Starting phenix.real_space_refine on Mon Mar 11 15:25:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8by8_16324/03_2024/8by8_16324.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8by8_16324/03_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_16324/03_2024/8by8_16324.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8by8_16324/03_2024/8by8_16324.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8by8_16324/03_2024/8by8_16324.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8by8_16324/03_2024/8by8_16324.pdb" } 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 Residue "A TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 41": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 49": "OE1" <-> "OE2" Residue "A ARG 52": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 60": "OE1" <-> "OE2" Residue "A GLU 69": "OE1" <-> "OE2" Residue "A ARG 172": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 236": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 277": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 315": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 315": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 375": "OE1" <-> "OE2" Residue "A ARG 420": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 471": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 512": "OE1" <-> "OE2" Residue "A TYR 522": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 616": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 618": "OE1" <-> "OE2" Residue "A GLU 652": "OE1" <-> "OE2" Residue "A GLU 735": "OE1" <-> "OE2" Residue "A ARG 781": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 827": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 869": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 898": "OE1" <-> "OE2" Residue "A ASP 901": "OD1" <-> "OD2" Residue "A ARG 908": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 938": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1057": "OE1" <-> "OE2" Residue "A GLU 1194": "OE1" <-> "OE2" Residue "A GLU 1244": "OE1" <-> "OE2" Residue "A PHE 1252": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1260": "OE1" <-> "OE2" Residue "B TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 30": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 52": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 236": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 277": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 277": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 330": "OD1" <-> "OD2" Residue "B PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 375": "OE1" <-> "OE2" Residue "B ARG 616": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 652": "OE1" <-> "OE2" Residue "B GLU 674": "OE1" <-> "OE2" Residue "B GLU 699": "OE1" <-> "OE2" Residue "B GLU 705": "OE1" <-> "OE2" Residue "B ARG 768": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 775": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 869": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 973": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 1013": "OE1" <-> "OE2" Residue "B TYR 1018": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 1073": "OE1" <-> "OE2" Residue "B PHE 1074": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1115": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 1182": "OE1" <-> "OE2" Residue "B PHE 1216": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 1237": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 1250": "OE1" <-> "OE2" Residue "B TYR 1275": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 23.75, 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 - 3.50 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: 23.03 Conformation dependent library (CDL) restraints added in 6.6 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: 2.47 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: 13.17 Time building geometry restraints manager: 24.45 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: 100.10 - 106.88: 846 106.88 - 113.67: 46685 113.67 - 120.45: 12205 120.45 - 127.23: 10855 127.23 - 134.02: 288 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 1.850 nonbonded pdb=" O VAL B 883 " pdb="HE22 GLN B 899 " model vdw 1.546 1.850 nonbonded pdb=" O SER A 841 " pdb="HD21 ASN A 845 " model vdw 1.574 1.850 nonbonded pdb=" O SER B 841 " pdb="HD21 ASN B 845 " model vdw 1.579 1.850 nonbonded pdb=" O VAL A 883 " pdb="HE22 GLN A 899 " model vdw 1.603 1.850 ... (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 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: 3.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.260 Construct map_model_manager: 0.440 Extract box with map and model: 12.100 Check model and map are aligned: 0.440 Set scattering table: 0.260 Process input model: 109.580 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.140 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: 0.000 Load rotamer database and sin/cos tables:9.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 137.090 ------------------------------------------------------------------------------- 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 : 2.218 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: 1.9654 time to fit residues: 530.7163 Evaluate side-chains 158 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 135 time to evaluate : 2.187 ------------------------------------------------------------------------------- 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: 4.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.8980 chunk 149 optimal weight: 0.0070 chunk 232 optimal weight: 10.0000 overall best weight: 1.9804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 891 GLN A 953 GLN ** A1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 GLN B 395 GLN B1083 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1861 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 20006 Z= 0.278 Angle : 0.541 6.211 27279 Z= 0.282 Chirality : 0.042 0.191 3104 Planarity : 0.004 0.078 3593 Dihedral : 8.114 179.834 2832 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.33 % Favored : 95.55 % Rotamer: Outliers : 2.40 % Allowed : 12.15 % Favored : 85.45 % 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: -0.14 (0.16), residues: 2606 helix: 1.06 (0.16), residues: 1126 sheet: -0.06 (0.33), residues: 244 loop : -1.20 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1226 HIS 0.004 0.001 HIS B 253 PHE 0.011 0.002 PHE A 944 TYR 0.010 0.001 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: 47 poor density : 142 time to evaluate : 2.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 36 residues processed: 183 average time/residue: 2.0467 time to fit residues: 439.2946 Evaluate side-chains 173 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 137 time to evaluate : 2.201 ------------------------------------------------------------------------------- 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 492 SER 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 697 SER 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 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 974 SER Chi-restraints excluded: chain A residue 1151 VAL 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 319 SER 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 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 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: 4.9990 chunk 72 optimal weight: 5.9990 chunk 193 optimal weight: 0.3980 chunk 158 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 232 optimal weight: 10.0000 chunk 251 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 230 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 186 optimal weight: 3.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1882 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 20006 Z= 0.344 Angle : 0.575 6.594 27279 Z= 0.302 Chirality : 0.043 0.185 3104 Planarity : 0.005 0.056 3593 Dihedral : 8.193 179.701 2831 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.01 % Favored : 93.88 % Rotamer: Outliers : 2.83 % Allowed : 13.45 % Favored : 83.72 % 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: -0.60 (0.16), residues: 2606 helix: 0.66 (0.15), residues: 1126 sheet: -0.34 (0.33), residues: 246 loop : -1.42 (0.17), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1226 HIS 0.004 0.001 HIS B 540 PHE 0.014 0.002 PHE B 944 TYR 0.072 0.002 TYR B1108 ARG 0.010 0.001 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 197 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 142 time to evaluate : 2.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 41 residues processed: 189 average time/residue: 1.8034 time to fit residues: 400.4916 Evaluate side-chains 175 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 134 time to evaluate : 2.208 ------------------------------------------------------------------------------- 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 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 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 89 CYS Chi-restraints excluded: chain B residue 119 CYS 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 673 THR Chi-restraints excluded: chain B residue 697 SER Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 808 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 Chi-restraints excluded: chain B residue 1222 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 230 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 120 optimal weight: 0.0980 chunk 25 optimal weight: 2.9990 chunk 111 optimal weight: 8.9990 chunk 156 optimal weight: 6.9990 chunk 233 optimal weight: 0.9990 chunk 247 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 221 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1877 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 20006 Z= 0.213 Angle : 0.525 6.800 27279 Z= 0.271 Chirality : 0.041 0.173 3104 Planarity : 0.004 0.076 3593 Dihedral : 8.064 179.732 2831 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.49 % Favored : 95.40 % Rotamer: Outliers : 2.50 % Allowed : 14.51 % Favored : 83.00 % 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: -0.25 (0.16), residues: 2606 helix: 1.05 (0.16), residues: 1128 sheet: -0.39 (0.33), residues: 248 loop : -1.29 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1226 HIS 0.004 0.001 HIS A 688 PHE 0.009 0.001 PHE B 944 TYR 0.033 0.001 TYR B1108 ARG 0.016 0.000 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 191 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 143 time to evaluate : 2.226 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: 0.4541 (mmt) cc_final: 0.4317 (mtt) outliers start: 48 outliers final: 36 residues processed: 184 average time/residue: 1.8797 time to fit residues: 406.9762 Evaluate side-chains 172 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 136 time to evaluate : 2.250 ------------------------------------------------------------------------------- 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 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 702 SER Chi-restraints excluded: chain A residue 729 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 119 CYS Chi-restraints excluded: chain B residue 241 THR 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 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 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 1085 LEU Chi-restraints excluded: chain B residue 1106 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 206 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 184 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 211 optimal weight: 1.9990 chunk 171 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 126 optimal weight: 0.5980 chunk 222 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 ASN ** A1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 GLN B 57 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1878 moved from start: 0.1550 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= 0.205 Angle : 0.515 6.833 27279 Z= 0.264 Chirality : 0.041 0.173 3104 Planarity : 0.004 0.044 3593 Dihedral : 7.966 179.808 2830 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.64 % Favored : 95.24 % Rotamer: Outliers : 2.40 % Allowed : 14.99 % Favored : 82.61 % 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: -0.11 (0.16), residues: 2606 helix: 1.21 (0.16), residues: 1116 sheet: -0.40 (0.33), residues: 248 loop : -1.22 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1226 HIS 0.004 0.001 HIS A 778 PHE 0.009 0.001 PHE B 944 TYR 0.014 0.001 TYR B1108 ARG 0.012 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 187 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 141 time to evaluate : 2.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 35 residues processed: 179 average time/residue: 1.9016 time to fit residues: 398.0677 Evaluate side-chains 171 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 136 time to evaluate : 2.173 ------------------------------------------------------------------------------- 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 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 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 1157 ASP 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 319 SER 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 697 SER 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 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: 0.9980 chunk 222 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 145 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 247 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1883 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 20006 Z= 0.247 Angle : 0.531 7.410 27279 Z= 0.274 Chirality : 0.041 0.165 3104 Planarity : 0.004 0.097 3593 Dihedral : 7.885 179.835 2825 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.99 % Favored : 94.89 % Rotamer: Outliers : 2.45 % Allowed : 15.37 % Favored : 82.18 % 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: -0.24 (0.16), residues: 2606 helix: 1.08 (0.16), residues: 1126 sheet: -0.36 (0.33), residues: 244 loop : -1.30 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1226 HIS 0.003 0.001 HIS B 100 PHE 0.013 0.001 PHE A1115 TYR 0.020 0.001 TYR B 614 ARG 0.017 0.001 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 186 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 139 time to evaluate : 2.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 35 residues processed: 178 average time/residue: 1.9108 time to fit residues: 397.2127 Evaluate side-chains 171 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 136 time to evaluate : 2.203 ------------------------------------------------------------------------------- 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 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 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 1157 ASP 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 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 808 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 238 optimal weight: 9.9990 chunk 27 optimal weight: 0.6980 chunk 141 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 208 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 chunk 246 optimal weight: 0.7980 chunk 154 optimal weight: 0.0970 chunk 150 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1876 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 20006 Z= 0.175 Angle : 0.506 7.587 27279 Z= 0.258 Chirality : 0.040 0.159 3104 Planarity : 0.004 0.059 3593 Dihedral : 7.745 179.724 2823 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.98 % Favored : 95.90 % Rotamer: Outliers : 1.97 % Allowed : 16.14 % 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: 0.07 (0.16), residues: 2606 helix: 1.38 (0.16), residues: 1128 sheet: -0.32 (0.32), residues: 254 loop : -1.17 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B1226 HIS 0.003 0.001 HIS B 100 PHE 0.013 0.001 PHE A1115 TYR 0.013 0.001 TYR B1275 ARG 0.013 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 178 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 141 time to evaluate : 2.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 33 residues processed: 174 average time/residue: 1.9209 time to fit residues: 392.8670 Evaluate side-chains 167 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 134 time to evaluate : 2.214 ------------------------------------------------------------------------------- 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 368 ILE 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 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 15 GLN Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 382 SER 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 808 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 152 optimal weight: 0.0170 chunk 98 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 156 optimal weight: 6.9990 chunk 168 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 22 optimal weight: 0.2980 chunk 193 optimal weight: 0.2980 overall best weight: 0.8820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1874 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 20006 Z= 0.176 Angle : 0.507 8.337 27279 Z= 0.257 Chirality : 0.040 0.159 3104 Planarity : 0.004 0.082 3593 Dihedral : 7.698 179.764 2823 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.02 % Favored : 95.90 % Rotamer: Outliers : 1.87 % Allowed : 16.33 % Favored : 81.80 % 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: 0.15 (0.16), residues: 2606 helix: 1.47 (0.16), residues: 1128 sheet: -0.31 (0.33), residues: 244 loop : -1.12 (0.17), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B1226 HIS 0.004 0.001 HIS B 100 PHE 0.017 0.001 PHE A1115 TYR 0.020 0.001 TYR B 614 ARG 0.017 0.000 ARG B 712 *********************** 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 172 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 137 time to evaluate : 2.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 32 residues processed: 167 average time/residue: 1.9168 time to fit residues: 374.7623 Evaluate side-chains 168 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 136 time to evaluate : 2.207 ------------------------------------------------------------------------------- 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 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 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 241 THR Chi-restraints excluded: chain B residue 382 SER 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 808 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 224 optimal weight: 2.9990 chunk 236 optimal weight: 0.8980 chunk 215 optimal weight: 3.9990 chunk 229 optimal weight: 2.9990 chunk 138 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 217 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1886 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 20006 Z= 0.267 Angle : 0.538 8.448 27279 Z= 0.276 Chirality : 0.041 0.152 3104 Planarity : 0.004 0.053 3593 Dihedral : 7.750 179.781 2823 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.38 % Favored : 94.54 % Rotamer: Outliers : 2.11 % Allowed : 16.19 % Favored : 81.70 % 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: 1.16 (0.16), residues: 1128 sheet: -0.44 (0.32), residues: 248 loop : -1.29 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A1226 HIS 0.003 0.001 HIS B 100 PHE 0.017 0.001 PHE A1115 TYR 0.010 0.001 TYR B 993 ARG 0.011 0.000 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 174 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 134 time to evaluate : 2.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 35 residues processed: 170 average time/residue: 1.9372 time to fit residues: 386.0343 Evaluate side-chains 168 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 133 time to evaluate : 2.191 ------------------------------------------------------------------------------- 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 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 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 319 SER Chi-restraints excluded: chain B residue 382 SER 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 808 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 243 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 169 optimal weight: 0.4980 chunk 255 optimal weight: 1.9990 chunk 234 optimal weight: 0.2980 chunk 203 optimal weight: 0.0970 chunk 21 optimal weight: 4.9990 chunk 156 optimal weight: 0.2980 chunk 124 optimal weight: 0.3980 chunk 161 optimal weight: 0.7980 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** A1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.1883 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.186 20006 Z= 0.298 Angle : 0.719 61.598 27279 Z= 0.353 Chirality : 0.043 0.782 3104 Planarity : 0.004 0.053 3593 Dihedral : 7.682 179.759 2820 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.34 % Favored : 94.54 % Rotamer: Outliers : 2.07 % Allowed : 16.33 % Favored : 81.60 % Cbeta Deviations : 0.04 % 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: -0.19 (0.16), residues: 2606 helix: 1.15 (0.16), residues: 1128 sheet: -0.45 (0.32), residues: 248 loop : -1.29 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1226 HIS 0.004 0.001 HIS B 100 PHE 0.016 0.001 PHE A1115 TYR 0.010 0.001 TYR B 993 ARG 0.008 0.000 ARG B1082 ********************** 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 171 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 132 time to evaluate : 2.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 36 residues processed: 165 average time/residue: 1.9303 time to fit residues: 371.4719 Evaluate side-chains 168 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 132 time to evaluate : 2.205 ------------------------------------------------------------------------------- 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 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 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 241 THR Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 461 ARG 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 790 LYS Chi-restraints excluded: chain B residue 808 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 187 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 203 optimal weight: 0.3980 chunk 85 optimal weight: 4.9990 chunk 208 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 chunk 178 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** A1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.108852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.088150 restraints weight = 197825.066| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 3.88 r_work: 0.3552 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3556 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3556 r_free = 0.3556 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3556 r_free = 0.3556 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3556 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.186 20006 Z= 0.298 Angle : 0.719 61.598 27279 Z= 0.353 Chirality : 0.043 0.782 3104 Planarity : 0.004 0.053 3593 Dihedral : 7.682 179.759 2820 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.34 % Favored : 94.54 % Rotamer: Outliers : 1.97 % Allowed : 16.43 % Favored : 81.60 % Cbeta Deviations : 0.04 % 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: -0.19 (0.16), residues: 2606 helix: 1.15 (0.16), residues: 1128 sheet: -0.45 (0.32), residues: 248 loop : -1.29 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1226 HIS 0.004 0.001 HIS B 100 PHE 0.016 0.001 PHE A1115 TYR 0.010 0.001 TYR B 993 ARG 0.008 0.000 ARG B1082 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10452.10 seconds wall clock time: 180 minutes 27.03 seconds (10827.03 seconds total)