues: 2606 helix: 1.60 (0.16), residues: 1108 sheet: -0.43 (0.32), residues: 246 loop : -1.18 (0.17), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B1226 HIS 0.004 0.001 HIS B 100 PHE 0.016 0.001 PHE A1115 TYR 0.020 0.001 TYR B 614 ARG 0.013 0.000 ARG B 712 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 130 time to evaluate : 2.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 23 residues processed: 152 average time/residue: 1.9697 time to fit residues: 354.1553 Evaluate side-chains 150 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 127 time to evaluate : 2.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1215 THR Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 809 CYS Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 1085 LEU Chi-restraints excluded: chain B residue 1106 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 203 optimal weight: 0.5980 chunk 85 optimal weight: 4.9990 chunk 208 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 37 optimal weight: 0.0040 chunk 178 optimal weight: 4.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.110834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.090219 restraints weight = 198083.717| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 3.89 r_work: 0.3599 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3602 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3602 r_free = 0.3602 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3602 r_free = 0.3602 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3602 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.081 20006 Z= 0.160 Angle : 0.502 9.736 27279 Z= 0.255 Chirality : 0.040 0.151 3104 Planarity : 0.004 0.055 3593 Dihedral : 7.331 179.954 2813 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.78 % Favored : 96.14 % Rotamer: Outliers : 1.34 % Allowed : 16.91 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: 0.33 (0.17), residues: 2606 helix: 1.75 (0.16), residues: 1108 sheet: -0.40 (0.32), residues: 246 loop : -1.10 (0.17), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B1226 HIS 0.005 0.001 HIS B1048 PHE 0.013 0.001 PHE A1115 TYR 0.009 0.001 TYR A1162 ARG 0.012 0.000 ARG B 712 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10558.99 seconds wall clock time: 179 minutes 43.99 seconds (10783.99 seconds total)