Starting phenix.real_space_refine on Sat Dec 16 10:42:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mip_23859/12_2023/7mip_23859_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mip_23859/12_2023/7mip_23859.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mip_23859/12_2023/7mip_23859_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mip_23859/12_2023/7mip_23859_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mip_23859/12_2023/7mip_23859_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mip_23859/12_2023/7mip_23859.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mip_23859/12_2023/7mip_23859.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mip_23859/12_2023/7mip_23859_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mip_23859/12_2023/7mip_23859_trim_updated.pdb" } resolution = 2.4 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= 0.263 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 96 5.16 5 C 11116 2.51 5 N 2976 2.21 5 O 3268 1.98 5 H 17328 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C ASP 134": "OD1" <-> "OD2" Residue "C ARG 164": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 173": "OE1" <-> "OE2" Residue "C GLU 259": "OE1" <-> "OE2" Residue "C ARG 268": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 287": "OE1" <-> "OE2" Residue "C GLU 297": "OE1" <-> "OE2" Residue "C TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 356": "OE1" <-> "OE2" Residue "C PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 470": "OD1" <-> "OD2" Residue "C GLU 475": "OE1" <-> "OE2" Residue "C GLU 476": "OE1" <-> "OE2" Residue "C GLU 493": "OE1" <-> "OE2" Residue "C GLU 494": "OE1" <-> "OE2" Residue "C ASP 503": "OD1" <-> "OD2" Residue "C GLU 505": "OE1" <-> "OE2" Residue "C GLU 507": "OE1" <-> "OE2" Residue "C ARG 508": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 510": "OE1" <-> "OE2" Residue "C GLU 513": "OE1" <-> "OE2" Residue "C GLU 515": "OE1" <-> "OE2" Residue "C ASP 516": "OD1" <-> "OD2" Residue "C GLU 528": "OE1" <-> "OE2" Residue "C ARG 550": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "D ASP 134": "OD1" <-> "OD2" Residue "D ARG 164": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 173": "OE1" <-> "OE2" Residue "D GLU 259": "OE1" <-> "OE2" Residue "D ARG 268": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 287": "OE1" <-> "OE2" Residue "D GLU 297": "OE1" <-> "OE2" Residue "D TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 356": "OE1" <-> "OE2" Residue "D PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 470": "OD1" <-> "OD2" Residue "D GLU 475": "OE1" <-> "OE2" Residue "D GLU 476": "OE1" <-> "OE2" Residue "D GLU 493": "OE1" <-> "OE2" Residue "D GLU 494": "OE1" <-> "OE2" Residue "D ASP 503": "OD1" <-> "OD2" Residue "D GLU 505": "OE1" <-> "OE2" Residue "D GLU 507": "OE1" <-> "OE2" Residue "D ARG 508": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 510": "OE1" <-> "OE2" Residue "D GLU 513": "OE1" <-> "OE2" Residue "D GLU 515": "OE1" <-> "OE2" Residue "D ASP 516": "OD1" <-> "OD2" Residue "D GLU 528": "OE1" <-> "OE2" Residue "D ARG 550": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 57": "OE1" <-> "OE2" Residue "G ASP 134": "OD1" <-> "OD2" Residue "G ARG 164": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 173": "OE1" <-> "OE2" Residue "G GLU 259": "OE1" <-> "OE2" Residue "G ARG 268": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 287": "OE1" <-> "OE2" Residue "G GLU 297": "OE1" <-> "OE2" Residue "G TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 356": "OE1" <-> "OE2" Residue "G PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 470": "OD1" <-> "OD2" Residue "G GLU 475": "OE1" <-> "OE2" Residue "G GLU 476": "OE1" <-> "OE2" Residue "G GLU 493": "OE1" <-> "OE2" Residue "G GLU 494": "OE1" <-> "OE2" Residue "G ASP 503": "OD1" <-> "OD2" Residue "G GLU 505": "OE1" <-> "OE2" Residue "G GLU 507": "OE1" <-> "OE2" Residue "G ARG 508": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 510": "OE1" <-> "OE2" Residue "G GLU 513": "OE1" <-> "OE2" Residue "G GLU 515": "OE1" <-> "OE2" Residue "G ASP 516": "OD1" <-> "OD2" Residue "G GLU 528": "OE1" <-> "OE2" Residue "G ARG 550": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 57": "OE1" <-> "OE2" Residue "I ASP 134": "OD1" <-> "OD2" Residue "I ARG 164": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 173": "OE1" <-> "OE2" Residue "I GLU 259": "OE1" <-> "OE2" Residue "I ARG 268": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 287": "OE1" <-> "OE2" Residue "I GLU 297": "OE1" <-> "OE2" Residue "I TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 356": "OE1" <-> "OE2" Residue "I PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ASP 470": "OD1" <-> "OD2" Residue "I GLU 475": "OE1" <-> "OE2" Residue "I GLU 476": "OE1" <-> "OE2" Residue "I GLU 493": "OE1" <-> "OE2" Residue "I GLU 494": "OE1" <-> "OE2" Residue "I ASP 503": "OD1" <-> "OD2" Residue "I GLU 505": "OE1" <-> "OE2" Residue "I GLU 507": "OE1" <-> "OE2" Residue "I ARG 508": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 510": "OE1" <-> "OE2" Residue "I GLU 513": "OE1" <-> "OE2" Residue "I GLU 515": "OE1" <-> "OE2" Residue "I ASP 516": "OD1" <-> "OD2" Residue "I GLU 528": "OE1" <-> "OE2" Residue "I ARG 550": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 34800 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 8617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 8617 Classifications: {'peptide': 540} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 510} Chain breaks: 2 Chain: "D" Number of atoms: 8617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 8617 Classifications: {'peptide': 540} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 510} Chain breaks: 2 Chain: "G" Number of atoms: 8617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 8617 Classifications: {'peptide': 540} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 510} Chain breaks: 2 Chain: "I" Number of atoms: 8617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 8617 Classifications: {'peptide': 540} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 510} Chain breaks: 2 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} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 3} Chain: "D" 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: "G" 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: "I" 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: 4 residue: pdb=" N ILE C 250 " occ=0.80 ... (17 atoms not shown) pdb="HD13 ILE C 250 " occ=0.80 residue: pdb=" N ILE D 250 " occ=0.80 ... (17 atoms not shown) pdb="HD13 ILE D 250 " occ=0.80 residue: pdb=" N ILE G 250 " occ=0.80 ... (17 atoms not shown) pdb="HD13 ILE G 250 " occ=0.80 residue: pdb=" N ILE I 250 " occ=0.80 ... (17 atoms not shown) pdb="HD13 ILE I 250 " occ=0.80 Time building chain proxies: 14.86, per 1000 atoms: 0.43 Number of scatterers: 34800 At special positions: 0 Unit cell: (124.95, 129.15, 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 96 16.00 P 12 15.00 Mg 4 11.99 O 3268 8.00 N 2976 7.00 C 11116 6.00 H 17328 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 243 " distance=2.04 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 243 " distance=2.04 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 243 " distance=2.04 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 243 " distance=2.04 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: 30.48 Conformation dependent library (CDL) restraints added in 3.6 seconds 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4000 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 96 helices and 16 sheets defined 42.0% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.98 Creating SS restraints... Processing helix chain 'C' and resid 16 through 29 Processing helix chain 'C' and resid 47 through 49 No H-bonds generated for 'chain 'C' and resid 47 through 49' Processing helix chain 'C' and resid 69 through 78 Processing helix chain 'C' and resid 84 through 86 No H-bonds generated for 'chain 'C' and resid 84 through 86' Processing helix chain 'C' and resid 90 through 102 Processing helix chain 'C' and resid 113 through 129 removed outlier: 7.089A pdb=" N THR C 118 " --> pdb=" O VAL C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 169 Proline residue: C 158 - end of helix removed outlier: 3.532A pdb=" N GLU C 161 " --> pdb=" O PRO C 158 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN C 167 " --> pdb=" O ARG C 164 " (cutoff:3.500A) 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 259 Proline residue: C 254 - end of helix removed outlier: 3.875A pdb=" N GLU C 259 " --> pdb=" O LEU C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 269 Processing helix chain 'C' and resid 283 through 294 Processing helix chain 'C' and resid 311 through 327 removed outlier: 6.473A pdb=" N SER C 316 " --> pdb=" O SER C 313 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HIS C 323 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA C 325 " --> pdb=" O GLU C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 341 No H-bonds generated for 'chain 'C' and resid 339 through 341' Processing helix chain 'C' and resid 345 through 349 Processing helix chain 'C' and resid 351 through 363 Processing helix chain 'C' and resid 378 through 390 Processing helix chain 'C' and resid 400 through 413 Processing helix chain 'C' and resid 463 through 467 Processing helix chain 'C' and resid 489 through 495 removed outlier: 3.983A pdb=" N GLN C 495 " --> pdb=" O CYS C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 527 through 529 No H-bonds generated for 'chain 'C' and resid 527 through 529' Processing helix chain 'C' and resid 538 through 547 Processing helix chain 'C' and resid 551 through 556 Processing helix chain 'D' and resid 16 through 29 Processing helix chain 'D' and resid 47 through 49 No H-bonds generated for 'chain 'D' and resid 47 through 49' Processing helix chain 'D' and resid 69 through 78 Processing helix chain 'D' and resid 84 through 86 No H-bonds generated for 'chain 'D' and resid 84 through 86' Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 113 through 129 removed outlier: 7.088A pdb=" N THR D 118 " --> pdb=" O VAL D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 169 Proline residue: D 158 - end of helix removed outlier: 3.532A pdb=" N GLU D 161 " --> pdb=" O PRO D 158 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLN D 167 " --> pdb=" O ARG D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 206 Processing helix chain 'D' and resid 224 through 233 Processing helix chain 'D' and resid 238 through 240 No H-bonds generated for 'chain 'D' and resid 238 through 240' Processing helix chain 'D' and resid 250 through 259 Proline residue: D 254 - end of helix removed outlier: 3.875A pdb=" N GLU D 259 " --> pdb=" O LEU D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 269 Processing helix chain 'D' and resid 283 through 294 Processing helix chain 'D' and resid 311 through 327 removed outlier: 6.473A pdb=" N SER D 316 " --> pdb=" O SER D 313 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HIS D 323 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA D 325 " --> pdb=" O GLU D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 341 No H-bonds generated for 'chain 'D' and resid 339 through 341' Processing helix chain 'D' and resid 345 through 349 Processing helix chain 'D' and resid 351 through 363 Processing helix chain 'D' and resid 378 through 390 Processing helix chain 'D' and resid 400 through 413 Processing helix chain 'D' and resid 463 through 467 Processing helix chain 'D' and resid 489 through 495 removed outlier: 3.983A pdb=" N GLN D 495 " --> pdb=" O CYS D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 527 through 529 No H-bonds generated for 'chain 'D' and resid 527 through 529' Processing helix chain 'D' and resid 538 through 547 Processing helix chain 'D' and resid 551 through 556 Processing helix chain 'G' and resid 16 through 29 Processing helix chain 'G' and resid 47 through 49 No H-bonds generated for 'chain 'G' and resid 47 through 49' Processing helix chain 'G' and resid 69 through 78 Processing helix chain 'G' and resid 84 through 86 No H-bonds generated for 'chain 'G' and resid 84 through 86' Processing helix chain 'G' and resid 90 through 102 Processing helix chain 'G' and resid 113 through 129 removed outlier: 7.089A pdb=" N THR G 118 " --> pdb=" O VAL G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 169 Proline residue: G 158 - end of helix removed outlier: 3.531A pdb=" N GLU G 161 " --> pdb=" O PRO G 158 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN G 167 " --> pdb=" O ARG G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 206 Processing helix chain 'G' and resid 224 through 233 Processing helix chain 'G' and resid 238 through 240 No H-bonds generated for 'chain 'G' and resid 238 through 240' Processing helix chain 'G' and resid 250 through 259 Proline residue: G 254 - end of helix removed outlier: 3.875A pdb=" N GLU G 259 " --> pdb=" O LEU G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 262 through 269 Processing helix chain 'G' and resid 283 through 294 Processing helix chain 'G' and resid 311 through 327 removed outlier: 6.474A pdb=" N SER G 316 " --> pdb=" O SER G 313 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS G 323 " --> pdb=" O ALA G 320 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA G 325 " --> pdb=" O GLU G 322 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 341 No H-bonds generated for 'chain 'G' and resid 339 through 341' Processing helix chain 'G' and resid 345 through 349 Processing helix chain 'G' and resid 351 through 363 Processing helix chain 'G' and resid 378 through 390 Processing helix chain 'G' and resid 400 through 413 Processing helix chain 'G' and resid 463 through 467 Processing helix chain 'G' and resid 489 through 495 removed outlier: 3.983A pdb=" N GLN G 495 " --> pdb=" O CYS G 491 " (cutoff:3.500A) Processing helix chain 'G' and resid 527 through 529 No H-bonds generated for 'chain 'G' and resid 527 through 529' Processing helix chain 'G' and resid 538 through 547 Processing helix chain 'G' and resid 551 through 556 Processing helix chain 'I' and resid 16 through 29 Processing helix chain 'I' and resid 47 through 49 No H-bonds generated for 'chain 'I' and resid 47 through 49' Processing helix chain 'I' and resid 69 through 78 Processing helix chain 'I' and resid 84 through 86 No H-bonds generated for 'chain 'I' and resid 84 through 86' Processing helix chain 'I' and resid 90 through 102 Processing helix chain 'I' and resid 113 through 129 removed outlier: 7.088A pdb=" N THR I 118 " --> pdb=" O VAL I 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 154 through 169 Proline residue: I 158 - end of helix removed outlier: 3.532A pdb=" N GLU I 161 " --> pdb=" O PRO I 158 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLN I 167 " --> pdb=" O ARG I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 206 Processing helix chain 'I' and resid 224 through 233 Processing helix chain 'I' and resid 238 through 240 No H-bonds generated for 'chain 'I' and resid 238 through 240' Processing helix chain 'I' and resid 250 through 259 Proline residue: I 254 - end of helix removed outlier: 3.875A pdb=" N GLU I 259 " --> pdb=" O LEU I 256 " (cutoff:3.500A) Processing helix chain 'I' and resid 262 through 269 Processing helix chain 'I' and resid 283 through 294 Processing helix chain 'I' and resid 311 through 327 removed outlier: 6.473A pdb=" N SER I 316 " --> pdb=" O SER I 313 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HIS I 323 " --> pdb=" O ALA I 320 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA I 325 " --> pdb=" O GLU I 322 " (cutoff:3.500A) Processing helix chain 'I' and resid 339 through 341 No H-bonds generated for 'chain 'I' and resid 339 through 341' Processing helix chain 'I' and resid 345 through 349 Processing helix chain 'I' and resid 351 through 363 Processing helix chain 'I' and resid 378 through 390 Processing helix chain 'I' and resid 400 through 413 Processing helix chain 'I' and resid 463 through 467 Processing helix chain 'I' and resid 489 through 495 removed outlier: 3.983A pdb=" N GLN I 495 " --> pdb=" O CYS I 491 " (cutoff:3.500A) Processing helix chain 'I' and resid 527 through 529 No H-bonds generated for 'chain 'I' and resid 527 through 529' Processing helix chain 'I' and resid 538 through 547 Processing helix chain 'I' and resid 551 through 556 Processing sheet with id= A, first strand: chain 'C' and resid 241 through 244 removed outlier: 6.228A pdb=" N VAL C 214 " --> pdb=" O ILE C 242 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N VAL C 244 " --> pdb=" O VAL C 214 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N CYS C 216 " --> pdb=" O VAL C 244 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N TYR C 3 " --> pdb=" O CYS C 176 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE C 178 " --> pdb=" O TYR C 3 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU C 5 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N VAL C 180 " --> pdb=" O LEU C 5 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N THR C 7 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N LEU C 182 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY C 8 " --> pdb=" O LEU C 147 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 331 through 338 removed outlier: 6.867A pdb=" N GLY C 366 " --> pdb=" O ALA C 302 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N VAL C 304 " --> pdb=" O GLY C 366 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU C 368 " --> pdb=" O VAL C 304 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 433 through 435 Processing sheet with id= D, first strand: chain 'C' and resid 473 through 480 Processing sheet with id= E, first strand: chain 'D' and resid 241 through 244 removed outlier: 6.229A pdb=" N VAL D 214 " --> pdb=" O ILE D 242 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N VAL D 244 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N CYS D 216 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TYR D 3 " --> pdb=" O CYS D 176 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ILE D 178 " --> pdb=" O TYR D 3 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU D 5 " --> pdb=" O ILE D 178 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL D 180 " --> pdb=" O LEU D 5 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N THR D 7 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N LEU D 182 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY D 8 " --> pdb=" O LEU D 147 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 331 through 338 removed outlier: 6.867A pdb=" N GLY D 366 " --> pdb=" O ALA D 302 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N VAL D 304 " --> pdb=" O GLY D 366 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU D 368 " --> pdb=" O VAL D 304 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 433 through 435 Processing sheet with id= H, first strand: chain 'D' and resid 473 through 480 Processing sheet with id= I, first strand: chain 'G' and resid 241 through 244 removed outlier: 6.229A pdb=" N VAL G 214 " --> pdb=" O ILE G 242 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N VAL G 244 " --> pdb=" O VAL G 214 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N CYS G 216 " --> pdb=" O VAL G 244 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N TYR G 3 " --> pdb=" O CYS G 176 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE G 178 " --> pdb=" O TYR G 3 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU G 5 " --> pdb=" O ILE G 178 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL G 180 " --> pdb=" O LEU G 5 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N THR G 7 " --> pdb=" O VAL G 180 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N LEU G 182 " --> pdb=" O THR G 7 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY G 8 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 331 through 338 removed outlier: 6.867A pdb=" N GLY G 366 " --> pdb=" O ALA G 302 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N VAL G 304 " --> pdb=" O GLY G 366 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU G 368 " --> pdb=" O VAL G 304 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 433 through 435 Processing sheet with id= L, first strand: chain 'G' and resid 473 through 480 Processing sheet with id= M, first strand: chain 'I' and resid 241 through 244 removed outlier: 6.229A pdb=" N VAL I 214 " --> pdb=" O ILE I 242 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N VAL I 244 " --> pdb=" O VAL I 214 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N CYS I 216 " --> pdb=" O VAL I 244 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N TYR I 3 " --> pdb=" O CYS I 176 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE I 178 " --> pdb=" O TYR I 3 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU I 5 " --> pdb=" O ILE I 178 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL I 180 " --> pdb=" O LEU I 5 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N THR I 7 " --> pdb=" O VAL I 180 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N LEU I 182 " --> pdb=" O THR I 7 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY I 8 " --> pdb=" O LEU I 147 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'I' and resid 331 through 338 removed outlier: 6.867A pdb=" N GLY I 366 " --> pdb=" O ALA I 302 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N VAL I 304 " --> pdb=" O GLY I 366 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU I 368 " --> pdb=" O VAL I 304 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'I' and resid 433 through 435 Processing sheet with id= P, first strand: chain 'I' and resid 473 through 480 676 hydrogen bonds defined for protein. 1740 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: 14.03 Time building geometry restraints manager: 31.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.14: 17292 1.14 - 1.33: 3228 1.33 - 1.51: 7089 1.51 - 1.70: 7423 1.70 - 1.88: 152 Bond restraints: 35184 Sorted by residual: bond pdb=" ND1 HIS G 526 " pdb=" CE1 HIS G 526 " ideal model delta sigma weight residual 1.321 1.456 -0.135 1.00e-02 1.00e+04 1.81e+02 bond pdb=" ND1 HIS C 526 " pdb=" CE1 HIS C 526 " ideal model delta sigma weight residual 1.321 1.455 -0.134 1.00e-02 1.00e+04 1.80e+02 bond pdb=" ND1 HIS D 526 " pdb=" CE1 HIS D 526 " ideal model delta sigma weight residual 1.321 1.455 -0.134 1.00e-02 1.00e+04 1.80e+02 bond pdb=" ND1 HIS I 526 " pdb=" CE1 HIS I 526 " ideal model delta sigma weight residual 1.321 1.455 -0.134 1.00e-02 1.00e+04 1.80e+02 bond pdb=" C2' UTP I 604 " pdb=" C3' UTP I 604 " ideal model delta sigma weight residual 1.301 1.528 -0.227 2.00e-02 2.50e+03 1.29e+02 ... (remaining 35179 not shown) Histogram of bond angle deviations from ideal: 59.52 - 75.60: 24 75.60 - 91.69: 4 91.69 - 107.78: 6245 107.78 - 123.87: 54508 123.87 - 139.96: 2967 Bond angle restraints: 63748 Sorted by residual: angle pdb=" N PRO G 538 " pdb=" CA PRO G 538 " pdb=" C PRO G 538 " ideal model delta sigma weight residual 110.70 120.16 -9.46 1.22e+00 6.72e-01 6.01e+01 angle pdb=" N PRO C 538 " pdb=" CA PRO C 538 " pdb=" C PRO C 538 " ideal model delta sigma weight residual 110.70 120.16 -9.46 1.22e+00 6.72e-01 6.01e+01 angle pdb=" N PRO I 538 " pdb=" CA PRO I 538 " pdb=" C PRO I 538 " ideal model delta sigma weight residual 110.70 120.09 -9.39 1.22e+00 6.72e-01 5.92e+01 angle pdb=" N PRO D 538 " pdb=" CA PRO D 538 " pdb=" C PRO D 538 " ideal model delta sigma weight residual 110.70 120.08 -9.38 1.22e+00 6.72e-01 5.92e+01 angle pdb=" CG HIS G 526 " pdb=" CD2 HIS G 526 " pdb=" NE2 HIS G 526 " ideal model delta sigma weight residual 107.20 114.59 -7.39 1.00e+00 1.00e+00 5.47e+01 ... (remaining 63743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 14283 17.91 - 35.82: 935 35.82 - 53.73: 454 53.73 - 71.64: 280 71.64 - 89.55: 60 Dihedral angle restraints: 16012 sinusoidal: 8724 harmonic: 7288 Sorted by residual: dihedral pdb=" CA PRO I 115 " pdb=" C PRO I 115 " pdb=" N HIS I 116 " pdb=" CA HIS I 116 " ideal model delta harmonic sigma weight residual -180.00 -153.06 -26.94 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA PRO D 115 " pdb=" C PRO D 115 " pdb=" N HIS D 116 " pdb=" CA HIS D 116 " ideal model delta harmonic sigma weight residual -180.00 -153.06 -26.94 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA PRO C 115 " pdb=" C PRO C 115 " pdb=" N HIS C 116 " pdb=" CA HIS C 116 " ideal model delta harmonic sigma weight residual -180.00 -153.07 -26.93 0 5.00e+00 4.00e-02 2.90e+01 ... (remaining 16009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1561 0.098 - 0.196: 833 0.196 - 0.293: 224 0.293 - 0.391: 34 0.391 - 0.489: 24 Chirality restraints: 2676 Sorted by residual: chirality pdb=" C1' UTP G 603 " pdb=" C2' UTP G 603 " pdb=" N1 UTP G 603 " pdb=" O4' UTP G 603 " both_signs ideal model delta sigma weight residual False 2.53 2.04 0.49 2.00e-01 2.50e+01 5.98e+00 chirality pdb=" C1' UTP C 603 " pdb=" C2' UTP C 603 " pdb=" N1 UTP C 603 " pdb=" O4' UTP C 603 " both_signs ideal model delta sigma weight residual False 2.53 2.04 0.49 2.00e-01 2.50e+01 5.95e+00 chirality pdb=" C1' UTP D 604 " pdb=" C2' UTP D 604 " pdb=" N1 UTP D 604 " pdb=" O4' UTP D 604 " both_signs ideal model delta sigma weight residual False 2.53 2.04 0.49 2.00e-01 2.50e+01 5.90e+00 ... (remaining 2673 not shown) Planarity restraints: 5116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 265 " -0.155 2.00e-02 2.50e+03 6.68e-02 1.34e+02 pdb=" CG TYR D 265 " -0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR D 265 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR D 265 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR D 265 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR D 265 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR D 265 " -0.022 2.00e-02 2.50e+03 pdb=" OH TYR D 265 " -0.122 2.00e-02 2.50e+03 pdb=" HD1 TYR D 265 " 0.064 2.00e-02 2.50e+03 pdb=" HD2 TYR D 265 " 0.070 2.00e-02 2.50e+03 pdb=" HE1 TYR D 265 " 0.039 2.00e-02 2.50e+03 pdb=" HE2 TYR D 265 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR I 265 " 0.155 2.00e-02 2.50e+03 6.68e-02 1.34e+02 pdb=" CG TYR I 265 " 0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR I 265 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR I 265 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR I 265 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR I 265 " -0.017 2.00e-02 2.50e+03 pdb=" CZ TYR I 265 " 0.023 2.00e-02 2.50e+03 pdb=" OH TYR I 265 " 0.122 2.00e-02 2.50e+03 pdb=" HD1 TYR I 265 " -0.064 2.00e-02 2.50e+03 pdb=" HD2 TYR I 265 " -0.069 2.00e-02 2.50e+03 pdb=" HE1 TYR I 265 " -0.039 2.00e-02 2.50e+03 pdb=" HE2 TYR I 265 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 265 " 0.155 2.00e-02 2.50e+03 6.66e-02 1.33e+02 pdb=" CG TYR C 265 " 0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR C 265 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR C 265 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR C 265 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR C 265 " -0.017 2.00e-02 2.50e+03 pdb=" CZ TYR C 265 " 0.022 2.00e-02 2.50e+03 pdb=" OH TYR C 265 " 0.121 2.00e-02 2.50e+03 pdb=" HD1 TYR C 265 " -0.065 2.00e-02 2.50e+03 pdb=" HD2 TYR C 265 " -0.068 2.00e-02 2.50e+03 pdb=" HE1 TYR C 265 " -0.038 2.00e-02 2.50e+03 pdb=" HE2 TYR C 265 " -0.036 2.00e-02 2.50e+03 ... (remaining 5113 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.07: 1727 2.07 - 2.71: 49698 2.71 - 3.34: 112875 3.34 - 3.97: 151208 3.97 - 4.60: 220332 Nonbonded interactions: 535840 Sorted by model distance: nonbonded pdb="HE21 GLN C 95 " pdb=" OE1 GLN G 95 " model vdw 1.443 1.850 nonbonded pdb=" OE1 GLN D 95 " pdb="HE22 GLN I 95 " model vdw 1.445 1.850 nonbonded pdb=" OE1 GLN C 95 " pdb="HE22 GLN G 95 " model vdw 1.459 1.850 nonbonded pdb="HE22 GLN D 95 " pdb=" OE1 GLN I 95 " model vdw 1.461 1.850 nonbonded pdb=" HA THR D 110 " pdb=" HE1 PHE I 50 " model vdw 1.553 2.270 ... (remaining 535835 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 'C' and (resid 1 through 557 or resid 601)) selection = (chain 'D' and (resid 1 through 557 or resid 601)) selection = (chain 'G' and (resid 1 through 557 or resid 601)) selection = (chain 'I' and (resid 1 through 557 or resid 601)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.80 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: 1.720 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: 7.160 Check model and map are aligned: 0.530 Set scattering table: 0.300 Process input model: 113.990 Find NCS groups from input model: 1.930 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 139.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.227 17856 Z= 0.975 Angle : 2.040 16.371 24196 Z= 1.341 Chirality : 0.125 0.489 2676 Planarity : 0.013 0.091 3084 Dihedral : 14.663 88.560 6808 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.37 % Favored : 96.44 % Rotamer: Outliers : 1.04 % Allowed : 5.87 % Favored : 93.09 % Cbeta Deviations : 0.40 % Peptide Plane: Cis-proline : 3.45 % 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: -1.24 (0.17), residues: 2136 helix: -0.94 (0.15), residues: 900 sheet: -0.74 (0.28), residues: 340 loop : -0.47 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.018 TRP D 387 HIS 0.028 0.006 HIS I 526 PHE 0.071 0.019 PHE G 482 TYR 0.120 0.020 TYR C 265 ARG 0.007 0.001 ARG G 252 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 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 506 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 486 time to evaluate : 2.836 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 outliers start: 20 outliers final: 4 residues processed: 494 average time/residue: 2.3744 time to fit residues: 1344.4206 Evaluate side-chains 380 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 376 time to evaluate : 2.816 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 3.6650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.6980 chunk 163 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 169 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 196 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 87 ASN C 348 GLN C 359 GLN C 412 ASN D 55 HIS D 87 ASN D 348 GLN D 359 GLN D 412 ASN G 87 ASN G 348 GLN I 87 ASN I 348 GLN I 359 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 17856 Z= 0.246 Angle : 0.657 6.030 24196 Z= 0.339 Chirality : 0.045 0.141 2676 Planarity : 0.005 0.055 3084 Dihedral : 7.613 53.377 2508 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.26 % Favored : 98.55 % Rotamer: Outliers : 2.39 % Allowed : 12.37 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.54 (0.17), residues: 2136 helix: 0.12 (0.16), residues: 912 sheet: -0.97 (0.25), residues: 404 loop : -0.34 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 358 HIS 0.003 0.001 HIS I 179 PHE 0.014 0.002 PHE D 163 TYR 0.016 0.002 TYR G 42 ARG 0.006 0.001 ARG C 465 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 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 418 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 372 time to evaluate : 2.734 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 outliers start: 46 outliers final: 19 residues processed: 392 average time/residue: 2.7212 time to fit residues: 1205.9715 Evaluate side-chains 365 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 346 time to evaluate : 2.731 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 11 residues processed: 8 average time/residue: 1.1381 time to fit residues: 15.4666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 chunk 175 optimal weight: 0.8980 chunk 194 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 359 GLN I 359 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 17856 Z= 0.336 Angle : 0.646 8.888 24196 Z= 0.329 Chirality : 0.046 0.175 2676 Planarity : 0.005 0.041 3084 Dihedral : 7.615 53.753 2508 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.29 % Favored : 97.52 % Rotamer: Outliers : 2.29 % Allowed : 13.51 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.18), residues: 2136 helix: 0.27 (0.16), residues: 924 sheet: -0.72 (0.25), residues: 404 loop : -0.13 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP G 358 HIS 0.009 0.002 HIS C 116 PHE 0.018 0.002 PHE D 163 TYR 0.015 0.002 TYR G 42 ARG 0.005 0.001 ARG I 252 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 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 394 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 350 time to evaluate : 2.722 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 outliers start: 44 outliers final: 26 residues processed: 370 average time/residue: 2.6016 time to fit residues: 1094.8976 Evaluate side-chains 354 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 328 time to evaluate : 2.628 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 13 residues processed: 13 average time/residue: 0.9597 time to fit residues: 20.1462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 101 optimal weight: 8.9990 chunk 21 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 197 optimal weight: 0.3980 chunk 208 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 186 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 165 GLN ** C 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 GLN G 165 GLN I 165 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17856 Z= 0.260 Angle : 0.581 8.445 24196 Z= 0.291 Chirality : 0.044 0.153 2676 Planarity : 0.005 0.042 3084 Dihedral : 7.058 52.517 2508 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.03 % Allowed : 14.03 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.18), residues: 2136 helix: 0.59 (0.17), residues: 920 sheet: -0.20 (0.27), residues: 364 loop : -0.05 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 358 HIS 0.007 0.002 HIS G 116 PHE 0.016 0.002 PHE G 163 TYR 0.014 0.002 TYR I 42 ARG 0.007 0.001 ARG G 550 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 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 404 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 365 time to evaluate : 2.812 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 outliers start: 39 outliers final: 24 residues processed: 384 average time/residue: 2.5608 time to fit residues: 1116.3191 Evaluate side-chains 361 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 337 time to evaluate : 2.873 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 15 residues processed: 9 average time/residue: 0.8680 time to fit residues: 14.6055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 0.9980 chunk 118 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 178 optimal weight: 0.9990 chunk 144 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 187 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 165 GLN ** I 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 17856 Z= 0.222 Angle : 0.572 7.099 24196 Z= 0.282 Chirality : 0.043 0.148 2676 Planarity : 0.005 0.047 3084 Dihedral : 6.798 52.584 2508 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.51 % Allowed : 15.12 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.38 (0.18), residues: 2136 helix: 0.77 (0.17), residues: 916 sheet: -0.27 (0.27), residues: 364 loop : 0.12 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 358 HIS 0.005 0.001 HIS I 116 PHE 0.013 0.001 PHE G 163 TYR 0.013 0.001 TYR D 42 ARG 0.007 0.001 ARG G 550 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 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 391 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 362 time to evaluate : 2.821 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 outliers start: 29 outliers final: 17 residues processed: 374 average time/residue: 2.5155 time to fit residues: 1075.1626 Evaluate side-chains 345 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 328 time to evaluate : 2.750 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 10 residues processed: 7 average time/residue: 1.3529 time to fit residues: 15.4780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 0.9980 chunk 188 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 208 optimal weight: 2.9990 chunk 173 optimal weight: 0.9980 chunk 96 optimal weight: 0.0370 chunk 17 optimal weight: 1.9990 chunk 69 optimal weight: 0.1980 chunk 109 optimal weight: 1.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17856 Z= 0.184 Angle : 0.538 6.362 24196 Z= 0.266 Chirality : 0.043 0.155 2676 Planarity : 0.004 0.049 3084 Dihedral : 6.527 51.611 2508 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.25 % Allowed : 15.49 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.51 (0.18), residues: 2136 helix: 0.86 (0.17), residues: 928 sheet: -0.22 (0.27), residues: 364 loop : 0.21 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 358 HIS 0.004 0.001 HIS I 116 PHE 0.012 0.001 PHE D 163 TYR 0.012 0.001 TYR C 42 ARG 0.008 0.000 ARG C 550 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 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 368 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 344 time to evaluate : 2.759 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 outliers start: 24 outliers final: 19 residues processed: 356 average time/residue: 2.6927 time to fit residues: 1083.7582 Evaluate side-chains 347 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 328 time to evaluate : 2.937 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 11 residues processed: 8 average time/residue: 0.6875 time to fit residues: 11.8945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 119 optimal weight: 0.4980 chunk 152 optimal weight: 0.3980 chunk 118 optimal weight: 0.8980 chunk 175 optimal weight: 0.0980 chunk 116 optimal weight: 0.7980 chunk 208 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 126 optimal weight: 0.8980 chunk 96 optimal weight: 0.0050 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 17856 Z= 0.148 Angle : 0.517 7.582 24196 Z= 0.254 Chirality : 0.042 0.144 2676 Planarity : 0.004 0.070 3084 Dihedral : 6.144 50.003 2508 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.35 % Allowed : 15.85 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.69 (0.18), residues: 2136 helix: 1.02 (0.17), residues: 928 sheet: -0.16 (0.28), residues: 364 loop : 0.31 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 358 HIS 0.003 0.001 HIS G 116 PHE 0.010 0.001 PHE D 163 TYR 0.011 0.001 TYR I 42 ARG 0.008 0.000 ARG G 550 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 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 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 354 time to evaluate : 2.798 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 outliers start: 26 outliers final: 15 residues processed: 365 average time/residue: 2.6338 time to fit residues: 1095.1705 Evaluate side-chains 350 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 335 time to evaluate : 2.463 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 10 residues processed: 5 average time/residue: 0.7446 time to fit residues: 8.7930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 163 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.4760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 17856 Z= 0.333 Angle : 0.605 8.129 24196 Z= 0.301 Chirality : 0.045 0.156 2676 Planarity : 0.005 0.057 3084 Dihedral : 7.003 53.650 2508 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.04 % Allowed : 16.58 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.41 (0.18), residues: 2136 helix: 0.75 (0.17), residues: 920 sheet: -0.12 (0.27), residues: 364 loop : 0.13 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP I 358 HIS 0.007 0.002 HIS G 116 PHE 0.018 0.002 PHE D 163 TYR 0.016 0.002 TYR D 314 ARG 0.015 0.001 ARG D 81 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 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 378 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 358 time to evaluate : 2.798 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 outliers start: 20 outliers final: 14 residues processed: 370 average time/residue: 2.6452 time to fit residues: 1111.1544 Evaluate side-chains 356 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 342 time to evaluate : 2.684 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 11 residues processed: 3 average time/residue: 0.4572 time to fit residues: 5.8790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 2.9990 chunk 181 optimal weight: 0.2980 chunk 194 optimal weight: 0.5980 chunk 116 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 152 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 175 optimal weight: 0.5980 chunk 183 optimal weight: 0.1980 chunk 193 optimal weight: 0.6980 chunk 127 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.4862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17856 Z= 0.160 Angle : 0.536 7.595 24196 Z= 0.264 Chirality : 0.042 0.145 2676 Planarity : 0.005 0.069 3084 Dihedral : 6.411 51.503 2508 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.09 % Allowed : 16.53 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.66 (0.18), residues: 2136 helix: 0.92 (0.17), residues: 928 sheet: -0.01 (0.27), residues: 360 loop : 0.30 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 358 HIS 0.004 0.001 HIS G 116 PHE 0.011 0.001 PHE G 163 TYR 0.011 0.001 TYR I 42 ARG 0.011 0.001 ARG D 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 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 377 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 356 time to evaluate : 2.571 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 outliers start: 21 outliers final: 19 residues processed: 368 average time/residue: 2.8978 time to fit residues: 1209.5862 Evaluate side-chains 369 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 350 time to evaluate : 3.034 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 12 residues processed: 7 average time/residue: 0.7204 time to fit residues: 11.1547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 142 optimal weight: 0.6980 chunk 215 optimal weight: 3.9990 chunk 198 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 chunk 136 optimal weight: 0.0010 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.4921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17856 Z= 0.218 Angle : 0.552 9.304 24196 Z= 0.273 Chirality : 0.043 0.147 2676 Planarity : 0.005 0.066 3084 Dihedral : 6.538 52.005 2508 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.09 % Allowed : 17.15 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.67 (0.18), residues: 2136 helix: 0.96 (0.17), residues: 920 sheet: -0.01 (0.27), residues: 360 loop : 0.27 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 358 HIS 0.005 0.001 HIS G 116 PHE 0.012 0.001 PHE G 163 TYR 0.012 0.001 TYR I 42 ARG 0.012 0.001 ARG G 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 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 383 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 362 time to evaluate : 2.621 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 outliers start: 21 outliers final: 14 residues processed: 374 average time/residue: 2.3588 time to fit residues: 995.1159 Evaluate side-chains 371 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 357 time to evaluate : 2.051 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 2 average time/residue: 1.2574 time to fit residues: 5.8508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 171 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: