Starting phenix.real_space_refine on Sun Apr 14 17:45:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mii_23852/04_2024/7mii_23852_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mii_23852/04_2024/7mii_23852.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mii_23852/04_2024/7mii_23852_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mii_23852/04_2024/7mii_23852_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mii_23852/04_2024/7mii_23852_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mii_23852/04_2024/7mii_23852.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mii_23852/04_2024/7mii_23852.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mii_23852/04_2024/7mii_23852_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mii_23852/04_2024/7mii_23852_trim_updated.pdb" } resolution = 2.7 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= 0.205 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 92 5.16 5 C 10284 2.51 5 N 2768 2.21 5 O 2928 1.98 5 F 12 1.80 5 H 16108 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 68": "OD1" <-> "OD2" Residue "A GLU 75": "OE1" <-> "OE2" Residue "A PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 138": "OE1" <-> "OE2" Residue "A GLU 139": "OE1" <-> "OE2" Residue "A GLU 155": "OE1" <-> "OE2" Residue "A GLU 259": "OE1" <-> "OE2" Residue "A TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 408": "OE1" <-> "OE2" Residue "A PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 476": "OE1" <-> "OE2" Residue "A PHE 482": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 510": "OE1" <-> "OE2" Residue "A PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 528": "OE1" <-> "OE2" Residue "A TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 68": "OD1" <-> "OD2" Residue "B GLU 75": "OE1" <-> "OE2" Residue "B PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B GLU 139": "OE1" <-> "OE2" Residue "B GLU 155": "OE1" <-> "OE2" Residue "B GLU 259": "OE1" <-> "OE2" Residue "B TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 408": "OE1" <-> "OE2" Residue "B PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 476": "OE1" <-> "OE2" Residue "B PHE 482": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 510": "OE1" <-> "OE2" Residue "B PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 528": "OE1" <-> "OE2" Residue "B TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 68": "OD1" <-> "OD2" Residue "C GLU 75": "OE1" <-> "OE2" Residue "C PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 138": "OE1" <-> "OE2" Residue "C GLU 139": "OE1" <-> "OE2" Residue "C GLU 155": "OE1" <-> "OE2" Residue "C GLU 259": "OE1" <-> "OE2" Residue "C TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 408": "OE1" <-> "OE2" Residue "C PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 476": "OE1" <-> "OE2" Residue "C PHE 482": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 510": "OE1" <-> "OE2" Residue "C PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 528": "OE1" <-> "OE2" Residue "C TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 68": "OD1" <-> "OD2" Residue "E GLU 75": "OE1" <-> "OE2" Residue "E PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 138": "OE1" <-> "OE2" Residue "E GLU 139": "OE1" <-> "OE2" Residue "E GLU 155": "OE1" <-> "OE2" Residue "E GLU 259": "OE1" <-> "OE2" Residue "E TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 408": "OE1" <-> "OE2" Residue "E PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 476": "OE1" <-> "OE2" Residue "E PHE 482": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 510": "OE1" <-> "OE2" Residue "E PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 528": "OE1" <-> "OE2" Residue "E TYR 540": "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-5288/modules/chem_data/mon_lib" Total number of atoms: 32208 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 7968 Classifications: {'peptide': 497} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 472} Chain breaks: 5 Chain: "B" Number of atoms: 7968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 7968 Classifications: {'peptide': 497} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 472} Chain breaks: 5 Chain: "C" Number of atoms: 7968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 7968 Classifications: {'peptide': 497} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 472} Chain breaks: 5 Chain: "E" Number of atoms: 7968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 7968 Classifications: {'peptide': 497} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 472} Chain breaks: 5 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Unusual residues: {' MG': 1, 'UTP': 1, 'ZFY': 1} Inner-chain residues flagged as termini: ['pdbres="GLN A 603 "'] Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 3} Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Unusual residues: {' MG': 1, 'UTP': 1, 'ZFY': 1} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 3} Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Unusual residues: {' MG': 1, 'UTP': 1, 'ZFY': 1} Inner-chain residues flagged as termini: ['pdbres="GLN C 603 "'] Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 3} Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Unusual residues: {' MG': 1, 'UTP': 1, 'ZFY': 1} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 3} Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N GLU A 155 " occ=0.75 ... (13 atoms not shown) pdb=" HG3 GLU A 155 " occ=0.75 residue: pdb=" N CYS A 243 " occ=0.75 ... (9 atoms not shown) pdb=" HG CYS A 243 " occ=0.75 residue: pdb=" N GLU B 155 " occ=0.75 ... (13 atoms not shown) pdb=" HG3 GLU B 155 " occ=0.75 residue: pdb=" N CYS B 243 " occ=0.75 ... (9 atoms not shown) pdb=" HG CYS B 243 " occ=0.75 residue: pdb=" N GLU C 155 " occ=0.75 ... (13 atoms not shown) pdb=" HG3 GLU C 155 " occ=0.75 residue: pdb=" N CYS C 243 " occ=0.75 ... (9 atoms not shown) pdb=" HG CYS C 243 " occ=0.75 residue: pdb=" N GLU E 155 " occ=0.75 ... (13 atoms not shown) pdb=" HG3 GLU E 155 " occ=0.75 residue: pdb=" N CYS E 243 " occ=0.75 ... (9 atoms not shown) pdb=" HG CYS E 243 " occ=0.75 Time building chain proxies: 14.46, per 1000 atoms: 0.45 Number of scatterers: 32208 At special positions: 0 Unit cell: (124.95, 133.35, 87.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 92 16.00 P 12 15.00 Mg 4 11.99 F 12 9.00 O 2928 8.00 N 2768 7.00 C 10284 6.00 H 16108 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: 27.55 Conformation dependent library (CDL) restraints added in 3.3 seconds 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 96 helices and 12 sheets defined 41.8% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.42 Creating SS restraints... Processing helix chain 'A' and resid 12 through 14 No H-bonds generated for 'chain 'A' and resid 12 through 14' Processing helix chain 'A' and resid 16 through 29 Processing helix chain 'A' and resid 47 through 49 No H-bonds generated for 'chain 'A' and resid 47 through 49' Processing helix chain 'A' and resid 69 through 78 removed outlier: 3.586A pdb=" N TYR A 74 " --> pdb=" O LEU A 71 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE A 77 " --> pdb=" O TYR A 74 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU A 78 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 86 No H-bonds generated for 'chain 'A' and resid 84 through 86' Processing helix chain 'A' and resid 90 through 102 Processing helix chain 'A' and resid 113 through 129 removed outlier: 7.149A pdb=" N THR A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 168 Proline residue: A 158 - end of helix removed outlier: 3.574A pdb=" N GLU A 161 " --> pdb=" O PRO A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 195 through 206 Processing helix chain 'A' and resid 224 through 233 Processing helix chain 'A' and resid 238 through 240 No H-bonds generated for 'chain 'A' and resid 238 through 240' Processing helix chain 'A' and resid 250 through 260 Proline residue: A 254 - end of helix Processing helix chain 'A' and resid 262 through 269 Processing helix chain 'A' and resid 284 through 294 removed outlier: 3.687A pdb=" N ARG A 294 " --> pdb=" O ASP A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 327 Processing helix chain 'A' and resid 339 through 342 No H-bonds generated for 'chain 'A' and resid 339 through 342' Processing helix chain 'A' and resid 352 through 362 removed outlier: 3.940A pdb=" N GLN A 359 " --> pdb=" O HIS A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 390 Processing helix chain 'A' and resid 399 through 410 removed outlier: 4.262A pdb=" N LEU A 404 " --> pdb=" O GLY A 401 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A 407 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 467 Processing helix chain 'A' and resid 489 through 491 No H-bonds generated for 'chain 'A' and resid 489 through 491' Processing helix chain 'A' and resid 538 through 547 Processing helix chain 'A' and resid 551 through 554 No H-bonds generated for 'chain 'A' and resid 551 through 554' Processing helix chain 'B' and resid 12 through 14 No H-bonds generated for 'chain 'B' and resid 12 through 14' Processing helix chain 'B' and resid 16 through 29 Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 69 through 78 removed outlier: 3.587A pdb=" N TYR B 74 " --> pdb=" O LEU B 71 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE B 77 " --> pdb=" O TYR B 74 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU B 78 " --> pdb=" O GLU B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 86 No H-bonds generated for 'chain 'B' and resid 84 through 86' Processing helix chain 'B' and resid 90 through 102 Processing helix chain 'B' and resid 113 through 129 removed outlier: 7.149A pdb=" N THR B 118 " --> pdb=" O VAL B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 168 Proline residue: B 158 - end of helix removed outlier: 3.574A pdb=" N GLU B 161 " --> pdb=" O PRO B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 195 through 206 Processing helix chain 'B' and resid 224 through 233 Processing helix chain 'B' and resid 238 through 240 No H-bonds generated for 'chain 'B' and resid 238 through 240' Processing helix chain 'B' and resid 250 through 260 Proline residue: B 254 - end of helix Processing helix chain 'B' and resid 262 through 269 Processing helix chain 'B' and resid 284 through 294 removed outlier: 3.687A pdb=" N ARG B 294 " --> pdb=" O ASP B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 327 Processing helix chain 'B' and resid 339 through 342 No H-bonds generated for 'chain 'B' and resid 339 through 342' Processing helix chain 'B' and resid 352 through 362 removed outlier: 3.939A pdb=" N GLN B 359 " --> pdb=" O HIS B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 390 Processing helix chain 'B' and resid 399 through 410 removed outlier: 4.261A pdb=" N LEU B 404 " --> pdb=" O GLY B 401 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE B 407 " --> pdb=" O LEU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 467 Processing helix chain 'B' and resid 489 through 491 No H-bonds generated for 'chain 'B' and resid 489 through 491' Processing helix chain 'B' and resid 538 through 547 Processing helix chain 'B' and resid 551 through 554 No H-bonds generated for 'chain 'B' and resid 551 through 554' Processing helix chain 'C' and resid 12 through 14 No H-bonds generated for 'chain 'C' and resid 12 through 14' Processing helix chain 'C' and resid 16 through 29 Processing helix chain 'C' and resid 47 through 49 No H-bonds generated for 'chain 'C' and resid 47 through 49' Processing helix chain 'C' and resid 69 through 78 removed outlier: 3.585A pdb=" N TYR C 74 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE C 77 " --> pdb=" O TYR C 74 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU C 78 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 86 No H-bonds generated for 'chain 'C' and resid 84 through 86' Processing helix chain 'C' and resid 90 through 102 Processing helix chain 'C' and resid 113 through 129 removed outlier: 7.149A pdb=" N THR C 118 " --> pdb=" O VAL C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 168 Proline residue: C 158 - end of helix removed outlier: 3.574A pdb=" N GLU C 161 " --> pdb=" O PRO C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 195 through 206 Processing helix chain 'C' and resid 224 through 233 Processing helix chain 'C' and resid 238 through 240 No H-bonds generated for 'chain 'C' and resid 238 through 240' Processing helix chain 'C' and resid 250 through 260 Proline residue: C 254 - end of helix Processing helix chain 'C' and resid 262 through 269 Processing helix chain 'C' and resid 284 through 294 removed outlier: 3.687A pdb=" N ARG C 294 " --> pdb=" O ASP C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 327 Processing helix chain 'C' and resid 339 through 342 No H-bonds generated for 'chain 'C' and resid 339 through 342' Processing helix chain 'C' and resid 352 through 362 removed outlier: 3.939A pdb=" N GLN C 359 " --> pdb=" O HIS C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 390 Processing helix chain 'C' and resid 399 through 410 removed outlier: 4.261A pdb=" N LEU C 404 " --> pdb=" O GLY C 401 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE C 407 " --> pdb=" O LEU C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 467 Processing helix chain 'C' and resid 489 through 491 No H-bonds generated for 'chain 'C' and resid 489 through 491' Processing helix chain 'C' and resid 538 through 547 Processing helix chain 'C' and resid 551 through 554 No H-bonds generated for 'chain 'C' and resid 551 through 554' Processing helix chain 'E' and resid 12 through 14 No H-bonds generated for 'chain 'E' and resid 12 through 14' Processing helix chain 'E' and resid 16 through 29 Processing helix chain 'E' and resid 47 through 49 No H-bonds generated for 'chain 'E' and resid 47 through 49' Processing helix chain 'E' and resid 69 through 78 removed outlier: 3.586A pdb=" N TYR E 74 " --> pdb=" O LEU E 71 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE E 77 " --> pdb=" O TYR E 74 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU E 78 " --> pdb=" O GLU E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 86 No H-bonds generated for 'chain 'E' and resid 84 through 86' Processing helix chain 'E' and resid 90 through 102 Processing helix chain 'E' and resid 113 through 129 removed outlier: 7.149A pdb=" N THR E 118 " --> pdb=" O VAL E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 168 Proline residue: E 158 - end of helix removed outlier: 3.576A pdb=" N GLU E 161 " --> pdb=" O PRO E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 195 through 206 Processing helix chain 'E' and resid 224 through 233 Processing helix chain 'E' and resid 238 through 240 No H-bonds generated for 'chain 'E' and resid 238 through 240' Processing helix chain 'E' and resid 250 through 260 Proline residue: E 254 - end of helix Processing helix chain 'E' and resid 262 through 269 Processing helix chain 'E' and resid 284 through 294 removed outlier: 3.687A pdb=" N ARG E 294 " --> pdb=" O ASP E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 327 Processing helix chain 'E' and resid 339 through 342 No H-bonds generated for 'chain 'E' and resid 339 through 342' Processing helix chain 'E' and resid 352 through 362 removed outlier: 3.939A pdb=" N GLN E 359 " --> pdb=" O HIS E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 390 Processing helix chain 'E' and resid 399 through 410 removed outlier: 4.262A pdb=" N LEU E 404 " --> pdb=" O GLY E 401 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE E 407 " --> pdb=" O LEU E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 463 through 467 Processing helix chain 'E' and resid 489 through 491 No H-bonds generated for 'chain 'E' and resid 489 through 491' Processing helix chain 'E' and resid 538 through 547 Processing helix chain 'E' and resid 551 through 554 No H-bonds generated for 'chain 'E' and resid 551 through 554' Processing sheet with id= A, first strand: chain 'A' and resid 241 through 245 removed outlier: 6.170A pdb=" N ILE A 214 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE A 244 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N CYS A 216 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TYR A 3 " --> pdb=" O CYS A 176 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE A 178 " --> pdb=" O TYR A 3 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU A 5 " --> pdb=" O ILE A 178 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL A 180 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR A 7 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N LEU A 182 " --> pdb=" O THR A 7 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N GLY A 9 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY A 8 " --> pdb=" O LEU A 147 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 58 through 60 Processing sheet with id= C, first strand: chain 'A' and resid 331 through 336 removed outlier: 6.702A pdb=" N GLY A 366 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N VAL A 369 " --> pdb=" O PRO A 394 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU A 396 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N PHE A 520 " --> pdb=" O LEU A 514 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLU A 513 " --> pdb=" O PHE A 499 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N PHE A 499 " --> pdb=" O GLU A 513 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 241 through 245 removed outlier: 6.170A pdb=" N ILE B 214 " --> pdb=" O ILE B 242 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE B 244 " --> pdb=" O ILE B 214 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N CYS B 216 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TYR B 3 " --> pdb=" O CYS B 176 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE B 178 " --> pdb=" O TYR B 3 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU B 5 " --> pdb=" O ILE B 178 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL B 180 " --> pdb=" O LEU B 5 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR B 7 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N LEU B 182 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N GLY B 9 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY B 8 " --> pdb=" O LEU B 147 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 58 through 60 Processing sheet with id= F, first strand: chain 'B' and resid 331 through 336 removed outlier: 6.702A pdb=" N GLY B 366 " --> pdb=" O ALA B 302 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N VAL B 369 " --> pdb=" O PRO B 394 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU B 396 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N PHE B 520 " --> pdb=" O LEU B 514 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLU B 513 " --> pdb=" O PHE B 499 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N PHE B 499 " --> pdb=" O GLU B 513 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 241 through 245 removed outlier: 6.170A pdb=" N ILE C 214 " --> pdb=" O ILE C 242 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE C 244 " --> pdb=" O ILE C 214 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N CYS C 216 " --> pdb=" O ILE C 244 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TYR C 3 " --> pdb=" O CYS C 176 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE C 178 " --> pdb=" O TYR C 3 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU C 5 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL C 180 " --> pdb=" O LEU C 5 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR C 7 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N LEU C 182 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N GLY C 9 " --> pdb=" O LEU C 182 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY C 8 " --> pdb=" O LEU C 147 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 58 through 60 Processing sheet with id= I, first strand: chain 'C' and resid 331 through 336 removed outlier: 6.702A pdb=" N GLY C 366 " --> pdb=" O ALA C 302 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL C 369 " --> pdb=" O PRO C 394 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU C 396 " --> pdb=" O VAL C 369 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N PHE C 520 " --> pdb=" O LEU C 514 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLU C 513 " --> pdb=" O PHE C 499 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N PHE C 499 " --> pdb=" O GLU C 513 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 241 through 245 removed outlier: 6.170A pdb=" N ILE E 214 " --> pdb=" O ILE E 242 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ILE E 244 " --> pdb=" O ILE E 214 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N CYS E 216 " --> pdb=" O ILE E 244 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TYR E 3 " --> pdb=" O CYS E 176 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE E 178 " --> pdb=" O TYR E 3 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU E 5 " --> pdb=" O ILE E 178 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL E 180 " --> pdb=" O LEU E 5 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N THR E 7 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N LEU E 182 " --> pdb=" O THR E 7 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N GLY E 9 " --> pdb=" O LEU E 182 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY E 8 " --> pdb=" O LEU E 147 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 58 through 60 Processing sheet with id= L, first strand: chain 'E' and resid 331 through 336 removed outlier: 6.702A pdb=" N GLY E 366 " --> pdb=" O ALA E 302 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL E 369 " --> pdb=" O PRO E 394 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU E 396 " --> pdb=" O VAL E 369 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N PHE E 520 " --> pdb=" O LEU E 514 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLU E 513 " --> pdb=" O PHE E 499 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N PHE E 499 " --> pdb=" O GLU E 513 " (cutoff:3.500A) 596 hydrogen bonds defined for protein. 1464 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: 13.20 Time building geometry restraints manager: 28.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.87 - 1.07: 3570 1.07 - 1.28: 15126 1.28 - 1.48: 6525 1.48 - 1.68: 7163 1.68 - 1.89: 152 Bond restraints: 32536 Sorted by residual: bond pdb=" C2' UTP A 602 " pdb=" C3' UTP A 602 " ideal model delta sigma weight residual 1.301 1.532 -0.231 2.00e-02 2.50e+03 1.33e+02 bond pdb=" C2' UTP C 602 " pdb=" C3' UTP C 602 " ideal model delta sigma weight residual 1.301 1.531 -0.230 2.00e-02 2.50e+03 1.33e+02 bond pdb=" C2' UTP E 603 " pdb=" C3' UTP E 603 " ideal model delta sigma weight residual 1.301 1.530 -0.229 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C2' UTP B 603 " pdb=" C3' UTP B 603 " ideal model delta sigma weight residual 1.301 1.530 -0.229 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C1' UTP E 603 " pdb=" O4' UTP E 603 " ideal model delta sigma weight residual 1.553 1.395 0.158 2.00e-02 2.50e+03 6.25e+01 ... (remaining 32531 not shown) Histogram of bond angle deviations from ideal: 59.61 - 75.33: 20 75.33 - 91.05: 20 91.05 - 106.77: 2245 106.77 - 122.49: 52530 122.49 - 138.21: 4101 Bond angle restraints: 58916 Sorted by residual: angle pdb=" CA ILE A 80 " pdb=" CB ILE A 80 " pdb=" CG1 ILE A 80 " ideal model delta sigma weight residual 110.40 131.81 -21.41 1.70e+00 3.46e-01 1.59e+02 angle pdb=" CA ILE E 80 " pdb=" CB ILE E 80 " pdb=" CG1 ILE E 80 " ideal model delta sigma weight residual 110.40 131.81 -21.41 1.70e+00 3.46e-01 1.59e+02 angle pdb=" CA ILE C 80 " pdb=" CB ILE C 80 " pdb=" CG1 ILE C 80 " ideal model delta sigma weight residual 110.40 131.78 -21.38 1.70e+00 3.46e-01 1.58e+02 angle pdb=" CA ILE B 80 " pdb=" CB ILE B 80 " pdb=" CG1 ILE B 80 " ideal model delta sigma weight residual 110.40 131.78 -21.38 1.70e+00 3.46e-01 1.58e+02 angle pdb=" CG1 ILE C 80 " pdb=" CB ILE C 80 " pdb=" HB ILE C 80 " ideal model delta sigma weight residual 109.00 71.83 37.17 3.00e+00 1.11e-01 1.53e+02 ... (remaining 58911 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.99: 13356 16.99 - 33.98: 986 33.98 - 50.97: 366 50.97 - 67.96: 424 67.96 - 84.96: 80 Dihedral angle restraints: 15212 sinusoidal: 8488 harmonic: 6724 Sorted by residual: dihedral pdb=" C ARG A 217 " pdb=" N ARG A 217 " pdb=" CA ARG A 217 " pdb=" CB ARG A 217 " ideal model delta harmonic sigma weight residual -122.60 -136.39 13.79 0 2.50e+00 1.60e-01 3.04e+01 dihedral pdb=" C ARG C 217 " pdb=" N ARG C 217 " pdb=" CA ARG C 217 " pdb=" CB ARG C 217 " ideal model delta harmonic sigma weight residual -122.60 -136.37 13.77 0 2.50e+00 1.60e-01 3.03e+01 dihedral pdb=" CA PRO A 115 " pdb=" C PRO A 115 " pdb=" N HIS A 116 " pdb=" CA HIS A 116 " ideal model delta harmonic sigma weight residual -180.00 -152.54 -27.46 0 5.00e+00 4.00e-02 3.02e+01 ... (remaining 15209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.194: 2239 0.194 - 0.388: 197 0.388 - 0.582: 24 0.582 - 0.776: 0 0.776 - 0.970: 4 Chirality restraints: 2464 Sorted by residual: chirality pdb=" CB ILE A 80 " pdb=" CA ILE A 80 " pdb=" CG1 ILE A 80 " pdb=" CG2 ILE A 80 " both_signs ideal model delta sigma weight residual False 2.64 1.68 0.97 2.00e-01 2.50e+01 2.35e+01 chirality pdb=" CB ILE B 80 " pdb=" CA ILE B 80 " pdb=" CG1 ILE B 80 " pdb=" CG2 ILE B 80 " both_signs ideal model delta sigma weight residual False 2.64 1.68 0.97 2.00e-01 2.50e+01 2.35e+01 chirality pdb=" CB ILE E 80 " pdb=" CA ILE E 80 " pdb=" CG1 ILE E 80 " pdb=" CG2 ILE E 80 " both_signs ideal model delta sigma weight residual False 2.64 1.68 0.97 2.00e-01 2.50e+01 2.34e+01 ... (remaining 2461 not shown) Planarity restraints: 4688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 285 " -0.153 2.00e-02 2.50e+03 7.10e-02 2.02e+02 pdb=" CG TRP A 285 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP A 285 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP A 285 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 285 " 0.035 2.00e-02 2.50e+03 pdb=" CE2 TRP A 285 " -0.021 2.00e-02 2.50e+03 pdb=" CE3 TRP A 285 " 0.037 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 285 " -0.059 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 285 " 0.031 2.00e-02 2.50e+03 pdb=" CH2 TRP A 285 " -0.035 2.00e-02 2.50e+03 pdb=" HD1 TRP A 285 " 0.009 2.00e-02 2.50e+03 pdb=" HE1 TRP A 285 " 0.156 2.00e-02 2.50e+03 pdb=" HE3 TRP A 285 " 0.083 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 285 " -0.084 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 285 " 0.075 2.00e-02 2.50e+03 pdb=" HH2 TRP A 285 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 285 " 0.153 2.00e-02 2.50e+03 7.10e-02 2.02e+02 pdb=" CG TRP E 285 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP E 285 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP E 285 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 285 " -0.035 2.00e-02 2.50e+03 pdb=" CE2 TRP E 285 " 0.021 2.00e-02 2.50e+03 pdb=" CE3 TRP E 285 " -0.037 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 285 " 0.059 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 285 " -0.032 2.00e-02 2.50e+03 pdb=" CH2 TRP E 285 " 0.035 2.00e-02 2.50e+03 pdb=" HD1 TRP E 285 " -0.008 2.00e-02 2.50e+03 pdb=" HE1 TRP E 285 " -0.156 2.00e-02 2.50e+03 pdb=" HE3 TRP E 285 " -0.083 2.00e-02 2.50e+03 pdb=" HZ2 TRP E 285 " 0.084 2.00e-02 2.50e+03 pdb=" HZ3 TRP E 285 " -0.075 2.00e-02 2.50e+03 pdb=" HH2 TRP E 285 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 285 " -0.153 2.00e-02 2.50e+03 7.09e-02 2.01e+02 pdb=" CG TRP B 285 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP B 285 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP B 285 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 285 " 0.036 2.00e-02 2.50e+03 pdb=" CE2 TRP B 285 " -0.021 2.00e-02 2.50e+03 pdb=" CE3 TRP B 285 " 0.037 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 285 " -0.059 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 285 " 0.031 2.00e-02 2.50e+03 pdb=" CH2 TRP B 285 " -0.036 2.00e-02 2.50e+03 pdb=" HD1 TRP B 285 " 0.008 2.00e-02 2.50e+03 pdb=" HE1 TRP B 285 " 0.156 2.00e-02 2.50e+03 pdb=" HE3 TRP B 285 " 0.083 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 285 " -0.083 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 285 " 0.075 2.00e-02 2.50e+03 pdb=" HH2 TRP B 285 " -0.059 2.00e-02 2.50e+03 ... (remaining 4685 not shown) Histogram of nonbonded interaction distances: 1.21 - 1.89: 468 1.89 - 2.56: 29431 2.56 - 3.24: 104237 3.24 - 3.92: 140046 3.92 - 4.60: 211154 Nonbonded interactions: 485336 Sorted by model distance: nonbonded pdb=" HG CYS C 399 " pdb=" HB2 GLN C 603 " model vdw 1.207 2.440 nonbonded pdb=" HG CYS A 399 " pdb=" HB2 GLN A 603 " model vdw 1.207 2.440 nonbonded pdb=" HG CYS B 399 " pdb=" HB2 GLN B 604 " model vdw 1.208 2.440 nonbonded pdb=" HG CYS E 399 " pdb=" HB2 GLN E 604 " model vdw 1.209 2.440 nonbonded pdb=" HE3 MET A 157 " pdb=" HE3 MET C 157 " model vdw 1.222 2.440 ... (remaining 485331 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 1 through 556) selection = (chain 'B' and resid 1 through 556) selection = (chain 'C' and resid 1 through 556) selection = (chain 'E' and resid 1 through 556) } 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=0.75 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.480 Extract box with map and model: 7.220 Check model and map are aligned: 0.450 Set scattering table: 0.260 Process input model: 108.450 Find NCS groups from input model: 1.720 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 135.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 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 : 0.015 0.231 16428 Z= 0.974 Angle : 2.118 21.408 22228 Z= 1.396 Chirality : 0.127 0.970 2464 Planarity : 0.014 0.112 2816 Dihedral : 15.499 84.956 6236 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.83 % Allowed : 4.13 % Favored : 94.04 % Cbeta Deviations : 1.95 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.16), residues: 1940 helix: -1.33 (0.14), residues: 892 sheet: -1.31 (0.24), residues: 372 loop : -1.10 (0.21), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.109 0.032 TRP B 387 HIS 0.013 0.004 HIS E 323 PHE 0.061 0.016 PHE A 409 TYR 0.155 0.024 TYR C 74 ARG 0.010 0.001 ARG E 205 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 495 time to evaluate : 2.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8132 (mt-10) REVERT: A 333 ASN cc_start: 0.8168 (t0) cc_final: 0.7921 (t0) REVERT: A 392 LYS cc_start: 0.7850 (mttt) cc_final: 0.7595 (mttp) REVERT: A 402 MET cc_start: 0.7837 (ttp) cc_final: 0.7611 (ttp) REVERT: B 75 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8124 (mt-10) REVERT: B 333 ASN cc_start: 0.8187 (t0) cc_final: 0.7933 (t0) REVERT: B 392 LYS cc_start: 0.7845 (mttt) cc_final: 0.7642 (mttp) REVERT: B 402 MET cc_start: 0.7827 (ttp) cc_final: 0.7592 (ttp) REVERT: B 454 ARG cc_start: 0.7853 (ttm170) cc_final: 0.7641 (ttm110) REVERT: C 75 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8116 (mt-10) REVERT: C 333 ASN cc_start: 0.8137 (t0) cc_final: 0.7876 (t0) REVERT: C 392 LYS cc_start: 0.7865 (mttt) cc_final: 0.7651 (mttp) REVERT: C 454 ARG cc_start: 0.7867 (ttm170) cc_final: 0.7614 (ttm110) REVERT: E 75 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8090 (mt-10) REVERT: E 392 LYS cc_start: 0.7838 (mttt) cc_final: 0.7624 (mttp) REVERT: E 402 MET cc_start: 0.7840 (ttp) cc_final: 0.7611 (ttp) REVERT: B 604 GLN cc_start: 0.7371 (pt0) cc_final: 0.7120 (pt0) REVERT: C 603 GLN cc_start: 0.7383 (pt0) cc_final: 0.7140 (pt0) outliers start: 32 outliers final: 4 residues processed: 523 average time/residue: 2.5951 time to fit residues: 1537.3284 Evaluate side-chains 353 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 349 time to evaluate : 2.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain E residue 55 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 0.7980 chunk 148 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 153 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 177 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS A 329 ASN A 359 GLN A 494 GLN A 556 GLN B 96 HIS B 329 ASN B 359 GLN B 494 GLN B 556 GLN C 96 HIS C 165 GLN C 329 ASN C 359 GLN C 494 GLN C 556 GLN E 96 HIS E 112 GLN E 240 GLN E 329 ASN E 359 GLN E 494 GLN E 556 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 16428 Z= 0.239 Angle : 0.646 13.595 22228 Z= 0.331 Chirality : 0.078 1.527 2464 Planarity : 0.005 0.059 2816 Dihedral : 8.895 49.953 2308 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.12 % Allowed : 12.33 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.84 (0.19), residues: 1940 helix: -0.14 (0.17), residues: 900 sheet: -1.03 (0.24), residues: 396 loop : -0.52 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 387 HIS 0.007 0.001 HIS A 235 PHE 0.016 0.002 PHE B 163 TYR 0.017 0.002 TYR E 42 ARG 0.005 0.001 ARG E 532 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 366 time to evaluate : 2.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 LYS cc_start: 0.7262 (mttt) cc_final: 0.6937 (mtpm) REVERT: A 312 ASP cc_start: 0.7344 (m-30) cc_final: 0.7119 (m-30) REVERT: A 392 LYS cc_start: 0.7361 (mttt) cc_final: 0.7124 (mttp) REVERT: A 393 ILE cc_start: 0.7619 (mt) cc_final: 0.7358 (mt) REVERT: B 228 GLU cc_start: 0.7231 (mm-30) cc_final: 0.6994 (mm-30) REVERT: B 312 ASP cc_start: 0.7286 (m-30) cc_final: 0.7057 (m-30) REVERT: B 392 LYS cc_start: 0.7357 (mttt) cc_final: 0.7119 (mttp) REVERT: C 228 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6947 (mm-30) REVERT: C 392 LYS cc_start: 0.7367 (mttt) cc_final: 0.7109 (mttp) REVERT: E 393 ILE cc_start: 0.7713 (mt) cc_final: 0.7465 (mt) REVERT: E 465 ARG cc_start: 0.7259 (ttt180) cc_final: 0.6992 (ttt-90) outliers start: 37 outliers final: 15 residues processed: 387 average time/residue: 2.5978 time to fit residues: 1127.4421 Evaluate side-chains 334 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 319 time to evaluate : 2.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain E residue 55 HIS Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 243 CYS Chi-restraints excluded: chain E residue 498 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 158 optimal weight: 0.4980 chunk 176 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 143 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS A 329 ASN B 179 HIS B 185 GLN B 237 ASN B 329 ASN C 177 ASN C 179 HIS C 185 GLN C 329 ASN E 177 ASN E 179 HIS E 185 GLN E 329 ASN E 502 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.4557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16428 Z= 0.273 Angle : 0.641 15.139 22228 Z= 0.320 Chirality : 0.080 1.589 2464 Planarity : 0.005 0.051 2816 Dihedral : 8.794 55.901 2308 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.64 % Allowed : 13.88 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.77 (0.19), residues: 1940 helix: -0.18 (0.17), residues: 892 sheet: -0.70 (0.25), residues: 392 loop : -0.55 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 387 HIS 0.006 0.002 HIS B 96 PHE 0.017 0.002 PHE A 163 TYR 0.015 0.002 TYR E 42 ARG 0.004 0.001 ARG B 164 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 338 time to evaluate : 2.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8356 (mmtt) cc_final: 0.8150 (mmtt) REVERT: A 284 LYS cc_start: 0.7317 (mttt) cc_final: 0.6981 (mtpm) REVERT: A 300 SER cc_start: 0.7989 (p) cc_final: 0.7778 (p) REVERT: A 392 LYS cc_start: 0.7532 (mttt) cc_final: 0.7211 (mttp) REVERT: A 448 MET cc_start: 0.7782 (ttp) cc_final: 0.7389 (ttp) REVERT: B 70 ASP cc_start: 0.6932 (t0) cc_final: 0.6701 (t70) REVERT: B 284 LYS cc_start: 0.7298 (mttt) cc_final: 0.6969 (mtpm) REVERT: B 312 ASP cc_start: 0.7304 (m-30) cc_final: 0.7041 (m-30) REVERT: C 228 GLU cc_start: 0.7326 (mm-30) cc_final: 0.7084 (mm-30) REVERT: C 284 LYS cc_start: 0.7327 (mttt) cc_final: 0.6973 (mtpm) REVERT: E 109 LYS cc_start: 0.8318 (mmtt) cc_final: 0.8031 (mmmt) REVERT: E 284 LYS cc_start: 0.7313 (mttt) cc_final: 0.6979 (mtpm) REVERT: E 300 SER cc_start: 0.8004 (p) cc_final: 0.7787 (p) outliers start: 46 outliers final: 20 residues processed: 369 average time/residue: 2.4998 time to fit residues: 1039.0107 Evaluate side-chains 328 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 308 time to evaluate : 2.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 55 HIS Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 243 CYS Chi-restraints excluded: chain E residue 498 SER Chi-restraints excluded: chain E residue 537 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 178 optimal weight: 0.9980 chunk 189 optimal weight: 0.7980 chunk 93 optimal weight: 0.0270 chunk 169 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.7638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN A 177 ASN A 329 ASN B 177 ASN B 185 GLN B 237 ASN B 329 ASN C 185 GLN C 240 GLN C 329 ASN E 112 GLN E 122 GLN E 185 GLN E 329 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.4933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16428 Z= 0.193 Angle : 0.566 14.886 22228 Z= 0.279 Chirality : 0.077 1.538 2464 Planarity : 0.004 0.039 2816 Dihedral : 8.021 50.523 2308 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.24 % Allowed : 15.08 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.55 (0.19), residues: 1940 helix: 0.11 (0.17), residues: 896 sheet: -0.53 (0.25), residues: 392 loop : -0.67 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 387 HIS 0.003 0.001 HIS C 116 PHE 0.013 0.001 PHE B 163 TYR 0.013 0.001 TYR A 42 ARG 0.004 0.000 ARG E 465 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 316 time to evaluate : 2.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8351 (mmtt) cc_final: 0.8147 (mmtt) REVERT: A 259 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7157 (mt-10) REVERT: A 284 LYS cc_start: 0.7425 (mttt) cc_final: 0.6988 (mtpm) REVERT: A 392 LYS cc_start: 0.7579 (mttt) cc_final: 0.7354 (mmtp) REVERT: B 191 GLU cc_start: 0.6747 (OUTLIER) cc_final: 0.6008 (tm-30) REVERT: B 259 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7168 (mt-10) REVERT: B 312 ASP cc_start: 0.7193 (m-30) cc_final: 0.6942 (m-30) REVERT: C 71 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8826 (mp) REVERT: C 191 GLU cc_start: 0.6704 (OUTLIER) cc_final: 0.5836 (tm-30) REVERT: C 228 GLU cc_start: 0.7335 (mm-30) cc_final: 0.7106 (mm-30) REVERT: C 259 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7166 (mt-10) REVERT: C 284 LYS cc_start: 0.7429 (mttt) cc_final: 0.6988 (mtpm) REVERT: E 109 LYS cc_start: 0.8306 (mmtt) cc_final: 0.8021 (mmmt) REVERT: E 191 GLU cc_start: 0.6788 (OUTLIER) cc_final: 0.5882 (tm-30) REVERT: E 259 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7150 (mt-10) REVERT: E 284 LYS cc_start: 0.7412 (mttt) cc_final: 0.6994 (mtpm) outliers start: 39 outliers final: 17 residues processed: 342 average time/residue: 2.6555 time to fit residues: 1020.7237 Evaluate side-chains 333 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 308 time to evaluate : 2.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 55 HIS Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain E residue 243 CYS Chi-restraints excluded: chain E residue 259 GLU Chi-restraints excluded: chain E residue 498 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN A 329 ASN A 412 ASN B 122 GLN B 198 GLN B 237 ASN B 329 ASN B 412 ASN C 185 GLN C 198 GLN C 237 ASN C 240 GLN C 329 ASN C 412 ASN E 185 GLN E 198 GLN E 329 ASN E 412 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.5404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 16428 Z= 0.395 Angle : 0.667 15.164 22228 Z= 0.335 Chirality : 0.079 1.540 2464 Planarity : 0.005 0.046 2816 Dihedral : 9.785 61.484 2308 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.04 % Allowed : 14.91 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.90 (0.18), residues: 1940 helix: -0.16 (0.17), residues: 872 sheet: -0.55 (0.26), residues: 368 loop : -0.95 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 387 HIS 0.006 0.002 HIS C 96 PHE 0.016 0.002 PHE B 163 TYR 0.014 0.002 TYR A 292 ARG 0.006 0.001 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 332 time to evaluate : 2.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7972 (OUTLIER) cc_final: 0.7584 (ttm) REVERT: A 71 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8889 (mp) REVERT: A 191 GLU cc_start: 0.6584 (OUTLIER) cc_final: 0.5842 (tm-30) REVERT: A 202 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.7300 (ttp-170) REVERT: A 223 GLU cc_start: 0.7025 (mp0) cc_final: 0.6714 (mt-10) REVERT: A 296 GLN cc_start: 0.7236 (mt0) cc_final: 0.6790 (mm110) REVERT: A 481 ARG cc_start: 0.7221 (OUTLIER) cc_final: 0.6887 (mtp85) REVERT: B 1 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7632 (ttm) REVERT: B 71 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8891 (mp) REVERT: B 191 GLU cc_start: 0.6704 (OUTLIER) cc_final: 0.5918 (tm-30) REVERT: B 202 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.7280 (ttp-170) REVERT: B 312 ASP cc_start: 0.7376 (m-30) cc_final: 0.7052 (m-30) REVERT: B 481 ARG cc_start: 0.7189 (OUTLIER) cc_final: 0.6860 (mtp85) REVERT: C 1 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7601 (ttm) REVERT: C 191 GLU cc_start: 0.6612 (OUTLIER) cc_final: 0.5760 (tm-30) REVERT: C 228 GLU cc_start: 0.7387 (mm-30) cc_final: 0.7148 (mm-30) REVERT: C 259 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7111 (mt-10) REVERT: C 448 MET cc_start: 0.7749 (ttp) cc_final: 0.7484 (ttp) REVERT: C 465 ARG cc_start: 0.7701 (tmt90) cc_final: 0.7419 (ttt-90) REVERT: C 481 ARG cc_start: 0.7255 (OUTLIER) cc_final: 0.6950 (mtp85) REVERT: E 1 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7595 (ttm) REVERT: E 71 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8884 (mp) REVERT: E 109 LYS cc_start: 0.8339 (mmtt) cc_final: 0.8041 (mmmt) REVERT: E 191 GLU cc_start: 0.6706 (OUTLIER) cc_final: 0.5929 (tm-30) REVERT: E 481 ARG cc_start: 0.7243 (OUTLIER) cc_final: 0.6926 (mtp85) outliers start: 53 outliers final: 28 residues processed: 356 average time/residue: 2.6354 time to fit residues: 1050.6290 Evaluate side-chains 368 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 322 time to evaluate : 2.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 481 ARG Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 202 ARG Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 392 LYS Chi-restraints excluded: chain B residue 481 ARG Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain C residue 481 ARG Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 55 HIS Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain E residue 243 CYS Chi-restraints excluded: chain E residue 481 ARG Chi-restraints excluded: chain E residue 498 SER Chi-restraints excluded: chain E residue 537 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 0.9990 chunk 170 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 189 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 62 optimal weight: 0.0770 chunk 99 optimal weight: 1.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN A 329 ASN B 198 GLN B 237 ASN B 329 ASN C 198 GLN C 329 ASN E 198 GLN E 329 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.5480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16428 Z= 0.180 Angle : 0.554 15.110 22228 Z= 0.271 Chirality : 0.076 1.512 2464 Planarity : 0.004 0.041 2816 Dihedral : 8.180 54.906 2308 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.12 % Allowed : 17.03 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 (0.19), residues: 1940 helix: 0.09 (0.17), residues: 896 sheet: -0.31 (0.26), residues: 376 loop : -0.90 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 387 HIS 0.003 0.001 HIS B 116 PHE 0.011 0.001 PHE B 163 TYR 0.012 0.001 TYR A 42 ARG 0.002 0.000 ARG C 479 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 327 time to evaluate : 2.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 GLN cc_start: 0.7212 (mt0) cc_final: 0.6782 (mm110) REVERT: A 481 ARG cc_start: 0.7199 (OUTLIER) cc_final: 0.6847 (mtp85) REVERT: B 259 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6965 (mt-10) REVERT: B 312 ASP cc_start: 0.7211 (m-30) cc_final: 0.6956 (m-30) REVERT: B 481 ARG cc_start: 0.7192 (OUTLIER) cc_final: 0.6865 (mtp85) REVERT: C 71 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8870 (mp) REVERT: C 191 GLU cc_start: 0.6596 (OUTLIER) cc_final: 0.5854 (tm-30) REVERT: C 228 GLU cc_start: 0.7320 (mm-30) cc_final: 0.7056 (mm-30) REVERT: C 448 MET cc_start: 0.7768 (ttp) cc_final: 0.7497 (ttp) REVERT: C 481 ARG cc_start: 0.7276 (OUTLIER) cc_final: 0.6983 (mtp85) REVERT: E 71 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8883 (mp) REVERT: E 109 LYS cc_start: 0.8341 (mmtt) cc_final: 0.8027 (mmmt) REVERT: E 191 GLU cc_start: 0.6589 (OUTLIER) cc_final: 0.5888 (tm-30) REVERT: E 259 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.6951 (mt-10) REVERT: E 481 ARG cc_start: 0.7249 (OUTLIER) cc_final: 0.6932 (mtp85) outliers start: 37 outliers final: 19 residues processed: 347 average time/residue: 2.8157 time to fit residues: 1117.7021 Evaluate side-chains 345 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 316 time to evaluate : 2.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 481 ARG Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 392 LYS Chi-restraints excluded: chain B residue 481 ARG Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 481 ARG Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 55 HIS Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain E residue 224 MET Chi-restraints excluded: chain E residue 243 CYS Chi-restraints excluded: chain E residue 259 GLU Chi-restraints excluded: chain E residue 481 ARG Chi-restraints excluded: chain E residue 498 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 138 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN A 329 ASN B 237 ASN B 329 ASN C 237 ASN C 240 GLN C 329 ASN E 185 GLN E 329 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.5661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16428 Z= 0.263 Angle : 0.587 15.095 22228 Z= 0.289 Chirality : 0.077 1.514 2464 Planarity : 0.005 0.040 2816 Dihedral : 8.633 55.311 2308 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.52 % Allowed : 17.20 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.53 (0.18), residues: 1940 helix: 0.20 (0.17), residues: 872 sheet: -0.36 (0.25), residues: 376 loop : -0.87 (0.22), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 387 HIS 0.005 0.001 HIS E 96 PHE 0.014 0.001 PHE E 163 TYR 0.011 0.002 TYR A 42 ARG 0.004 0.001 ARG C 465 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 324 time to evaluate : 2.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8879 (mp) REVERT: A 259 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6935 (mt-10) REVERT: A 296 GLN cc_start: 0.7194 (mt0) cc_final: 0.6756 (mm110) REVERT: A 448 MET cc_start: 0.7821 (ttp) cc_final: 0.7615 (ttp) REVERT: A 481 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.6922 (mtp85) REVERT: B 71 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8876 (mp) REVERT: B 191 GLU cc_start: 0.6635 (OUTLIER) cc_final: 0.5943 (tm-30) REVERT: B 296 GLN cc_start: 0.7138 (mt0) cc_final: 0.6812 (mm-40) REVERT: B 312 ASP cc_start: 0.7172 (m-30) cc_final: 0.6922 (m-30) REVERT: B 481 ARG cc_start: 0.7248 (OUTLIER) cc_final: 0.6915 (mtp85) REVERT: C 71 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8879 (mp) REVERT: C 191 GLU cc_start: 0.6595 (OUTLIER) cc_final: 0.5869 (tm-30) REVERT: C 228 GLU cc_start: 0.7311 (mm-30) cc_final: 0.7082 (mm-30) REVERT: C 296 GLN cc_start: 0.7202 (mt0) cc_final: 0.6863 (mm110) REVERT: C 448 MET cc_start: 0.7794 (ttp) cc_final: 0.7524 (ttp) REVERT: C 481 ARG cc_start: 0.7322 (OUTLIER) cc_final: 0.7036 (mtp85) REVERT: E 71 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8878 (mp) REVERT: E 109 LYS cc_start: 0.8359 (mmtt) cc_final: 0.8027 (mmmt) REVERT: E 191 GLU cc_start: 0.6596 (OUTLIER) cc_final: 0.5891 (tm-30) REVERT: E 481 ARG cc_start: 0.7236 (OUTLIER) cc_final: 0.6921 (mtp85) outliers start: 44 outliers final: 23 residues processed: 345 average time/residue: 2.5750 time to fit residues: 999.5748 Evaluate side-chains 353 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 318 time to evaluate : 2.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 481 ARG Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 481 ARG Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 481 ARG Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain E residue 224 MET Chi-restraints excluded: chain E residue 243 CYS Chi-restraints excluded: chain E residue 481 ARG Chi-restraints excluded: chain E residue 498 SER Chi-restraints excluded: chain E residue 537 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 148 optimal weight: 0.7980 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN A 329 ASN B 237 ASN B 329 ASN C 112 GLN C 240 GLN C 329 ASN E 185 GLN E 329 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.5763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16428 Z= 0.265 Angle : 0.581 15.119 22228 Z= 0.286 Chirality : 0.076 1.509 2464 Planarity : 0.005 0.041 2816 Dihedral : 8.438 55.442 2302 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.18 % Allowed : 17.89 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.52 (0.18), residues: 1940 helix: 0.21 (0.18), residues: 868 sheet: -0.29 (0.25), residues: 372 loop : -0.91 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 387 HIS 0.006 0.002 HIS B 55 PHE 0.013 0.001 PHE B 163 TYR 0.012 0.002 TYR E 42 ARG 0.008 0.001 ARG C 465 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 324 time to evaluate : 2.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8881 (mp) REVERT: A 191 GLU cc_start: 0.6532 (OUTLIER) cc_final: 0.5836 (tm-30) REVERT: A 259 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6914 (mt-10) REVERT: A 296 GLN cc_start: 0.7183 (mt0) cc_final: 0.6791 (mm110) REVERT: A 448 MET cc_start: 0.7873 (ttp) cc_final: 0.7628 (ttp) REVERT: A 481 ARG cc_start: 0.7207 (OUTLIER) cc_final: 0.6905 (mtp85) REVERT: B 71 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8877 (mp) REVERT: B 191 GLU cc_start: 0.6581 (OUTLIER) cc_final: 0.5896 (tm-30) REVERT: B 259 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6928 (mt-10) REVERT: B 296 GLN cc_start: 0.7156 (mt0) cc_final: 0.6801 (mm-40) REVERT: B 481 ARG cc_start: 0.7159 (OUTLIER) cc_final: 0.6851 (mtp85) REVERT: C 71 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8887 (mp) REVERT: C 191 GLU cc_start: 0.6520 (OUTLIER) cc_final: 0.5836 (tm-30) REVERT: C 228 GLU cc_start: 0.7317 (mm-30) cc_final: 0.7071 (mm-30) REVERT: C 296 GLN cc_start: 0.7183 (mt0) cc_final: 0.6860 (mm110) REVERT: C 448 MET cc_start: 0.7789 (ttp) cc_final: 0.7529 (ttp) REVERT: C 481 ARG cc_start: 0.7244 (OUTLIER) cc_final: 0.6976 (mtp85) REVERT: E 71 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8875 (mp) REVERT: E 109 LYS cc_start: 0.8355 (mmtt) cc_final: 0.8024 (mmmt) REVERT: E 191 GLU cc_start: 0.6594 (OUTLIER) cc_final: 0.5892 (tm-30) REVERT: E 259 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6931 (mt-10) REVERT: E 481 ARG cc_start: 0.7232 (OUTLIER) cc_final: 0.6950 (mtp85) outliers start: 38 outliers final: 18 residues processed: 346 average time/residue: 2.6529 time to fit residues: 1029.4580 Evaluate side-chains 350 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 317 time to evaluate : 2.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 481 ARG Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 481 ARG Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 481 ARG Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain E residue 243 CYS Chi-restraints excluded: chain E residue 259 GLU Chi-restraints excluded: chain E residue 481 ARG Chi-restraints excluded: chain E residue 498 SER Chi-restraints excluded: chain E residue 537 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 1.9990 chunk 180 optimal weight: 5.9990 chunk 165 optimal weight: 0.9990 chunk 176 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 chunk 175 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN A 329 ASN B 112 GLN B 237 ASN B 329 ASN C 237 ASN C 240 GLN C 329 ASN E 329 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.5895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16428 Z= 0.304 Angle : 0.603 15.177 22228 Z= 0.298 Chirality : 0.077 1.517 2464 Planarity : 0.005 0.040 2816 Dihedral : 8.821 56.043 2300 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.12 % Allowed : 18.12 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 (0.18), residues: 1940 helix: 0.13 (0.17), residues: 868 sheet: -0.31 (0.26), residues: 372 loop : -0.94 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 387 HIS 0.005 0.002 HIS B 96 PHE 0.015 0.001 PHE E 163 TYR 0.012 0.002 TYR B 265 ARG 0.007 0.001 ARG A 465 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 322 time to evaluate : 2.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8890 (mp) REVERT: A 110 THR cc_start: 0.8547 (m) cc_final: 0.8331 (m) REVERT: A 191 GLU cc_start: 0.6515 (OUTLIER) cc_final: 0.5827 (tm-30) REVERT: A 259 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6904 (mt-10) REVERT: A 296 GLN cc_start: 0.7193 (mt0) cc_final: 0.6795 (mm110) REVERT: A 448 MET cc_start: 0.7843 (ttp) cc_final: 0.7609 (ttp) REVERT: A 481 ARG cc_start: 0.7200 (OUTLIER) cc_final: 0.6903 (mtp85) REVERT: B 71 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8885 (mp) REVERT: B 191 GLU cc_start: 0.6630 (OUTLIER) cc_final: 0.5915 (tm-30) REVERT: B 259 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6922 (mt-10) REVERT: B 296 GLN cc_start: 0.7131 (mt0) cc_final: 0.6792 (mm-40) REVERT: B 481 ARG cc_start: 0.7154 (OUTLIER) cc_final: 0.6841 (mtp85) REVERT: C 71 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8892 (mp) REVERT: C 191 GLU cc_start: 0.6613 (OUTLIER) cc_final: 0.5881 (tm-30) REVERT: C 228 GLU cc_start: 0.7338 (mm-30) cc_final: 0.7121 (mm-30) REVERT: C 296 GLN cc_start: 0.7198 (mt0) cc_final: 0.6897 (mm110) REVERT: C 448 MET cc_start: 0.7789 (ttp) cc_final: 0.7470 (ttp) REVERT: C 481 ARG cc_start: 0.7235 (OUTLIER) cc_final: 0.6973 (mtp85) REVERT: E 71 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8886 (mp) REVERT: E 109 LYS cc_start: 0.8371 (mmtt) cc_final: 0.8043 (mmmt) REVERT: E 191 GLU cc_start: 0.6597 (OUTLIER) cc_final: 0.5896 (tm-30) REVERT: E 259 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6931 (mt-10) REVERT: E 296 GLN cc_start: 0.7188 (mt0) cc_final: 0.6746 (mm110) REVERT: E 481 ARG cc_start: 0.7228 (OUTLIER) cc_final: 0.6955 (mtp85) outliers start: 37 outliers final: 19 residues processed: 344 average time/residue: 2.6565 time to fit residues: 1024.8000 Evaluate side-chains 354 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 320 time to evaluate : 2.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 481 ARG Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 481 ARG Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 481 ARG Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain E residue 243 CYS Chi-restraints excluded: chain E residue 259 GLU Chi-restraints excluded: chain E residue 481 ARG Chi-restraints excluded: chain E residue 498 SER Chi-restraints excluded: chain E residue 537 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 195 optimal weight: 0.9980 chunk 179 optimal weight: 0.1980 chunk 155 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 120 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN A 329 ASN B 237 ASN B 329 ASN C 240 GLN C 329 ASN E 329 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.5917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16428 Z= 0.196 Angle : 0.557 15.177 22228 Z= 0.272 Chirality : 0.076 1.517 2464 Planarity : 0.004 0.042 2816 Dihedral : 7.889 55.255 2300 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.18 % Allowed : 17.95 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.48 (0.19), residues: 1940 helix: 0.23 (0.18), residues: 892 sheet: -0.22 (0.26), residues: 372 loop : -0.93 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 387 HIS 0.003 0.001 HIS B 96 PHE 0.011 0.001 PHE E 163 TYR 0.012 0.001 TYR E 42 ARG 0.003 0.000 ARG E 465 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 324 time to evaluate : 2.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 HIS cc_start: 0.7709 (m90) cc_final: 0.7477 (m90) REVERT: A 71 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8882 (mp) REVERT: A 259 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6919 (mt-10) REVERT: A 284 LYS cc_start: 0.7546 (mmtp) cc_final: 0.6870 (ptmm) REVERT: A 296 GLN cc_start: 0.7204 (mt0) cc_final: 0.6906 (mm110) REVERT: A 448 MET cc_start: 0.7744 (ttp) cc_final: 0.7462 (ttp) REVERT: A 481 ARG cc_start: 0.7207 (OUTLIER) cc_final: 0.6907 (mtp85) REVERT: B 71 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8879 (mp) REVERT: B 191 GLU cc_start: 0.6625 (OUTLIER) cc_final: 0.5904 (tm-30) REVERT: B 259 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6915 (mt-10) REVERT: B 296 GLN cc_start: 0.7146 (mt0) cc_final: 0.6802 (mm-40) REVERT: B 465 ARG cc_start: 0.7659 (ttt-90) cc_final: 0.7447 (ttt-90) REVERT: B 481 ARG cc_start: 0.7157 (OUTLIER) cc_final: 0.6850 (mtp85) REVERT: C 71 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8886 (mp) REVERT: C 191 GLU cc_start: 0.6568 (OUTLIER) cc_final: 0.5898 (tm-30) REVERT: C 228 GLU cc_start: 0.7355 (mm-30) cc_final: 0.7124 (mm-30) REVERT: C 296 GLN cc_start: 0.7208 (mt0) cc_final: 0.6922 (mm110) REVERT: C 448 MET cc_start: 0.7764 (ttp) cc_final: 0.7507 (ttp) REVERT: C 481 ARG cc_start: 0.7246 (OUTLIER) cc_final: 0.6978 (mtp85) REVERT: E 71 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8877 (mp) REVERT: E 109 LYS cc_start: 0.8336 (mmtt) cc_final: 0.7995 (mmmt) REVERT: E 191 GLU cc_start: 0.6595 (OUTLIER) cc_final: 0.5910 (tm-30) REVERT: E 259 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6918 (mt-10) REVERT: E 296 GLN cc_start: 0.7194 (mt0) cc_final: 0.6768 (mm110) REVERT: E 481 ARG cc_start: 0.7254 (OUTLIER) cc_final: 0.6981 (mtp85) outliers start: 38 outliers final: 15 residues processed: 348 average time/residue: 2.6089 time to fit residues: 1018.9638 Evaluate side-chains 349 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 320 time to evaluate : 2.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 481 ARG Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 481 ARG Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 481 ARG Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain E residue 243 CYS Chi-restraints excluded: chain E residue 259 GLU Chi-restraints excluded: chain E residue 481 ARG Chi-restraints excluded: chain E residue 498 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 0.0970 chunk 165 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 155 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 159 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN A 329 ASN B 237 ASN B 329 ASN C 185 GLN C 240 GLN C 329 ASN E 329 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.156429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.128676 restraints weight = 49382.927| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.57 r_work: 0.3302 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3150 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.5994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16428 Z= 0.173 Angle : 0.548 15.253 22228 Z= 0.265 Chirality : 0.076 1.522 2464 Planarity : 0.004 0.041 2816 Dihedral : 7.262 54.428 2300 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.61 % Allowed : 18.98 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 (0.19), residues: 1940 helix: 0.45 (0.18), residues: 892 sheet: -0.13 (0.26), residues: 372 loop : -0.86 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 387 HIS 0.003 0.001 HIS A 96 PHE 0.012 0.001 PHE C 163 TYR 0.012 0.001 TYR E 42 ARG 0.005 0.000 ARG A 465 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15450.45 seconds wall clock time: 272 minutes 47.67 seconds (16367.67 seconds total)