Starting phenix.real_space_refine on Wed Feb 21 17:10:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mih_23851/02_2024/7mih_23851_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mih_23851/02_2024/7mih_23851.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mih_23851/02_2024/7mih_23851_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mih_23851/02_2024/7mih_23851_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mih_23851/02_2024/7mih_23851_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mih_23851/02_2024/7mih_23851.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mih_23851/02_2024/7mih_23851.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mih_23851/02_2024/7mih_23851_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mih_23851/02_2024/7mih_23851_trim_updated.pdb" } resolution = 2.8 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= 0.202 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: 7 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 92 5.16 5 C 9984 2.51 5 N 2684 2.21 5 O 2840 1.98 5 H 15640 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 75": "OE1" <-> "OE2" Residue "A GLU 138": "OE1" <-> "OE2" Residue "A GLU 139": "OE1" <-> "OE2" Residue "A GLU 155": "OE1" <-> "OE2" Residue "A GLU 173": "OE1" <-> "OE2" Residue "A GLU 223": "OE1" <-> "OE2" Residue "A GLU 259": "OE1" <-> "OE2" Residue "A TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 513": "OE1" <-> "OE2" Residue "A PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 554": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 75": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B GLU 139": "OE1" <-> "OE2" Residue "B GLU 155": "OE1" <-> "OE2" Residue "B GLU 173": "OE1" <-> "OE2" Residue "B GLU 223": "OE1" <-> "OE2" Residue "B GLU 259": "OE1" <-> "OE2" Residue "B TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 513": "OE1" <-> "OE2" Residue "B PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 554": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 75": "OE1" <-> "OE2" Residue "C GLU 138": "OE1" <-> "OE2" Residue "C GLU 139": "OE1" <-> "OE2" Residue "C GLU 155": "OE1" <-> "OE2" Residue "C GLU 173": "OE1" <-> "OE2" Residue "C GLU 223": "OE1" <-> "OE2" Residue "C GLU 259": "OE1" <-> "OE2" Residue "C TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 513": "OE1" <-> "OE2" Residue "C PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 554": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 75": "OE1" <-> "OE2" Residue "E GLU 138": "OE1" <-> "OE2" Residue "E GLU 139": "OE1" <-> "OE2" Residue "E GLU 155": "OE1" <-> "OE2" Residue "E GLU 173": "OE1" <-> "OE2" Residue "E GLU 223": "OE1" <-> "OE2" Residue "E GLU 259": "OE1" <-> "OE2" Residue "E TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 513": "OE1" <-> "OE2" Residue "E PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 554": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 31256 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 7731 Classifications: {'peptide': 483} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 459} Chain breaks: 6 Chain: "B" Number of atoms: 7731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 7731 Classifications: {'peptide': 483} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 459} Chain breaks: 6 Chain: "C" Number of atoms: 7731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 7731 Classifications: {'peptide': 483} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 459} Chain breaks: 6 Chain: "E" Number of atoms: 7731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 7731 Classifications: {'peptide': 483} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 459} Chain breaks: 6 Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 83 Unusual residues: {' MG': 1, 'UTP': 1, 'ZG4': 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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 83 Unusual residues: {' MG': 1, 'UTP': 1, 'ZG4': 1} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 3} Chain: "C" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 83 Unusual residues: {' MG': 1, 'UTP': 1, 'ZG4': 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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 83 Unusual residues: {' MG': 1, 'UTP': 1, 'ZG4': 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: 15.20, per 1000 atoms: 0.49 Number of scatterers: 31256 At special positions: 0 Unit cell: (124.95, 139.65, 87.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 92 16.00 P 12 15.00 Mg 4 11.99 O 2840 8.00 N 2684 7.00 C 9984 6.00 H 15640 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: 26.45 Conformation dependent library (CDL) restraints added in 3.4 seconds 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3584 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 88 helices and 8 sheets defined 42.1% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.08 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 69 through 78 removed outlier: 3.739A pdb=" N PHE A 77 " --> pdb=" O TYR A 74 " (cutoff:3.500A) removed outlier: 3.633A 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 103 Processing helix chain 'A' and resid 113 through 129 removed outlier: 7.115A 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: 3.732A pdb=" N GLU A 161 " --> pdb=" O PRO A 158 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN A 167 " --> pdb=" O ARG A 164 " (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 270 Processing helix chain 'A' and resid 284 through 294 Processing helix chain 'A' and resid 315 through 328 Processing helix chain 'A' and resid 357 through 362 Processing helix chain 'A' and resid 380 through 391 removed outlier: 3.567A pdb=" N ILE A 385 " --> pdb=" O LEU A 382 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER A 386 " --> pdb=" O GLN A 383 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TRP A 387 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS A 391 " --> pdb=" O ALA A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 409 removed outlier: 4.042A pdb=" N LEU A 404 " --> pdb=" O GLY A 401 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE A 409 " --> pdb=" O VAL A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 467 Processing helix chain 'A' and resid 486 through 491 removed outlier: 3.529A pdb=" N ILE A 489 " --> pdb=" O PRO A 486 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LYS A 490 " --> pdb=" O ASN A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 548 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 69 through 78 removed outlier: 3.739A pdb=" N PHE B 77 " --> pdb=" O TYR B 74 " (cutoff:3.500A) removed outlier: 3.633A 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 103 Processing helix chain 'B' and resid 113 through 129 removed outlier: 7.115A 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: 3.731A pdb=" N GLU B 161 " --> pdb=" O PRO B 158 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN B 167 " --> pdb=" O ARG B 164 " (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 270 Processing helix chain 'B' and resid 284 through 294 Processing helix chain 'B' and resid 315 through 328 Processing helix chain 'B' and resid 357 through 362 Processing helix chain 'B' and resid 380 through 391 removed outlier: 3.567A pdb=" N ILE B 385 " --> pdb=" O LEU B 382 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER B 386 " --> pdb=" O GLN B 383 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TRP B 387 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS B 391 " --> pdb=" O ALA B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 409 removed outlier: 4.042A pdb=" N LEU B 404 " --> pdb=" O GLY B 401 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE B 409 " --> pdb=" O VAL B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 467 Processing helix chain 'B' and resid 486 through 491 removed outlier: 3.529A pdb=" N ILE B 489 " --> pdb=" O PRO B 486 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LYS B 490 " --> pdb=" O ASN B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 548 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 69 through 78 removed outlier: 3.739A pdb=" N PHE C 77 " --> pdb=" O TYR C 74 " (cutoff:3.500A) removed outlier: 3.633A 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 103 Processing helix chain 'C' and resid 113 through 129 removed outlier: 7.115A 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: 3.732A pdb=" N GLU C 161 " --> pdb=" O PRO C 158 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN C 167 " --> pdb=" O ARG C 164 " (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 270 Processing helix chain 'C' and resid 284 through 294 Processing helix chain 'C' and resid 315 through 328 Processing helix chain 'C' and resid 357 through 362 Processing helix chain 'C' and resid 380 through 391 removed outlier: 3.567A pdb=" N ILE C 385 " --> pdb=" O LEU C 382 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER C 386 " --> pdb=" O GLN C 383 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TRP C 387 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS C 391 " --> pdb=" O ALA C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 409 removed outlier: 4.042A pdb=" N LEU C 404 " --> pdb=" O GLY C 401 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE C 409 " --> pdb=" O VAL C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 467 Processing helix chain 'C' and resid 486 through 491 removed outlier: 3.530A pdb=" N ILE C 489 " --> pdb=" O PRO C 486 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LYS C 490 " --> pdb=" O ASN C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 548 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 69 through 78 removed outlier: 3.739A pdb=" N PHE E 77 " --> pdb=" O TYR E 74 " (cutoff:3.500A) removed outlier: 3.633A 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 103 Processing helix chain 'E' and resid 113 through 129 removed outlier: 7.116A 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: 3.732A pdb=" N GLU E 161 " --> pdb=" O PRO E 158 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN E 167 " --> pdb=" O ARG E 164 " (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 270 Processing helix chain 'E' and resid 284 through 294 Processing helix chain 'E' and resid 315 through 328 Processing helix chain 'E' and resid 357 through 362 Processing helix chain 'E' and resid 380 through 391 removed outlier: 3.567A pdb=" N ILE E 385 " --> pdb=" O LEU E 382 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER E 386 " --> pdb=" O GLN E 383 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TRP E 387 " --> pdb=" O ALA E 384 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS E 391 " --> pdb=" O ALA E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 409 removed outlier: 4.042A pdb=" N LEU E 404 " --> pdb=" O GLY E 401 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE E 409 " --> pdb=" O VAL E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 463 through 467 Processing helix chain 'E' and resid 486 through 491 removed outlier: 3.529A pdb=" N ILE E 489 " --> pdb=" O PRO E 486 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LYS E 490 " --> pdb=" O ASN E 487 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 548 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: 6.267A pdb=" N ILE A 214 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ILE A 244 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N CYS A 216 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 213 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N TYR A 3 " --> pdb=" O CYS A 176 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ILE A 178 " --> pdb=" O TYR A 3 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU A 5 " --> pdb=" O ILE A 178 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N VAL A 180 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR A 7 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N LEU A 182 " --> pdb=" O THR A 7 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLY A 8 " --> pdb=" O LEU A 147 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 330 through 336 removed outlier: 6.516A pdb=" N LYS A 297 " --> pdb=" O LYS A 331 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ASN A 333 " --> pdb=" O LYS A 297 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N CYS A 299 " --> pdb=" O ASN A 333 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N MET A 335 " --> pdb=" O CYS A 299 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE A 301 " --> pdb=" O MET A 335 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLY A 366 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N VAL A 369 " --> pdb=" O PRO A 394 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU A 396 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE A 520 " --> pdb=" O LEU A 514 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLU A 513 " --> pdb=" O PHE A 499 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N PHE A 499 " --> pdb=" O GLU A 513 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 241 through 245 removed outlier: 6.267A pdb=" N ILE B 214 " --> pdb=" O ILE B 242 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ILE B 244 " --> pdb=" O ILE B 214 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N CYS B 216 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 213 " --> pdb=" O ASN B 177 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N TYR B 3 " --> pdb=" O CYS B 176 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ILE B 178 " --> pdb=" O TYR B 3 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU B 5 " --> pdb=" O ILE B 178 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL B 180 " --> pdb=" O LEU B 5 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR B 7 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N LEU B 182 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLY B 8 " --> pdb=" O LEU B 147 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 330 through 336 removed outlier: 6.515A pdb=" N LYS B 297 " --> pdb=" O LYS B 331 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ASN B 333 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N CYS B 299 " --> pdb=" O ASN B 333 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N MET B 335 " --> pdb=" O CYS B 299 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE B 301 " --> pdb=" O MET B 335 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLY B 366 " --> pdb=" O ALA B 302 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N VAL B 369 " --> pdb=" O PRO B 394 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU B 396 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE B 520 " --> pdb=" O LEU B 514 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLU B 513 " --> pdb=" O PHE B 499 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N PHE B 499 " --> pdb=" O GLU B 513 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 241 through 245 removed outlier: 6.268A pdb=" N ILE C 214 " --> pdb=" O ILE C 242 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ILE C 244 " --> pdb=" O ILE C 214 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N CYS C 216 " --> pdb=" O ILE C 244 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU C 213 " --> pdb=" O ASN C 177 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N TYR C 3 " --> pdb=" O CYS C 176 " (cutoff:3.500A) removed outlier: 7.782A 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: 7.575A pdb=" N VAL C 180 " --> pdb=" O LEU C 5 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR C 7 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N LEU C 182 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLY C 8 " --> pdb=" O LEU C 147 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 330 through 336 removed outlier: 6.515A pdb=" N LYS C 297 " --> pdb=" O LYS C 331 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ASN C 333 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N CYS C 299 " --> pdb=" O ASN C 333 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N MET C 335 " --> pdb=" O CYS C 299 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE C 301 " --> pdb=" O MET C 335 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLY C 366 " --> pdb=" O ALA C 302 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N VAL C 369 " --> pdb=" O PRO C 394 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU C 396 " --> pdb=" O VAL C 369 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE C 520 " --> pdb=" O LEU C 514 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLU C 513 " --> pdb=" O PHE C 499 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N PHE C 499 " --> pdb=" O GLU C 513 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 241 through 245 removed outlier: 6.267A pdb=" N ILE E 214 " --> pdb=" O ILE E 242 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ILE E 244 " --> pdb=" O ILE E 214 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N CYS E 216 " --> pdb=" O ILE E 244 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU E 213 " --> pdb=" O ASN E 177 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N TYR E 3 " --> pdb=" O CYS E 176 " (cutoff:3.500A) removed outlier: 7.781A 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: 7.576A pdb=" N VAL E 180 " --> pdb=" O LEU E 5 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR E 7 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N LEU E 182 " --> pdb=" O THR E 7 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLY E 8 " --> pdb=" O LEU E 147 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 330 through 336 removed outlier: 6.516A pdb=" N LYS E 297 " --> pdb=" O LYS E 331 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ASN E 333 " --> pdb=" O LYS E 297 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N CYS E 299 " --> pdb=" O ASN E 333 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N MET E 335 " --> pdb=" O CYS E 299 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE E 301 " --> pdb=" O MET E 335 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLY E 366 " --> pdb=" O ALA E 302 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N VAL E 369 " --> pdb=" O PRO E 394 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU E 396 " --> pdb=" O VAL E 369 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE E 520 " --> pdb=" O LEU E 514 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLU E 513 " --> pdb=" O PHE E 499 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N PHE E 499 " --> pdb=" O GLU E 513 " (cutoff:3.500A) 564 hydrogen bonds defined for protein. 1320 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: 13.38 Time building geometry restraints manager: 27.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.90 - 1.09: 15600 1.09 - 1.29: 2540 1.29 - 1.49: 6384 1.49 - 1.69: 6900 1.69 - 1.88: 148 Bond restraints: 31572 Sorted by residual: bond pdb=" C2' UTP C 602 " pdb=" C3' UTP C 602 " ideal model delta sigma weight residual 1.301 1.525 -0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C2' UTP B 603 " pdb=" C3' UTP B 603 " ideal model delta sigma weight residual 1.301 1.525 -0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C2' UTP E 603 " pdb=" C3' UTP E 603 " ideal model delta sigma weight residual 1.301 1.525 -0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C2' UTP A 602 " pdb=" C3' UTP A 602 " ideal model delta sigma weight residual 1.301 1.525 -0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C1' UTP A 602 " pdb=" O4' UTP A 602 " ideal model delta sigma weight residual 1.553 1.389 0.164 2.00e-02 2.50e+03 6.72e+01 ... (remaining 31567 not shown) Histogram of bond angle deviations from ideal: 59.64 - 79.00: 32 79.00 - 98.36: 32 98.36 - 117.71: 42552 117.71 - 137.07: 14512 137.07 - 156.43: 8 Bond angle restraints: 57136 Sorted by residual: angle pdb=" CA MET C 448 " pdb=" N MET C 448 " pdb=" H MET C 448 " ideal model delta sigma weight residual 114.00 156.43 -42.43 3.00e+00 1.11e-01 2.00e+02 angle pdb=" CA MET B 448 " pdb=" N MET B 448 " pdb=" H MET B 448 " ideal model delta sigma weight residual 114.00 156.43 -42.43 3.00e+00 1.11e-01 2.00e+02 angle pdb=" CA MET A 448 " pdb=" N MET A 448 " pdb=" H MET A 448 " ideal model delta sigma weight residual 114.00 156.43 -42.43 3.00e+00 1.11e-01 2.00e+02 angle pdb=" CA MET E 448 " pdb=" N MET E 448 " pdb=" H MET E 448 " ideal model delta sigma weight residual 114.00 156.43 -42.43 3.00e+00 1.11e-01 2.00e+02 angle pdb=" C ARG B 217 " pdb=" CA ARG B 217 " pdb=" HA ARG B 217 " ideal model delta sigma weight residual 109.00 72.91 36.09 3.00e+00 1.11e-01 1.45e+02 ... (remaining 57131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 13156 17.50 - 35.00: 874 35.00 - 52.51: 306 52.51 - 70.01: 372 70.01 - 87.51: 48 Dihedral angle restraints: 14756 sinusoidal: 8236 harmonic: 6520 Sorted by residual: dihedral pdb=" CA VAL B 133 " pdb=" C VAL B 133 " pdb=" N ASP B 134 " pdb=" CA ASP B 134 " ideal model delta harmonic sigma weight residual 180.00 147.27 32.73 0 5.00e+00 4.00e-02 4.29e+01 dihedral pdb=" CA VAL C 133 " pdb=" C VAL C 133 " pdb=" N ASP C 134 " pdb=" CA ASP C 134 " ideal model delta harmonic sigma weight residual 180.00 147.27 32.73 0 5.00e+00 4.00e-02 4.29e+01 dihedral pdb=" CA VAL A 133 " pdb=" C VAL A 133 " pdb=" N ASP A 134 " pdb=" CA ASP A 134 " ideal model delta harmonic sigma weight residual 180.00 147.27 32.73 0 5.00e+00 4.00e-02 4.29e+01 ... (remaining 14753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1345 0.098 - 0.196: 774 0.196 - 0.294: 196 0.294 - 0.392: 57 0.392 - 0.490: 28 Chirality restraints: 2400 Sorted by residual: chirality pdb=" CB THR C 118 " pdb=" CA THR C 118 " pdb=" OG1 THR C 118 " pdb=" CG2 THR C 118 " both_signs ideal model delta sigma weight residual False 2.55 2.06 0.49 2.00e-01 2.50e+01 6.00e+00 chirality pdb=" CB THR A 118 " pdb=" CA THR A 118 " pdb=" OG1 THR A 118 " pdb=" CG2 THR A 118 " both_signs ideal model delta sigma weight residual False 2.55 2.06 0.49 2.00e-01 2.50e+01 6.00e+00 chirality pdb=" CB THR B 118 " pdb=" CA THR B 118 " pdb=" OG1 THR B 118 " pdb=" CG2 THR B 118 " both_signs ideal model delta sigma weight residual False 2.55 2.06 0.49 2.00e-01 2.50e+01 5.94e+00 ... (remaining 2397 not shown) Planarity restraints: 4536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 74 " 0.319 2.00e-02 2.50e+03 1.43e-01 6.17e+02 pdb=" CG TYR C 74 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR C 74 " -0.056 2.00e-02 2.50e+03 pdb=" CD2 TYR C 74 " -0.062 2.00e-02 2.50e+03 pdb=" CE1 TYR C 74 " -0.040 2.00e-02 2.50e+03 pdb=" CE2 TYR C 74 " -0.030 2.00e-02 2.50e+03 pdb=" CZ TYR C 74 " 0.058 2.00e-02 2.50e+03 pdb=" OH TYR C 74 " 0.255 2.00e-02 2.50e+03 pdb=" HD1 TYR C 74 " -0.144 2.00e-02 2.50e+03 pdb=" HD2 TYR C 74 " -0.169 2.00e-02 2.50e+03 pdb=" HE1 TYR C 74 " -0.103 2.00e-02 2.50e+03 pdb=" HE2 TYR C 74 " -0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 74 " -0.318 2.00e-02 2.50e+03 1.43e-01 6.17e+02 pdb=" CG TYR A 74 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR A 74 " 0.056 2.00e-02 2.50e+03 pdb=" CD2 TYR A 74 " 0.062 2.00e-02 2.50e+03 pdb=" CE1 TYR A 74 " 0.040 2.00e-02 2.50e+03 pdb=" CE2 TYR A 74 " 0.030 2.00e-02 2.50e+03 pdb=" CZ TYR A 74 " -0.059 2.00e-02 2.50e+03 pdb=" OH TYR A 74 " -0.255 2.00e-02 2.50e+03 pdb=" HD1 TYR A 74 " 0.144 2.00e-02 2.50e+03 pdb=" HD2 TYR A 74 " 0.169 2.00e-02 2.50e+03 pdb=" HE1 TYR A 74 " 0.104 2.00e-02 2.50e+03 pdb=" HE2 TYR A 74 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 74 " 0.318 2.00e-02 2.50e+03 1.43e-01 6.16e+02 pdb=" CG TYR E 74 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR E 74 " -0.055 2.00e-02 2.50e+03 pdb=" CD2 TYR E 74 " -0.062 2.00e-02 2.50e+03 pdb=" CE1 TYR E 74 " -0.040 2.00e-02 2.50e+03 pdb=" CE2 TYR E 74 " -0.030 2.00e-02 2.50e+03 pdb=" CZ TYR E 74 " 0.059 2.00e-02 2.50e+03 pdb=" OH TYR E 74 " 0.255 2.00e-02 2.50e+03 pdb=" HD1 TYR E 74 " -0.144 2.00e-02 2.50e+03 pdb=" HD2 TYR E 74 " -0.169 2.00e-02 2.50e+03 pdb=" HE1 TYR E 74 " -0.104 2.00e-02 2.50e+03 pdb=" HE2 TYR E 74 " -0.073 2.00e-02 2.50e+03 ... (remaining 4533 not shown) Histogram of nonbonded interaction distances: 1.18 - 1.86: 374 1.86 - 2.55: 26798 2.55 - 3.23: 100328 3.23 - 3.92: 135895 3.92 - 4.60: 206228 Nonbonded interactions: 469623 Sorted by model distance: nonbonded pdb=" HD1 PHE E 373 " pdb=" H1 GLN E 604 " model vdw 1.177 2.100 nonbonded pdb=" HD1 PHE C 373 " pdb=" H1 GLN C 603 " model vdw 1.177 2.100 nonbonded pdb=" HD1 PHE A 373 " pdb=" H1 GLN A 603 " model vdw 1.177 2.100 nonbonded pdb=" HD1 PHE B 373 " pdb=" H1 GLN B 604 " model vdw 1.177 2.100 nonbonded pdb="HE22 GLN A 95 " pdb=" OE1 GLN C 95 " model vdw 1.373 1.850 ... (remaining 469618 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: 2.000 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: 0.500 Extract box with map and model: 7.400 Check model and map are aligned: 0.520 Set scattering table: 0.310 Process input model: 106.780 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 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 : 0.014 0.224 15932 Z= 0.893 Angle : 2.098 16.970 21548 Z= 1.375 Chirality : 0.132 0.490 2400 Planarity : 0.014 0.137 2724 Dihedral : 14.402 87.512 6036 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.84 % Allowed : 5.81 % Favored : 92.36 % Cbeta Deviations : 1.56 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -2.16 (0.17), residues: 1876 helix: -1.61 (0.14), residues: 832 sheet: -1.26 (0.24), residues: 388 loop : -0.91 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.100 0.036 TRP B 387 HIS 0.024 0.006 HIS C 323 PHE 0.066 0.018 PHE B 163 TYR 0.236 0.025 TYR C 74 ARG 0.008 0.001 ARG E 205 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Evaluate side-chains 481 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 450 time to evaluate : 2.632 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7533 (mt-10) REVERT: A 169 LYS cc_start: 0.6881 (mtpt) cc_final: 0.6534 (mttt) REVERT: A 205 ARG cc_start: 0.7532 (ttm170) cc_final: 0.7218 (mtm110) REVERT: A 288 MET cc_start: 0.7656 (mtm) cc_final: 0.7335 (mtt) REVERT: A 450 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8430 (tp) REVERT: B 75 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7559 (mt-10) REVERT: B 169 LYS cc_start: 0.6852 (mtpt) cc_final: 0.6536 (mttt) REVERT: B 205 ARG cc_start: 0.7521 (ttm170) cc_final: 0.7235 (mtm110) REVERT: B 288 MET cc_start: 0.7658 (mtm) cc_final: 0.7337 (mtt) REVERT: C 75 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7556 (mt-10) REVERT: C 169 LYS cc_start: 0.6821 (mtpt) cc_final: 0.6495 (mttt) REVERT: C 205 ARG cc_start: 0.7533 (ttm170) cc_final: 0.7256 (mtm110) REVERT: C 283 PHE cc_start: 0.5638 (t80) cc_final: 0.5435 (t80) REVERT: C 288 MET cc_start: 0.7622 (mtm) cc_final: 0.7309 (mtt) REVERT: E 75 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7577 (mt-10) REVERT: E 169 LYS cc_start: 0.6812 (mtpt) cc_final: 0.6499 (mttt) REVERT: E 205 ARG cc_start: 0.7535 (ttm170) cc_final: 0.7241 (mtm110) REVERT: E 288 MET cc_start: 0.7660 (mtm) cc_final: 0.7325 (mtt) outliers start: 31 outliers final: 12 residues processed: 469 average time/residue: 2.3121 time to fit residues: 1222.6980 Evaluate side-chains 315 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 302 time to evaluate : 2.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain B residue 524 GLN Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 483 GLU Chi-restraints excluded: chain C residue 524 GLN Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 483 GLU Chi-restraints excluded: chain E residue 524 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.7980 chunk 145 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 150 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 chunk 174 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN A 165 GLN A 271 HIS A 383 GLN A 491 GLN A 502 GLN A 556 GLN B 128 GLN B 165 GLN B 383 GLN B 491 GLN B 502 GLN B 556 GLN C 128 GLN C 165 GLN C 271 HIS C 383 GLN C 491 GLN C 502 GLN C 556 GLN E 128 GLN E 165 GLN E 383 GLN E 491 GLN E 502 GLN E 556 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15932 Z= 0.250 Angle : 0.614 5.201 21548 Z= 0.322 Chirality : 0.048 0.378 2400 Planarity : 0.005 0.054 2724 Dihedral : 8.149 58.775 2270 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.73 % Allowed : 14.51 % Favored : 82.76 % 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: -1.17 (0.19), residues: 1876 helix: -0.53 (0.17), residues: 832 sheet: -1.29 (0.24), residues: 364 loop : -0.46 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 387 HIS 0.005 0.002 HIS A 478 PHE 0.015 0.002 PHE C 318 TYR 0.019 0.002 TYR B 42 ARG 0.005 0.001 ARG A 532 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Evaluate side-chains 380 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 334 time to evaluate : 2.636 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: A 46 ASP cc_start: 0.6863 (OUTLIER) cc_final: 0.6571 (p0) REVERT: A 79 ASP cc_start: 0.7281 (t0) cc_final: 0.7017 (t0) REVERT: A 153 ASP cc_start: 0.7506 (p0) cc_final: 0.7251 (p0) REVERT: A 169 LYS cc_start: 0.6885 (mtpt) cc_final: 0.6616 (mttt) REVERT: A 202 ARG cc_start: 0.7657 (mtm110) cc_final: 0.7432 (ttp-110) REVERT: A 223 GLU cc_start: 0.6569 (OUTLIER) cc_final: 0.5699 (mp0) REVERT: A 258 GLU cc_start: 0.6285 (mm-30) cc_final: 0.6009 (mm-30) REVERT: A 288 MET cc_start: 0.7778 (mtm) cc_final: 0.7578 (mtt) REVERT: A 512 ILE cc_start: 0.8226 (pt) cc_final: 0.7954 (pp) REVERT: B 79 ASP cc_start: 0.7274 (t0) cc_final: 0.7069 (t0) REVERT: B 153 ASP cc_start: 0.7480 (p0) cc_final: 0.7195 (p0) REVERT: B 191 GLU cc_start: 0.7209 (tt0) cc_final: 0.6958 (tp30) REVERT: B 205 ARG cc_start: 0.7873 (ttm170) cc_final: 0.7527 (mtm110) REVERT: B 365 ASP cc_start: 0.7946 (OUTLIER) cc_final: 0.7725 (m-30) REVERT: C 79 ASP cc_start: 0.7220 (t0) cc_final: 0.7017 (t0) REVERT: C 102 ARG cc_start: 0.7796 (mmp80) cc_final: 0.7410 (mmp-170) REVERT: C 153 ASP cc_start: 0.7447 (p0) cc_final: 0.7189 (p0) REVERT: C 169 LYS cc_start: 0.6817 (mtpt) cc_final: 0.6546 (mttt) REVERT: C 191 GLU cc_start: 0.7182 (tt0) cc_final: 0.6979 (tp30) REVERT: C 205 ARG cc_start: 0.7871 (ttm170) cc_final: 0.7530 (mtm110) REVERT: C 258 GLU cc_start: 0.6314 (mm-30) cc_final: 0.6034 (mm-30) REVERT: C 512 ILE cc_start: 0.8167 (pt) cc_final: 0.7900 (pp) REVERT: E 79 ASP cc_start: 0.7280 (t0) cc_final: 0.7065 (t0) REVERT: E 153 ASP cc_start: 0.7459 (p0) cc_final: 0.7198 (p0) REVERT: E 191 GLU cc_start: 0.7206 (tt0) cc_final: 0.6958 (tp30) REVERT: E 202 ARG cc_start: 0.7618 (mtm110) cc_final: 0.7370 (ttp-110) REVERT: E 288 MET cc_start: 0.7775 (mtm) cc_final: 0.7550 (mtt) REVERT: E 454 ARG cc_start: 0.7574 (ttm170) cc_final: 0.7343 (ttm170) REVERT: E 512 ILE cc_start: 0.8175 (pt) cc_final: 0.7916 (pp) outliers start: 46 outliers final: 11 residues processed: 357 average time/residue: 2.6720 time to fit residues: 1060.6122 Evaluate side-chains 301 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 287 time to evaluate : 2.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 365 ASP Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 243 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 188 optimal weight: 4.9990 chunk 155 optimal weight: 0.9990 chunk 173 optimal weight: 3.9990 chunk 59 optimal weight: 0.4980 chunk 140 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 HIS ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 HIS ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 HIS ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 235 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15932 Z= 0.264 Angle : 0.584 5.800 21548 Z= 0.306 Chirality : 0.049 0.380 2400 Planarity : 0.005 0.039 2724 Dihedral : 7.164 51.927 2240 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.67 % Allowed : 15.05 % Favored : 81.28 % 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: -0.95 (0.19), residues: 1876 helix: -0.41 (0.17), residues: 828 sheet: -1.12 (0.25), residues: 356 loop : -0.32 (0.25), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 387 HIS 0.005 0.002 HIS A 235 PHE 0.014 0.002 PHE C 163 TYR 0.016 0.002 TYR B 42 ARG 0.009 0.001 ARG C 76 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Evaluate side-chains 357 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 295 time to evaluate : 2.454 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: A 46 ASP cc_start: 0.7468 (OUTLIER) cc_final: 0.7236 (p0) REVERT: A 123 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6981 (tm-30) REVERT: A 169 LYS cc_start: 0.7097 (mtpt) cc_final: 0.6766 (mttt) REVERT: A 258 GLU cc_start: 0.6400 (mm-30) cc_final: 0.6004 (mm-30) REVERT: A 512 ILE cc_start: 0.8218 (pt) cc_final: 0.7964 (pp) REVERT: B 123 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6961 (tm-30) REVERT: B 169 LYS cc_start: 0.7135 (mtpt) cc_final: 0.6919 (mttm) REVERT: B 512 ILE cc_start: 0.8176 (pt) cc_final: 0.7899 (pp) REVERT: C 123 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6951 (tm-30) REVERT: C 169 LYS cc_start: 0.7108 (mtpt) cc_final: 0.6812 (mttt) REVERT: C 223 GLU cc_start: 0.6870 (OUTLIER) cc_final: 0.5971 (mp0) REVERT: C 258 GLU cc_start: 0.6382 (mm-30) cc_final: 0.5966 (mm-30) REVERT: C 512 ILE cc_start: 0.8213 (pt) cc_final: 0.7954 (pp) REVERT: E 123 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6962 (tm-30) REVERT: E 169 LYS cc_start: 0.7076 (mtpt) cc_final: 0.6852 (mttt) REVERT: E 389 ARG cc_start: 0.6696 (ttp-110) cc_final: 0.6471 (ttp-110) REVERT: E 512 ILE cc_start: 0.8208 (pt) cc_final: 0.7960 (pp) outliers start: 62 outliers final: 22 residues processed: 335 average time/residue: 2.4336 time to fit residues: 917.8634 Evaluate side-chains 302 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 274 time to evaluate : 2.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 483 GLU Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 243 CYS Chi-restraints excluded: chain E residue 258 GLU Chi-restraints excluded: chain E residue 483 GLU Chi-restraints excluded: chain E residue 528 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 175 optimal weight: 0.8980 chunk 185 optimal weight: 0.7980 chunk 91 optimal weight: 0.5980 chunk 166 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 HIS C 55 HIS E 55 HIS E 271 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.4622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15932 Z= 0.303 Angle : 0.577 5.713 21548 Z= 0.299 Chirality : 0.048 0.365 2400 Planarity : 0.004 0.034 2724 Dihedral : 7.232 53.411 2240 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.50 % Allowed : 15.23 % Favored : 81.28 % 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: -0.90 (0.19), residues: 1876 helix: -0.41 (0.18), residues: 828 sheet: -0.99 (0.25), residues: 368 loop : -0.28 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 387 HIS 0.007 0.002 HIS C 235 PHE 0.011 0.001 PHE C 163 TYR 0.013 0.002 TYR C 42 ARG 0.004 0.001 ARG C 76 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Evaluate side-chains 345 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 286 time to evaluate : 2.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.7659 (OUTLIER) cc_final: 0.7414 (p0) REVERT: A 123 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.7013 (tm-30) REVERT: A 169 LYS cc_start: 0.7100 (mtpt) cc_final: 0.6827 (mttt) REVERT: B 123 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6969 (tm-30) REVERT: B 169 LYS cc_start: 0.7121 (mtpt) cc_final: 0.6870 (mttt) REVERT: B 363 LYS cc_start: 0.7390 (ptmt) cc_final: 0.7187 (ptmm) REVERT: B 521 VAL cc_start: 0.8370 (OUTLIER) cc_final: 0.8163 (m) REVERT: C 46 ASP cc_start: 0.7561 (OUTLIER) cc_final: 0.6801 (p0) REVERT: C 57 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.6934 (pp20) REVERT: C 103 ARG cc_start: 0.7979 (mtm-85) cc_final: 0.7733 (mtp180) REVERT: C 123 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6977 (tm-30) REVERT: C 155 GLU cc_start: 0.7728 (mp0) cc_final: 0.7463 (pm20) REVERT: C 169 LYS cc_start: 0.7088 (mtpt) cc_final: 0.6820 (mttt) REVERT: E 46 ASP cc_start: 0.7572 (OUTLIER) cc_final: 0.6822 (p0) REVERT: E 79 ASP cc_start: 0.7415 (t0) cc_final: 0.7069 (t0) REVERT: E 123 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6968 (tm-30) REVERT: E 169 LYS cc_start: 0.7059 (mtpt) cc_final: 0.6833 (mttt) outliers start: 59 outliers final: 28 residues processed: 319 average time/residue: 2.3463 time to fit residues: 845.0706 Evaluate side-chains 315 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 278 time to evaluate : 2.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 283 PHE Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 283 PHE Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 243 CYS Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 283 PHE Chi-restraints excluded: chain E residue 483 GLU Chi-restraints excluded: chain E residue 528 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 138 optimal weight: 0.0270 chunk 76 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 chunk 128 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 overall best weight: 1.1242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS B 55 HIS ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 55 HIS ** C 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 HIS ** E 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.4858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15932 Z= 0.276 Angle : 0.550 5.373 21548 Z= 0.286 Chirality : 0.047 0.361 2400 Planarity : 0.004 0.034 2724 Dihedral : 7.051 52.233 2240 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.08 % Allowed : 16.17 % Favored : 80.75 % 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: -0.82 (0.19), residues: 1876 helix: -0.38 (0.18), residues: 828 sheet: -0.83 (0.26), residues: 368 loop : -0.27 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 387 HIS 0.006 0.001 HIS C 235 PHE 0.010 0.001 PHE A 163 TYR 0.015 0.002 TYR B 42 ARG 0.003 0.000 ARG E 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Evaluate side-chains 344 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 292 time to evaluate : 2.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.7684 (OUTLIER) cc_final: 0.7418 (p0) REVERT: A 79 ASP cc_start: 0.7667 (t0) cc_final: 0.7425 (t0) REVERT: A 123 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.7018 (tm-30) REVERT: A 169 LYS cc_start: 0.7104 (mtpt) cc_final: 0.6838 (mttt) REVERT: A 483 GLU cc_start: 0.4557 (OUTLIER) cc_final: 0.4293 (pm20) REVERT: B 46 ASP cc_start: 0.7512 (OUTLIER) cc_final: 0.7288 (p0) REVERT: B 123 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6979 (tm-30) REVERT: B 169 LYS cc_start: 0.7122 (mtpt) cc_final: 0.6902 (mttm) REVERT: B 191 GLU cc_start: 0.7456 (tt0) cc_final: 0.7108 (tm-30) REVERT: B 521 VAL cc_start: 0.8376 (OUTLIER) cc_final: 0.8169 (m) REVERT: C 46 ASP cc_start: 0.7556 (OUTLIER) cc_final: 0.6872 (p0) REVERT: C 123 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6978 (tm-30) REVERT: C 169 LYS cc_start: 0.7083 (mtpt) cc_final: 0.6805 (mttt) REVERT: E 46 ASP cc_start: 0.7572 (OUTLIER) cc_final: 0.6902 (p0) REVERT: E 123 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6980 (tm-30) REVERT: E 169 LYS cc_start: 0.7059 (mtpt) cc_final: 0.6815 (mttt) REVERT: E 258 GLU cc_start: 0.5791 (OUTLIER) cc_final: 0.5528 (mt-10) REVERT: E 483 GLU cc_start: 0.4500 (OUTLIER) cc_final: 0.4252 (pm20) outliers start: 52 outliers final: 25 residues processed: 322 average time/residue: 2.4160 time to fit residues: 892.0380 Evaluate side-chains 322 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 285 time to evaluate : 2.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 283 PHE Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 283 PHE Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 243 CYS Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 258 GLU Chi-restraints excluded: chain E residue 283 PHE Chi-restraints excluded: chain E residue 483 GLU Chi-restraints excluded: chain E residue 528 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 0.9990 chunk 167 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 185 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 15 optimal weight: 0.0870 chunk 61 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS A 271 HIS B 55 HIS B 240 GLN C 55 HIS C 271 HIS E 55 HIS E 240 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.5004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15932 Z= 0.195 Angle : 0.514 5.608 21548 Z= 0.264 Chirality : 0.046 0.356 2400 Planarity : 0.004 0.047 2724 Dihedral : 6.705 50.109 2240 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.43 % Allowed : 18.78 % Favored : 78.79 % 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 (0.20), residues: 1876 helix: -0.25 (0.18), residues: 836 sheet: -0.68 (0.26), residues: 368 loop : -0.09 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 387 HIS 0.006 0.001 HIS C 235 PHE 0.009 0.001 PHE C 163 TYR 0.014 0.001 TYR A 42 ARG 0.007 0.000 ARG E 465 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Evaluate side-chains 335 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 294 time to evaluate : 2.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.7683 (OUTLIER) cc_final: 0.7422 (p0) REVERT: A 79 ASP cc_start: 0.7679 (t0) cc_final: 0.7421 (t0) REVERT: A 103 ARG cc_start: 0.7806 (mtm-85) cc_final: 0.7453 (mtm110) REVERT: A 123 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.7004 (tm-30) REVERT: A 169 LYS cc_start: 0.7082 (mtpt) cc_final: 0.6828 (mttt) REVERT: A 318 PHE cc_start: 0.8478 (t80) cc_final: 0.8100 (t80) REVERT: A 510 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.5900 (mt-10) REVERT: B 123 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7047 (tm-30) REVERT: B 169 LYS cc_start: 0.7105 (mtpt) cc_final: 0.6893 (mttm) REVERT: B 365 ASP cc_start: 0.8013 (m-30) cc_final: 0.7807 (m-30) REVERT: C 46 ASP cc_start: 0.7563 (OUTLIER) cc_final: 0.6877 (p0) REVERT: C 123 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7043 (tm-30) REVERT: C 169 LYS cc_start: 0.7063 (mtpt) cc_final: 0.6816 (mttt) REVERT: C 510 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6122 (mt-10) REVERT: E 46 ASP cc_start: 0.7564 (OUTLIER) cc_final: 0.6891 (p0) REVERT: E 123 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.7037 (tm-30) REVERT: E 169 LYS cc_start: 0.7038 (mtpt) cc_final: 0.6820 (mttt) REVERT: E 258 GLU cc_start: 0.5768 (OUTLIER) cc_final: 0.5551 (mt-10) REVERT: E 483 GLU cc_start: 0.4451 (OUTLIER) cc_final: 0.4248 (pm20) outliers start: 41 outliers final: 26 residues processed: 320 average time/residue: 2.2922 time to fit residues: 830.4458 Evaluate side-chains 318 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 281 time to evaluate : 2.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 283 PHE Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 283 PHE Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 243 CYS Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 258 GLU Chi-restraints excluded: chain E residue 283 PHE Chi-restraints excluded: chain E residue 483 GLU Chi-restraints excluded: chain E residue 528 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 112 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 240 GLN E 55 HIS ** E 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.5107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15932 Z= 0.279 Angle : 0.549 5.642 21548 Z= 0.283 Chirality : 0.047 0.355 2400 Planarity : 0.004 0.076 2724 Dihedral : 6.957 52.087 2240 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.67 % Allowed : 19.02 % Favored : 78.32 % 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: -0.70 (0.19), residues: 1876 helix: -0.33 (0.18), residues: 836 sheet: -0.73 (0.26), residues: 368 loop : -0.14 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 387 HIS 0.006 0.001 HIS E 235 PHE 0.010 0.001 PHE C 163 TYR 0.014 0.002 TYR B 42 ARG 0.011 0.001 ARG E 465 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Evaluate side-chains 331 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 286 time to evaluate : 2.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.7753 (OUTLIER) cc_final: 0.7483 (p0) REVERT: A 79 ASP cc_start: 0.7705 (t0) cc_final: 0.7449 (t0) REVERT: A 123 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.7016 (tm-30) REVERT: A 169 LYS cc_start: 0.7059 (mtpt) cc_final: 0.6802 (mttt) REVERT: B 123 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6985 (tm-30) REVERT: B 169 LYS cc_start: 0.7108 (mtpt) cc_final: 0.6891 (mttm) REVERT: B 365 ASP cc_start: 0.7966 (m-30) cc_final: 0.7742 (m-30) REVERT: B 521 VAL cc_start: 0.8324 (OUTLIER) cc_final: 0.8108 (m) REVERT: C 46 ASP cc_start: 0.7659 (OUTLIER) cc_final: 0.6930 (p0) REVERT: C 123 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6985 (tm-30) REVERT: C 169 LYS cc_start: 0.7075 (mtpt) cc_final: 0.6850 (mttt) REVERT: C 509 MET cc_start: 0.7693 (mmm) cc_final: 0.7489 (mmp) REVERT: C 510 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6048 (mt-10) REVERT: E 46 ASP cc_start: 0.7583 (OUTLIER) cc_final: 0.6878 (p0) REVERT: E 123 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6982 (tm-30) REVERT: E 169 LYS cc_start: 0.7052 (mtpt) cc_final: 0.6820 (mttt) REVERT: E 258 GLU cc_start: 0.5770 (OUTLIER) cc_final: 0.5545 (mt-10) outliers start: 45 outliers final: 28 residues processed: 313 average time/residue: 2.1939 time to fit residues: 781.0254 Evaluate side-chains 320 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 282 time to evaluate : 2.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 283 PHE Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 283 PHE Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 243 CYS Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 258 GLU Chi-restraints excluded: chain E residue 283 PHE Chi-restraints excluded: chain E residue 528 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 0.9980 chunk 110 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 117 optimal weight: 0.1980 chunk 126 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 chunk 168 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 HIS ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.5170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15932 Z= 0.192 Angle : 0.513 5.469 21548 Z= 0.263 Chirality : 0.046 0.354 2400 Planarity : 0.004 0.059 2724 Dihedral : 6.634 49.791 2240 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.55 % Allowed : 19.02 % Favored : 78.44 % 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: -0.49 (0.20), residues: 1876 helix: -0.14 (0.18), residues: 836 sheet: -0.66 (0.26), residues: 368 loop : -0.05 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 387 HIS 0.006 0.001 HIS C 235 PHE 0.009 0.001 PHE E 163 TYR 0.014 0.001 TYR B 42 ARG 0.010 0.000 ARG E 465 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Evaluate side-chains 332 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 289 time to evaluate : 2.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.7760 (OUTLIER) cc_final: 0.7508 (p0) REVERT: A 79 ASP cc_start: 0.7696 (t0) cc_final: 0.7428 (t0) REVERT: A 103 ARG cc_start: 0.7825 (mtm-85) cc_final: 0.7458 (mtm110) REVERT: A 123 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.7011 (tm-30) REVERT: A 130 LYS cc_start: 0.8478 (mtmt) cc_final: 0.8228 (mtmt) REVERT: A 510 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.5960 (mt-10) REVERT: B 123 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.7044 (tm-30) REVERT: B 365 ASP cc_start: 0.7959 (m-30) cc_final: 0.7737 (m-30) REVERT: B 510 GLU cc_start: 0.6920 (OUTLIER) cc_final: 0.5891 (mt-10) REVERT: C 46 ASP cc_start: 0.7666 (OUTLIER) cc_final: 0.6951 (p0) REVERT: C 123 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7051 (tm-30) REVERT: C 510 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.5940 (mt-10) REVERT: E 46 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.6921 (p0) REVERT: E 123 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.7042 (tm-30) REVERT: E 312 ASP cc_start: 0.7212 (m-30) cc_final: 0.6996 (m-30) REVERT: E 510 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6215 (mt-10) outliers start: 43 outliers final: 29 residues processed: 313 average time/residue: 2.1856 time to fit residues: 778.0056 Evaluate side-chains 321 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 281 time to evaluate : 2.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 283 PHE Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 283 PHE Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 243 CYS Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 283 PHE Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain E residue 528 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 155 optimal weight: 0.2980 chunk 163 optimal weight: 0.9980 chunk 171 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 240 GLN E 240 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.5270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15932 Z= 0.201 Angle : 0.516 5.220 21548 Z= 0.264 Chirality : 0.046 0.352 2400 Planarity : 0.005 0.067 2724 Dihedral : 6.592 49.355 2240 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.43 % Allowed : 19.37 % Favored : 78.20 % 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: -0.40 (0.20), residues: 1876 helix: -0.07 (0.18), residues: 836 sheet: -0.59 (0.26), residues: 364 loop : -0.03 (0.25), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 387 HIS 0.006 0.001 HIS C 235 PHE 0.011 0.001 PHE B 473 TYR 0.013 0.001 TYR C 42 ARG 0.011 0.001 ARG E 465 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Evaluate side-chains 328 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 287 time to evaluate : 2.659 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: A 79 ASP cc_start: 0.7675 (t0) cc_final: 0.7415 (t0) REVERT: A 103 ARG cc_start: 0.7785 (mtm-85) cc_final: 0.7399 (mtm110) REVERT: A 123 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.7012 (tm-30) REVERT: A 130 LYS cc_start: 0.8488 (mtmt) cc_final: 0.8244 (mtmt) REVERT: A 318 PHE cc_start: 0.8496 (t80) cc_final: 0.8118 (t80) REVERT: B 123 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6955 (tm-30) REVERT: B 365 ASP cc_start: 0.7952 (m-30) cc_final: 0.7728 (m-30) REVERT: B 510 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.5833 (mt-10) REVERT: C 46 ASP cc_start: 0.7705 (OUTLIER) cc_final: 0.6955 (p0) REVERT: C 123 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6954 (tm-30) REVERT: C 510 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.5969 (mt-10) REVERT: E 46 ASP cc_start: 0.7652 (OUTLIER) cc_final: 0.6957 (p0) REVERT: E 123 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6950 (tm-30) outliers start: 41 outliers final: 29 residues processed: 309 average time/residue: 2.2771 time to fit residues: 797.1422 Evaluate side-chains 317 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 280 time to evaluate : 2.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 283 PHE Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 283 PHE Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 243 CYS Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 283 PHE Chi-restraints excluded: chain E residue 528 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 191 optimal weight: 0.9980 chunk 176 optimal weight: 0.1980 chunk 152 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 117 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 GLN B 240 GLN E 165 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.5321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15932 Z= 0.206 Angle : 0.516 4.963 21548 Z= 0.264 Chirality : 0.046 0.351 2400 Planarity : 0.005 0.101 2724 Dihedral : 6.594 49.690 2240 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.43 % Allowed : 19.61 % Favored : 77.96 % 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: -0.30 (0.20), residues: 1876 helix: 0.01 (0.18), residues: 832 sheet: -0.52 (0.26), residues: 364 loop : 0.03 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 387 HIS 0.006 0.001 HIS C 235 PHE 0.026 0.001 PHE B 473 TYR 0.013 0.001 TYR E 42 ARG 0.015 0.001 ARG B 465 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Evaluate side-chains 317 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 276 time to evaluate : 2.846 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: A 46 ASP cc_start: 0.7802 (OUTLIER) cc_final: 0.7539 (p0) REVERT: A 79 ASP cc_start: 0.7676 (t0) cc_final: 0.7416 (t0) REVERT: A 103 ARG cc_start: 0.7855 (mtm-85) cc_final: 0.7495 (mtm110) REVERT: A 123 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.7016 (tm-30) REVERT: A 130 LYS cc_start: 0.8480 (mtmt) cc_final: 0.8239 (mtmt) REVERT: A 219 SER cc_start: 0.8627 (m) cc_final: 0.8400 (p) REVERT: A 318 PHE cc_start: 0.8497 (t80) cc_final: 0.8127 (t80) REVERT: A 365 ASP cc_start: 0.7845 (m-30) cc_final: 0.7467 (m-30) REVERT: B 123 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6965 (tm-30) REVERT: B 365 ASP cc_start: 0.7957 (m-30) cc_final: 0.7732 (m-30) REVERT: B 510 GLU cc_start: 0.6963 (OUTLIER) cc_final: 0.5885 (mt-10) REVERT: C 46 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.6975 (p0) REVERT: C 123 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6960 (tm-30) REVERT: E 46 ASP cc_start: 0.7691 (OUTLIER) cc_final: 0.6994 (p0) REVERT: E 123 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.6959 (tm-30) REVERT: E 510 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.5872 (mt-10) outliers start: 41 outliers final: 29 residues processed: 301 average time/residue: 2.2187 time to fit residues: 759.2492 Evaluate side-chains 310 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 272 time to evaluate : 2.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 283 PHE Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 283 PHE Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 243 CYS Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 283 PHE Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain E residue 528 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.5980 chunk 46 optimal weight: 0.2980 chunk 140 optimal weight: 0.4980 chunk 22 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 156 optimal weight: 0.8980 chunk 19 optimal weight: 0.4980 chunk 28 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.158656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.132720 restraints weight = 49750.016| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.62 r_work: 0.3293 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3159 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3159 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.5381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15932 Z= 0.171 Angle : 0.501 5.366 21548 Z= 0.255 Chirality : 0.045 0.352 2400 Planarity : 0.005 0.095 2724 Dihedral : 6.391 47.851 2240 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.25 % Allowed : 19.91 % Favored : 77.84 % 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: -0.08 (0.20), residues: 1876 helix: 0.14 (0.19), residues: 832 sheet: -0.31 (0.27), residues: 356 loop : 0.15 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 387 HIS 0.005 0.001 HIS C 235 PHE 0.013 0.001 PHE B 473 TYR 0.013 0.001 TYR E 42 ARG 0.014 0.001 ARG B 465 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13477.00 seconds wall clock time: 236 minutes 34.77 seconds (14194.77 seconds total)