Starting phenix.real_space_refine on Sat Feb 17 05:54:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yzi_14388/02_2024/7yzi_14388_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yzi_14388/02_2024/7yzi_14388.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yzi_14388/02_2024/7yzi_14388_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yzi_14388/02_2024/7yzi_14388_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yzi_14388/02_2024/7yzi_14388_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yzi_14388/02_2024/7yzi_14388.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yzi_14388/02_2024/7yzi_14388.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yzi_14388/02_2024/7yzi_14388_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yzi_14388/02_2024/7yzi_14388_trim_updated.pdb" } resolution = 3.83 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 800 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 6 5.49 5 S 30 5.16 5 C 5402 2.51 5 N 1473 2.21 5 O 1601 1.98 5 H 8375 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 49": "OE1" <-> "OE2" Residue "C ARG 50": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 49": "OE1" <-> "OE2" Residue "D ARG 50": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 49": "OE1" <-> "OE2" Residue "E ARG 50": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16891 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5775 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 5774 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 17, 'TRANS': 360} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 378, 5774 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 17, 'TRANS': 360} Chain breaks: 1 bond proxies already assigned to first conformer: 5835 Chain: "B" Number of atoms: 5775 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 5774 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 17, 'TRANS': 360} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 378, 5774 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 17, 'TRANS': 360} Chain breaks: 1 bond proxies already assigned to first conformer: 5835 Chain: "C" Number of atoms: 1752 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 117, 1711 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Conformer: "B" Number of residues, atoms: 117, 1711 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} bond proxies already assigned to first conformer: 1686 Chain: "D" Number of atoms: 1752 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 117, 1711 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Conformer: "B" Number of residues, atoms: 117, 1711 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} bond proxies already assigned to first conformer: 1686 Chain: "E" Number of atoms: 1749 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 117, 1708 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Conformer: "B" Number of residues, atoms: 117, 1708 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} bond proxies already assigned to first conformer: 1683 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 44 Unusual residues: {' MN': 2, 'ONM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 44 Unusual residues: {' MN': 2, 'ONM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N AARG C 24 " occ=0.55 ... (46 atoms not shown) pdb="HH22BARG C 24 " occ=0.45 residue: pdb=" N AGLU C 93 " occ=0.50 ... (28 atoms not shown) pdb=" HG3BGLU C 93 " occ=0.50 residue: pdb=" N AARG D 24 " occ=0.55 ... (46 atoms not shown) pdb="HH22BARG D 24 " occ=0.45 residue: pdb=" N AGLU D 93 " occ=0.50 ... (28 atoms not shown) pdb=" HG3BGLU D 93 " occ=0.50 residue: pdb=" N AARG E 24 " occ=0.55 ... (46 atoms not shown) pdb="HH22BARG E 24 " occ=0.45 residue: pdb=" N AGLU E 93 " occ=0.50 ... (28 atoms not shown) pdb=" HG3BGLU E 93 " occ=0.50 residue: pdb="MN MN A 503 " occ=0.99 residue: pdb="MN MN B 503 " occ=0.99 Time building chain proxies: 14.39, per 1000 atoms: 0.85 Number of scatterers: 16891 At special positions: 0 Unit cell: (84.48, 100.98, 159.06, 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) Mn 4 24.99 S 30 16.00 P 6 15.00 O 1601 8.00 N 1473 7.00 C 5402 6.00 H 8375 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 27 " - pdb=" SG CYS C 100 " distance=2.02 Simple disulfide: pdb=" SG CYS D 27 " - pdb=" SG CYS D 100 " distance=2.02 Simple disulfide: pdb=" SG CYS E 27 " - pdb=" SG CYS E 100 " distance=2.02 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.75 Conformation dependent library (CDL) restraints added in 3.5 seconds 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2022 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 15 sheets defined 45.3% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.62 Creating SS restraints... Processing helix chain 'A' and resid 43 through 68 removed outlier: 3.503A pdb=" N LEU A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 92 removed outlier: 4.158A pdb=" N ILE A 79 " --> pdb=" O TYR A 75 " (cutoff:3.500A) Proline residue: A 91 - end of helix Processing helix chain 'A' and resid 100 through 119 removed outlier: 3.703A pdb=" N ASP A 119 " --> pdb=" O ALA A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 124 No H-bonds generated for 'chain 'A' and resid 122 through 124' Processing helix chain 'A' and resid 126 through 140 removed outlier: 3.725A pdb=" N PHE A 130 " --> pdb=" O ALA A 126 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU A 131 " --> pdb=" O GLN A 127 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL A 138 " --> pdb=" O ALA A 134 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 165 removed outlier: 5.319A pdb=" N ALA A 147 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE A 161 " --> pdb=" O GLY A 158 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLU A 164 " --> pdb=" O ILE A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 226 removed outlier: 3.766A pdb=" N ALA A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER A 219 " --> pdb=" O GLU A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 236 removed outlier: 3.504A pdb=" N GLU A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG A 234 " --> pdb=" O SER A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 265 Processing helix chain 'A' and resid 269 through 290 Processing helix chain 'A' and resid 315 through 332 Processing helix chain 'A' and resid 369 through 379 Processing helix chain 'A' and resid 390 through 396 Processing helix chain 'B' and resid 43 through 68 removed outlier: 3.503A pdb=" N LEU B 64 " --> pdb=" O GLY B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 92 removed outlier: 4.158A pdb=" N ILE B 79 " --> pdb=" O TYR B 75 " (cutoff:3.500A) Proline residue: B 91 - end of helix Processing helix chain 'B' and resid 100 through 119 removed outlier: 3.704A pdb=" N ASP B 119 " --> pdb=" O ALA B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 124 No H-bonds generated for 'chain 'B' and resid 122 through 124' Processing helix chain 'B' and resid 126 through 140 removed outlier: 3.725A pdb=" N PHE B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 131 " --> pdb=" O GLN B 127 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL B 138 " --> pdb=" O ALA B 134 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 165 removed outlier: 5.319A pdb=" N ALA B 147 " --> pdb=" O GLU B 144 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE B 161 " --> pdb=" O GLY B 158 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLU B 164 " --> pdb=" O ILE B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 226 removed outlier: 3.766A pdb=" N ALA B 194 " --> pdb=" O ALA B 190 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER B 219 " --> pdb=" O GLU B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 236 removed outlier: 3.503A pdb=" N GLU B 233 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG B 234 " --> pdb=" O SER B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 265 Processing helix chain 'B' and resid 269 through 290 Processing helix chain 'B' and resid 315 through 332 Processing helix chain 'B' and resid 369 through 379 Processing helix chain 'B' and resid 390 through 396 Processing helix chain 'C' and resid 34 through 36 No H-bonds generated for 'chain 'C' and resid 34 through 36' Processing helix chain 'C' and resid 66 through 68 No H-bonds generated for 'chain 'C' and resid 66 through 68' Processing helix chain 'C' and resid 92 through 94 No H-bonds generated for 'chain 'C' and resid 92 through 94' Processing helix chain 'C' and resid 103 through 108 Processing helix chain 'D' and resid 34 through 36 No H-bonds generated for 'chain 'D' and resid 34 through 36' Processing helix chain 'D' and resid 66 through 68 No H-bonds generated for 'chain 'D' and resid 66 through 68' Processing helix chain 'D' and resid 92 through 94 No H-bonds generated for 'chain 'D' and resid 92 through 94' Processing helix chain 'D' and resid 103 through 108 Processing helix chain 'E' and resid 34 through 36 No H-bonds generated for 'chain 'E' and resid 34 through 36' Processing helix chain 'E' and resid 66 through 68 No H-bonds generated for 'chain 'E' and resid 66 through 68' Processing helix chain 'E' and resid 92 through 94 No H-bonds generated for 'chain 'E' and resid 92 through 94' Processing helix chain 'E' and resid 103 through 108 Processing sheet with id= A, first strand: chain 'A' and resid 245 through 247 Processing sheet with id= B, first strand: chain 'A' and resid 302 through 306 removed outlier: 3.531A pdb=" N SER A 251 " --> pdb=" O SER A 306 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N GLN A 385 " --> pdb=" O VAL A 345 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N LEU A 347 " --> pdb=" O GLN A 385 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLN A 387 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N THR A 349 " --> pdb=" O GLN A 387 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 401 through 403 removed outlier: 6.804A pdb=" N ARG A 403 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N LEU A 421 " --> pdb=" O ARG A 403 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 245 through 247 Processing sheet with id= E, first strand: chain 'B' and resid 302 through 306 removed outlier: 3.531A pdb=" N SER B 251 " --> pdb=" O SER B 306 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLN B 385 " --> pdb=" O VAL B 345 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LEU B 347 " --> pdb=" O GLN B 385 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLN B 387 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N THR B 349 " --> pdb=" O GLN B 387 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 401 through 403 removed outlier: 6.804A pdb=" N ARG B 403 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N LEU B 421 " --> pdb=" O ARG B 403 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 8 through 12 Processing sheet with id= H, first strand: chain 'C' and resid 40 through 44 Processing sheet with id= I, first strand: chain 'C' and resid 54 through 56 Processing sheet with id= J, first strand: chain 'D' and resid 8 through 12 Processing sheet with id= K, first strand: chain 'D' and resid 40 through 44 Processing sheet with id= L, first strand: chain 'D' and resid 54 through 56 Processing sheet with id= M, first strand: chain 'E' and resid 8 through 12 Processing sheet with id= N, first strand: chain 'E' and resid 40 through 44 Processing sheet with id= O, first strand: chain 'E' and resid 54 through 56 456 hydrogen bonds defined for protein. 1194 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: 5.76 Time building geometry restraints manager: 13.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.80 - 1.00: 8366 1.00 - 1.20: 15 1.20 - 1.40: 3569 1.40 - 1.60: 5063 1.60 - 1.80: 64 Bond restraints: 17077 Sorted by residual: bond pdb=" NH1 ARG A 44 " pdb="HH11 ARG A 44 " ideal model delta sigma weight residual 0.860 0.953 -0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" CG PRO A 176 " pdb=" CD PRO A 176 " ideal model delta sigma weight residual 1.503 1.350 0.153 3.40e-02 8.65e+02 2.02e+01 bond pdb=" CG PRO B 176 " pdb=" CD PRO B 176 " ideal model delta sigma weight residual 1.503 1.350 0.153 3.40e-02 8.65e+02 2.01e+01 bond pdb=" N PRO B 176 " pdb=" CD PRO B 176 " ideal model delta sigma weight residual 1.473 1.534 -0.061 1.40e-02 5.10e+03 1.87e+01 bond pdb=" N PRO A 176 " pdb=" CD PRO A 176 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.85e+01 ... (remaining 17072 not shown) Histogram of bond angle deviations from ideal: 58.82 - 78.62: 41 78.62 - 98.42: 139 98.42 - 118.21: 22661 118.21 - 138.01: 7928 138.01 - 157.81: 6 Bond angle restraints: 30775 Sorted by residual: angle pdb=" CD GLN A 66 " pdb=" CG GLN A 66 " pdb=" HG3 GLN A 66 " ideal model delta sigma weight residual 108.00 58.82 49.18 3.00e+00 1.11e-01 2.69e+02 angle pdb=" CG ARG A 403 " pdb=" CB ARG A 403 " pdb=" HB2 ARG A 403 " ideal model delta sigma weight residual 108.00 62.13 45.87 3.00e+00 1.11e-01 2.34e+02 angle pdb=" CD GLU A 293 " pdb=" CG GLU A 293 " pdb=" HG3 GLU A 293 " ideal model delta sigma weight residual 108.00 62.42 45.58 3.00e+00 1.11e-01 2.31e+02 angle pdb=" NE ARG A 95 " pdb=" CD ARG A 95 " pdb=" HD2 ARG A 95 " ideal model delta sigma weight residual 108.00 62.74 45.26 3.00e+00 1.11e-01 2.28e+02 angle pdb=" CA ARG A 403 " pdb=" CB ARG A 403 " pdb=" HB2 ARG A 403 " ideal model delta sigma weight residual 109.00 64.17 44.83 3.00e+00 1.11e-01 2.23e+02 ... (remaining 30770 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.33: 7098 18.33 - 36.67: 555 36.67 - 55.00: 282 55.00 - 73.34: 58 73.34 - 91.67: 29 Dihedral angle restraints: 8022 sinusoidal: 4308 harmonic: 3714 Sorted by residual: dihedral pdb=" C ARG B 44 " pdb=" N ARG B 44 " pdb=" CA ARG B 44 " pdb=" CB ARG B 44 " ideal model delta harmonic sigma weight residual -122.60 -96.82 -25.78 0 2.50e+00 1.60e-01 1.06e+02 dihedral pdb=" C ARG A 44 " pdb=" N ARG A 44 " pdb=" CA ARG A 44 " pdb=" CB ARG A 44 " ideal model delta harmonic sigma weight residual -122.60 -96.83 -25.77 0 2.50e+00 1.60e-01 1.06e+02 dihedral pdb=" CD ARG C 50 " pdb=" NE ARG C 50 " pdb=" CZ ARG C 50 " pdb=" NH1 ARG C 50 " ideal model delta sinusoidal sigma weight residual 0.00 -91.42 91.42 1 1.00e+01 1.00e-02 9.84e+01 ... (remaining 8019 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.224: 1351 0.224 - 0.448: 7 0.448 - 0.672: 2 0.672 - 0.897: 5 0.897 - 1.121: 2 Chirality restraints: 1367 Sorted by residual: chirality pdb=" CB VAL A 308 " pdb=" CA VAL A 308 " pdb=" CG1 VAL A 308 " pdb=" CG2 VAL A 308 " both_signs ideal model delta sigma weight residual False -2.63 -1.51 -1.12 2.00e-01 2.50e+01 3.14e+01 chirality pdb=" CB VAL B 308 " pdb=" CA VAL B 308 " pdb=" CG1 VAL B 308 " pdb=" CG2 VAL B 308 " both_signs ideal model delta sigma weight residual False -2.63 -1.51 -1.12 2.00e-01 2.50e+01 3.13e+01 chirality pdb=" CG LEU B 333 " pdb=" CB LEU B 333 " pdb=" CD1 LEU B 333 " pdb=" CD2 LEU B 333 " both_signs ideal model delta sigma weight residual False -2.59 -1.83 -0.76 2.00e-01 2.50e+01 1.43e+01 ... (remaining 1364 not shown) Planarity restraints: 2586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 177 " -0.026 2.00e-02 2.50e+03 7.10e-02 2.02e+02 pdb=" CG TRP A 177 " 0.206 2.00e-02 2.50e+03 pdb=" CD1 TRP A 177 " -0.158 2.00e-02 2.50e+03 pdb=" CD2 TRP A 177 " 0.032 2.00e-02 2.50e+03 pdb=" NE1 TRP A 177 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 TRP A 177 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 177 " -0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 177 " 0.011 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 177 " -0.023 2.00e-02 2.50e+03 pdb=" CH2 TRP A 177 " 0.017 2.00e-02 2.50e+03 pdb=" HD1 TRP A 177 " -0.060 2.00e-02 2.50e+03 pdb=" HE1 TRP A 177 " 0.025 2.00e-02 2.50e+03 pdb=" HE3 TRP A 177 " -0.029 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 177 " 0.021 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 177 " 0.011 2.00e-02 2.50e+03 pdb=" HH2 TRP A 177 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 177 " -0.030 2.00e-02 2.50e+03 6.79e-02 1.84e+02 pdb=" CG TRP B 177 " 0.203 2.00e-02 2.50e+03 pdb=" CD1 TRP B 177 " -0.161 2.00e-02 2.50e+03 pdb=" CD2 TRP B 177 " 0.027 2.00e-02 2.50e+03 pdb=" NE1 TRP B 177 " 0.034 2.00e-02 2.50e+03 pdb=" CE2 TRP B 177 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 177 " -0.021 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 177 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 177 " -0.031 2.00e-02 2.50e+03 pdb=" CH2 TRP B 177 " 0.009 2.00e-02 2.50e+03 pdb=" HD1 TRP B 177 " -0.028 2.00e-02 2.50e+03 pdb=" HE1 TRP B 177 " 0.016 2.00e-02 2.50e+03 pdb=" HE3 TRP B 177 " -0.025 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 177 " 0.008 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 177 " 0.017 2.00e-02 2.50e+03 pdb=" HH2 TRP B 177 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 360 " -1.008 9.50e-02 1.11e+02 3.37e-01 1.37e+02 pdb=" NE ARG A 360 " 0.082 2.00e-02 2.50e+03 pdb=" CZ ARG A 360 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 360 " -0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG A 360 " -0.024 2.00e-02 2.50e+03 pdb="HH11 ARG A 360 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG A 360 " -0.014 2.00e-02 2.50e+03 pdb="HH21 ARG A 360 " -0.025 2.00e-02 2.50e+03 pdb="HH22 ARG A 360 " 0.039 2.00e-02 2.50e+03 ... (remaining 2583 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.92: 253 1.92 - 2.59: 18828 2.59 - 3.26: 49974 3.26 - 3.93: 62205 3.93 - 4.60: 96880 Nonbonded interactions: 228140 Sorted by model distance: nonbonded pdb=" HG3 ARG A 44 " pdb=" HD2 ARG A 44 " model vdw 1.256 1.952 nonbonded pdb=" HB3 ASP B 170 " pdb=" OD1 ASN E 37 " model vdw 1.333 2.620 nonbonded pdb=" O GLY A 172 " pdb=" HE1 TRP E 52 " model vdw 1.390 1.850 nonbonded pdb=" HG LEU A 333 " pdb="HD13 LEU A 333 " model vdw 1.394 1.952 nonbonded pdb=" HD2 LYS B 334 " pdb=" HE2 LYS B 334 " model vdw 1.402 1.952 ... (remaining 228135 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 41 through 171 or (resid 172 and (name N or name CA or nam \ e C or name O or name HA2 or name HA3)) or resid 173 through 365 or resid 367 th \ rough 428 or resid 501 through 503)) selection = (chain 'B' and (resid 41 through 179 or (resid 180 and (name N or name CA or nam \ e C or name O or name CB or name OG or name H or name HA or name HB2 or name HB3 \ )) or resid 181 through 365 or resid 367 through 428 or resid 501 through 503)) } ncs_group { reference = (chain 'C' and (resid 6 through 23 or resid 26 through 36 or (resid 37 and (name \ N or name CA or name C or name O or name CB or name CG or name OD1 or name ND2 \ or name H or name HA or name HB2 or name HB3 or name HD21)) or resid 38 through \ 92 or resid 95 through 105 or (resid 106 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name NE or name CZ or name NH1 or name N \ H2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name \ HD2 or name HD3 or name HE or name HH11 or name HH21)) or resid 107 through 122) \ ) selection = (chain 'D' and (resid 6 through 23 or resid 26 through 36 or (resid 37 and (name \ N or name CA or name C or name O or name CB or name CG or name OD1 or name ND2 \ or name H or name HA or name HB2 or name HB3 or name HD21)) or resid 38 through \ 92 or resid 95 through 105 or (resid 106 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name NE or name CZ or name NH1 or name N \ H2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name \ HD2 or name HD3 or name HE or name HH11 or name HH21)) or resid 107 through 122) \ ) selection = (chain 'E' and (resid 6 through 23 or resid 26 through 92 or resid 95 through 12 \ 2)) } 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=0.32 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 4.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.270 Extract box with map and model: 13.740 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 64.440 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.090 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 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 : 0.009 0.153 8702 Z= 0.602 Angle : 1.670 33.796 11886 Z= 0.847 Chirality : 0.087 1.121 1367 Planarity : 0.037 0.463 1516 Dihedral : 18.277 91.672 3024 Min Nonbonded Distance : 1.618 Molprobity Statistics. All-atom Clashscore : 25.57 Ramachandran Plot: Outliers : 0.82 % Allowed : 4.94 % Favored : 94.24 % Rotamer: Outliers : 11.24 % Allowed : 2.29 % Favored : 86.47 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -0.97 (0.23), residues: 1111 helix: 0.56 (0.23), residues: 484 sheet: -1.16 (0.33), residues: 198 loop : -1.72 (0.25), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.196 0.008 TRP B 177 HIS 0.024 0.005 HIS A 216 PHE 0.107 0.006 PHE C 72 TYR 0.083 0.009 TYR C 98 ARG 0.137 0.006 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 180 is missing expected H atoms. Skipping. Evaluate side-chains 296 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 203 time to evaluate : 1.260 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: A 332 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7606 (tm-30) REVERT: B 65 MET cc_start: 0.8212 (ttm) cc_final: 0.8002 (tmm) REVERT: B 376 ARG cc_start: 0.7148 (OUTLIER) cc_final: 0.6484 (mtp180) REVERT: C 48 ASN cc_start: 0.5061 (p0) cc_final: 0.4286 (p0) REVERT: D 33 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7897 (mm) REVERT: D 62 THR cc_start: 0.7660 (OUTLIER) cc_final: 0.7445 (p) outliers start: 93 outliers final: 33 residues processed: 269 average time/residue: 0.4908 time to fit residues: 175.4685 Evaluate side-chains 165 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 128 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 66 GLN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 239 GLU Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 376 ARG Chi-restraints excluded: chain B residue 391 GLU Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 89 SER Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 50 ARG Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 76 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 174 GLN ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 8702 Z= 0.286 Angle : 0.844 17.394 11886 Z= 0.436 Chirality : 0.115 1.713 1367 Planarity : 0.009 0.161 1516 Dihedral : 11.249 101.476 1330 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.55 % Allowed : 3.39 % Favored : 96.07 % Rotamer: Outliers : 5.05 % Allowed : 12.50 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.29 (0.24), residues: 1111 helix: 1.06 (0.23), residues: 496 sheet: -1.18 (0.33), residues: 207 loop : -1.12 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 177 HIS 0.002 0.001 HIS B 94 PHE 0.022 0.002 PHE B 62 TYR 0.016 0.002 TYR C 42 ARG 0.010 0.001 ARG B 360 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 180 is missing expected H atoms. Skipping. Evaluate side-chains 180 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 141 time to evaluate : 1.430 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: A 186 THR cc_start: 0.8699 (m) cc_final: 0.8491 (m) REVERT: B 65 MET cc_start: 0.8462 (ttm) cc_final: 0.8196 (tmm) REVERT: B 177 TRP cc_start: 0.6906 (OUTLIER) cc_final: 0.6453 (p-90) REVERT: B 376 ARG cc_start: 0.7232 (OUTLIER) cc_final: 0.6667 (mtp180) REVERT: E 33 ILE cc_start: 0.6468 (mp) cc_final: 0.5994 (tp) outliers start: 39 outliers final: 24 residues processed: 175 average time/residue: 0.4729 time to fit residues: 112.0038 Evaluate side-chains 141 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 115 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 177 TRP Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 363 PHE Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 177 TRP Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 376 ARG Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 50 ARG Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain E residue 113 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 105 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 ASN ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8702 Z= 0.243 Angle : 0.744 11.847 11886 Z= 0.380 Chirality : 0.117 1.773 1367 Planarity : 0.005 0.048 1516 Dihedral : 8.028 58.553 1261 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.46 % Allowed : 2.84 % Favored : 96.71 % Rotamer: Outliers : 4.13 % Allowed : 14.56 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.34 (0.25), residues: 1111 helix: 1.53 (0.23), residues: 491 sheet: -0.57 (0.34), residues: 191 loop : -0.88 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 177 HIS 0.003 0.001 HIS B 290 PHE 0.023 0.002 PHE E 55 TYR 0.021 0.002 TYR C 42 ARG 0.006 0.001 ARG C 50 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 180 is missing expected H atoms. Skipping. Evaluate side-chains 150 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 119 time to evaluate : 1.226 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: B 65 MET cc_start: 0.8600 (ttm) cc_final: 0.8390 (tmm) REVERT: B 376 ARG cc_start: 0.7151 (OUTLIER) cc_final: 0.6266 (mtp180) REVERT: C 34 LEU cc_start: 0.7777 (tt) cc_final: 0.7545 (tt) REVERT: E 9 LEU cc_start: 0.6381 (mm) cc_final: 0.5969 (mp) REVERT: E 33 ILE cc_start: 0.6750 (mp) cc_final: 0.6359 (tp) outliers start: 31 outliers final: 19 residues processed: 146 average time/residue: 0.4513 time to fit residues: 91.5541 Evaluate side-chains 127 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 107 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 177 TRP Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain B residue 376 ARG Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 50 ARG Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 80 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 10 optimal weight: 0.4980 chunk 46 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 97 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 51 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 GLN B 317 GLN ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.4631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8702 Z= 0.216 Angle : 0.694 11.786 11886 Z= 0.354 Chirality : 0.116 1.725 1367 Planarity : 0.004 0.044 1516 Dihedral : 6.988 58.818 1249 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.46 % Allowed : 2.84 % Favored : 96.71 % Rotamer: Outliers : 2.64 % Allowed : 17.78 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.62 (0.25), residues: 1111 helix: 1.70 (0.23), residues: 497 sheet: -0.43 (0.34), residues: 209 loop : -0.68 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 367 HIS 0.001 0.000 HIS B 94 PHE 0.010 0.001 PHE B 62 TYR 0.012 0.002 TYR C 42 ARG 0.007 0.001 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 180 is missing expected H atoms. Skipping. Evaluate side-chains 125 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 107 time to evaluate : 1.297 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: B 376 ARG cc_start: 0.7078 (OUTLIER) cc_final: 0.6080 (mtp180) REVERT: E 33 ILE cc_start: 0.6957 (mp) cc_final: 0.6559 (tp) outliers start: 18 outliers final: 13 residues processed: 122 average time/residue: 0.4313 time to fit residues: 72.9175 Evaluate side-chains 115 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 101 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 376 ARG Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 50 ARG Chi-restraints excluded: chain E residue 77 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 88 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.5484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 8702 Z= 0.327 Angle : 0.761 11.877 11886 Z= 0.391 Chirality : 0.117 1.724 1367 Planarity : 0.004 0.044 1516 Dihedral : 6.351 59.114 1241 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.46 % Allowed : 4.12 % Favored : 95.43 % Rotamer: Outliers : 3.21 % Allowed : 18.35 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.24), residues: 1111 helix: 1.21 (0.22), residues: 485 sheet: -0.48 (0.34), residues: 209 loop : -0.98 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 52 HIS 0.007 0.001 HIS A 315 PHE 0.024 0.002 PHE B 283 TYR 0.022 0.002 TYR C 98 ARG 0.009 0.001 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 180 is missing expected H atoms. Skipping. Evaluate side-chains 132 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 109 time to evaluate : 1.432 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: E 33 ILE cc_start: 0.7313 (mp) cc_final: 0.6935 (tp) outliers start: 23 outliers final: 20 residues processed: 128 average time/residue: 0.4063 time to fit residues: 74.4176 Evaluate side-chains 125 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 105 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 177 TRP Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 82 PHE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 50 ARG Chi-restraints excluded: chain E residue 77 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 99 optimal weight: 9.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.5727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8702 Z= 0.219 Angle : 0.694 11.704 11886 Z= 0.351 Chirality : 0.116 1.735 1367 Planarity : 0.004 0.045 1516 Dihedral : 5.583 55.938 1236 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.46 % Allowed : 3.11 % Favored : 96.43 % Rotamer: Outliers : 2.87 % Allowed : 19.61 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.33 % 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: 0.57 (0.25), residues: 1111 helix: 1.58 (0.22), residues: 483 sheet: -0.05 (0.35), residues: 207 loop : -0.76 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 52 HIS 0.001 0.000 HIS A 94 PHE 0.016 0.001 PHE B 283 TYR 0.013 0.002 TYR C 98 ARG 0.005 0.000 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 180 is missing expected H atoms. Skipping. Evaluate side-chains 128 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 1.738 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 outliers start: 20 outliers final: 18 residues processed: 125 average time/residue: 0.4175 time to fit residues: 77.6411 Evaluate side-chains 120 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 102 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 177 TRP Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 363 PHE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 50 ARG Chi-restraints excluded: chain E residue 77 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.5998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8702 Z= 0.206 Angle : 0.684 11.722 11886 Z= 0.346 Chirality : 0.116 1.745 1367 Planarity : 0.004 0.047 1516 Dihedral : 5.472 53.942 1236 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.46 % Allowed : 3.29 % Favored : 96.25 % Rotamer: Outliers : 2.64 % Allowed : 20.07 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.33 % 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: 0.79 (0.25), residues: 1111 helix: 1.80 (0.22), residues: 483 sheet: 0.05 (0.35), residues: 207 loop : -0.68 (0.32), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 52 HIS 0.002 0.000 HIS B 290 PHE 0.018 0.001 PHE B 283 TYR 0.012 0.001 TYR C 98 ARG 0.006 0.000 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 180 is missing expected H atoms. Skipping. Evaluate side-chains 123 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 104 time to evaluate : 1.251 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: B 45 GLN cc_start: 0.8242 (tm-30) cc_final: 0.8028 (tm-30) outliers start: 19 outliers final: 18 residues processed: 120 average time/residue: 0.3694 time to fit residues: 65.0619 Evaluate side-chains 120 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 102 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 177 TRP Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 82 PHE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 50 ARG Chi-restraints excluded: chain E residue 77 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 81 optimal weight: 8.9990 chunk 93 optimal weight: 0.4980 chunk 98 optimal weight: 6.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.6147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8702 Z= 0.193 Angle : 0.679 11.700 11886 Z= 0.342 Chirality : 0.116 1.751 1367 Planarity : 0.004 0.044 1516 Dihedral : 5.301 50.002 1236 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.46 % Allowed : 2.93 % Favored : 96.61 % Rotamer: Outliers : 2.64 % Allowed : 19.95 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.33 % 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 (0.26), residues: 1111 helix: 1.97 (0.22), residues: 496 sheet: 0.14 (0.36), residues: 207 loop : -0.77 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 52 HIS 0.001 0.000 HIS B 290 PHE 0.018 0.001 PHE B 283 TYR 0.012 0.001 TYR C 98 ARG 0.005 0.000 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 180 is missing expected H atoms. Skipping. Evaluate side-chains 124 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 105 time to evaluate : 1.298 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: B 45 GLN cc_start: 0.8242 (tm-30) cc_final: 0.8040 (tm-30) outliers start: 19 outliers final: 19 residues processed: 121 average time/residue: 0.3469 time to fit residues: 62.3496 Evaluate side-chains 121 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 102 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 177 TRP Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain D residue 100 CYS Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 50 ARG Chi-restraints excluded: chain E residue 77 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 7.9990 chunk 96 optimal weight: 20.0000 chunk 98 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 41 optimal weight: 0.0770 chunk 75 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 86 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 overall best weight: 2.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.6533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8702 Z= 0.261 Angle : 0.715 11.755 11886 Z= 0.364 Chirality : 0.117 1.745 1367 Planarity : 0.004 0.042 1516 Dihedral : 5.649 54.210 1236 Min Nonbonded Distance : 1.336 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.46 % Allowed : 4.21 % Favored : 95.33 % Rotamer: Outliers : 3.10 % Allowed : 19.72 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.33 % 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 (0.25), residues: 1111 helix: 1.65 (0.22), residues: 491 sheet: -0.20 (0.35), residues: 213 loop : -0.88 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 41 HIS 0.004 0.001 HIS B 315 PHE 0.017 0.001 PHE B 283 TYR 0.020 0.002 TYR C 98 ARG 0.005 0.001 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 180 is missing expected H atoms. Skipping. Evaluate side-chains 128 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 105 time to evaluate : 1.228 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: B 45 GLN cc_start: 0.8290 (tm-30) cc_final: 0.8077 (tm-30) outliers start: 23 outliers final: 23 residues processed: 122 average time/residue: 0.3552 time to fit residues: 64.1642 Evaluate side-chains 128 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 105 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 177 TRP Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 363 PHE Chi-restraints excluded: chain B residue 82 PHE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 100 CYS Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 50 ARG Chi-restraints excluded: chain E residue 77 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 8 optimal weight: 0.3980 chunk 65 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.6573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8702 Z= 0.196 Angle : 0.689 11.621 11886 Z= 0.344 Chirality : 0.116 1.754 1367 Planarity : 0.004 0.042 1516 Dihedral : 5.498 55.657 1236 Min Nonbonded Distance : 1.577 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.46 % Allowed : 3.02 % Favored : 96.52 % Rotamer: Outliers : 2.75 % Allowed : 20.30 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.33 % 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: 0.93 (0.26), residues: 1111 helix: 2.01 (0.22), residues: 487 sheet: 0.09 (0.36), residues: 207 loop : -0.76 (0.33), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 52 HIS 0.002 0.000 HIS B 290 PHE 0.019 0.001 PHE B 283 TYR 0.012 0.001 TYR D 42 ARG 0.004 0.000 ARG E 71 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 180 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 107 time to evaluate : 1.204 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: B 45 GLN cc_start: 0.8273 (tm-30) cc_final: 0.8053 (tm-30) outliers start: 20 outliers final: 20 residues processed: 123 average time/residue: 0.3535 time to fit residues: 64.4084 Evaluate side-chains 125 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 105 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 177 TRP Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 363 PHE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain D residue 100 CYS Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 50 ARG Chi-restraints excluded: chain E residue 77 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.068473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.052687 restraints weight = 301287.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.056012 restraints weight = 96195.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.058164 restraints weight = 48283.866| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3348 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3348 r_free = 0.3348 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.3341 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.6662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8702 Z= 0.211 Angle : 0.687 11.596 11886 Z= 0.344 Chirality : 0.116 1.748 1367 Planarity : 0.004 0.041 1516 Dihedral : 5.440 56.938 1236 Min Nonbonded Distance : 1.410 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.46 % Allowed : 3.29 % Favored : 96.25 % Rotamer: Outliers : 2.64 % Allowed : 20.30 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.33 % 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: 0.94 (0.26), residues: 1111 helix: 2.05 (0.22), residues: 487 sheet: 0.07 (0.36), residues: 207 loop : -0.79 (0.33), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 52 HIS 0.002 0.001 HIS A 315 PHE 0.019 0.001 PHE B 283 TYR 0.017 0.002 TYR D 42 ARG 0.004 0.000 ARG D 76 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4023.14 seconds wall clock time: 72 minutes 18.03 seconds (4338.03 seconds total)