Starting phenix.real_space_refine on Tue Feb 13 18:42:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g04_29644/02_2024/8g04_29644_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g04_29644/02_2024/8g04_29644.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g04_29644/02_2024/8g04_29644.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g04_29644/02_2024/8g04_29644.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g04_29644/02_2024/8g04_29644_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g04_29644/02_2024/8g04_29644_updated.pdb" } resolution = 3.4 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= 0.001 sd= 0.042 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: 4 Type Number sf(0) Gaussians S 39 5.16 5 C 4664 2.51 5 N 1236 2.21 5 O 1375 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7314 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1136 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 11, 'TRANS': 139} Chain: "B" Number of atoms: 3027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3027 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 34, 'TRANS': 363} Chain breaks: 5 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 2, 'PCA:plan-2': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 3, 'TYR:plan': 1, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 141 Chain: "C" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3001 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 34, 'TRANS': 360} Chain breaks: 5 Unresolved non-hydrogen bonds: 184 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'PCA:plan-2': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'TYR:plan': 1, 'GLU:plan': 9, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 141 Chain: "B" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'MAN': 3, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'MAN': 3, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 4.53, per 1000 atoms: 0.62 Number of scatterers: 7314 At special positions: 0 Unit cell: (83.006, 116.424, 130.438, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 39 16.00 O 1375 8.00 N 1236 7.00 C 4664 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 28 " - pdb=" SG CYS A 172 " distance=2.03 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 106 " distance=2.03 Simple disulfide: pdb=" SG CYS B 40 " - pdb=" SG CYS B 50 " distance=2.03 Simple disulfide: pdb=" SG CYS B 77 " - pdb=" SG CYS B 93 " distance=2.03 Simple disulfide: pdb=" SG CYS B 193 " - pdb=" SG CYS B 323 " distance=2.03 Simple disulfide: pdb=" SG CYS B 194 " - pdb=" SG CYS B 241 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 352 " distance=2.03 Simple disulfide: pdb=" SG CYS C 40 " - pdb=" SG CYS C 50 " distance=2.03 Simple disulfide: pdb=" SG CYS C 77 " - pdb=" SG CYS C 93 " distance=2.03 Simple disulfide: pdb=" SG CYS C 193 " - pdb=" SG CYS C 323 " distance=2.03 Simple disulfide: pdb=" SG CYS C 194 " - pdb=" SG CYS C 241 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 334 " - pdb=" SG CYS C 352 " distance=2.03 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=6, symmetry=0 Links applied NAG-ASN " NAG B1001 " - " ASN B 117 " " NAG B1002 " - " ASN B 298 " " NAG B1003 " - " ASN B 358 " " NAG C1001 " - " ASN C 117 " " NAG C1002 " - " ASN C 298 " " NAG C1003 " - " ASN C 358 " Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.88 Conformation dependent library (CDL) restraints added in 2.0 seconds 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1756 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 21 helices and 17 sheets defined 15.6% alpha, 27.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'A' and resid 26 through 28 No H-bonds generated for 'chain 'A' and resid 26 through 28' Processing helix chain 'A' and resid 30 through 49 removed outlier: 3.798A pdb=" N SER A 48 " --> pdb=" O HIS A 44 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLN A 49 " --> pdb=" O SER A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 74 removed outlier: 3.758A pdb=" N THR A 74 " --> pdb=" O GLY A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 101 removed outlier: 3.599A pdb=" N GLY A 100 " --> pdb=" O MET A 96 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLN A 101 " --> pdb=" O ALA A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 129 removed outlier: 3.849A pdb=" N LEU A 128 " --> pdb=" O ALA A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 157 removed outlier: 3.850A pdb=" N PHE A 149 " --> pdb=" O PRO A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 166 Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'B' and resid 28 through 30 No H-bonds generated for 'chain 'B' and resid 28 through 30' Processing helix chain 'B' and resid 127 through 129 No H-bonds generated for 'chain 'B' and resid 127 through 129' Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'B' and resid 190 through 192 No H-bonds generated for 'chain 'B' and resid 190 through 192' Processing helix chain 'B' and resid 284 through 287 Processing helix chain 'B' and resid 385 through 387 No H-bonds generated for 'chain 'B' and resid 385 through 387' Processing helix chain 'C' and resid 28 through 32 removed outlier: 4.274A pdb=" N ALA C 32 " --> pdb=" O SER C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 127 through 129 No H-bonds generated for 'chain 'C' and resid 127 through 129' Processing helix chain 'C' and resid 159 through 164 removed outlier: 5.348A pdb=" N ASP C 163 " --> pdb=" O GLU C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 287 No H-bonds generated for 'chain 'C' and resid 285 through 287' Processing helix chain 'C' and resid 385 through 387 No H-bonds generated for 'chain 'C' and resid 385 through 387' Processing helix chain 'C' and resid 415 through 417 No H-bonds generated for 'chain 'C' and resid 415 through 417' Processing sheet with id= A, first strand: chain 'A' and resid 60 through 62 Processing sheet with id= B, first strand: chain 'B' and resid 39 through 41 removed outlier: 3.550A pdb=" N THR B 49 " --> pdb=" O PHE B 41 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 75 through 77 removed outlier: 4.562A pdb=" N LEU B 65 " --> pdb=" O CYS B 77 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR B 121 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ASN B 113 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N THR B 119 " --> pdb=" O ASN B 113 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 139 through 143 removed outlier: 3.576A pdb=" N TRP B 154 " --> pdb=" O GLY B 239 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 183 through 187 removed outlier: 4.564A pdb=" N TYR B 167 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 292 through 294 removed outlier: 3.774A pdb=" N PHE B 292 " --> pdb=" O THR B 300 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR B 300 " --> pdb=" O PHE B 292 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 310 through 318 removed outlier: 3.696A pdb=" N SER B 310 " --> pdb=" O THR B 369 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 396 through 399 Processing sheet with id= I, first strand: chain 'B' and resid 458 through 465 removed outlier: 3.939A pdb=" N THR B 428 " --> pdb=" O ARG B 458 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS B 436 " --> pdb=" O TYR B 427 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 39 through 41 removed outlier: 3.535A pdb=" N THR C 49 " --> pdb=" O PHE C 41 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 63 through 68 Processing sheet with id= L, first strand: chain 'C' and resid 138 through 143 removed outlier: 4.697A pdb=" N ILE C 138 " --> pdb=" O GLU C 155 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU C 155 " --> pdb=" O ILE C 138 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET C 142 " --> pdb=" O GLN C 151 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 183 through 186 Processing sheet with id= N, first strand: chain 'C' and resid 290 through 294 removed outlier: 4.096A pdb=" N ASN C 298 " --> pdb=" O LEU C 294 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 310 through 318 removed outlier: 3.930A pdb=" N SER C 310 " --> pdb=" O THR C 369 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 395 through 399 removed outlier: 4.163A pdb=" N ASN C 395 " --> pdb=" O GLN C 411 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLN C 411 " --> pdb=" O ASN C 395 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG C 399 " --> pdb=" O GLU C 407 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU C 407 " --> pdb=" O ARG C 399 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 425 through 428 244 hydrogen bonds defined for protein. 654 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: 2.21 Time building geometry restraints manager: 3.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2349 1.34 - 1.46: 1813 1.46 - 1.58: 3316 1.58 - 1.70: 0 1.70 - 1.82: 46 Bond restraints: 7524 Sorted by residual: bond pdb=" N PCA B 26 " pdb=" CD PCA B 26 " ideal model delta sigma weight residual 1.345 1.464 -0.119 2.00e-02 2.50e+03 3.56e+01 bond pdb=" N PCA C 26 " pdb=" CD PCA C 26 " ideal model delta sigma weight residual 1.345 1.463 -0.118 2.00e-02 2.50e+03 3.51e+01 bond pdb=" CG TRP B 474 " pdb=" CD1 TRP B 474 " ideal model delta sigma weight residual 1.365 1.477 -0.112 2.50e-02 1.60e+03 2.01e+01 bond pdb=" CG TRP B 272 " pdb=" CD1 TRP B 272 " ideal model delta sigma weight residual 1.365 1.476 -0.111 2.50e-02 1.60e+03 1.98e+01 bond pdb=" CG TRP C 272 " pdb=" CD1 TRP C 272 " ideal model delta sigma weight residual 1.365 1.476 -0.111 2.50e-02 1.60e+03 1.97e+01 ... (remaining 7519 not shown) Histogram of bond angle deviations from ideal: 100.67 - 107.33: 444 107.33 - 113.99: 4202 113.99 - 120.65: 2644 120.65 - 127.30: 2841 127.30 - 133.96: 162 Bond angle restraints: 10293 Sorted by residual: angle pdb=" CD2 TRP C 269 " pdb=" CE2 TRP C 269 " pdb=" CZ2 TRP C 269 " ideal model delta sigma weight residual 122.40 118.01 4.39 1.00e+00 1.00e+00 1.92e+01 angle pdb=" CD2 TRP B 269 " pdb=" CE2 TRP B 269 " pdb=" CZ2 TRP B 269 " ideal model delta sigma weight residual 122.40 118.04 4.36 1.00e+00 1.00e+00 1.90e+01 angle pdb=" CD2 TRP C 272 " pdb=" CE2 TRP C 272 " pdb=" CZ2 TRP C 272 " ideal model delta sigma weight residual 122.40 118.12 4.28 1.00e+00 1.00e+00 1.84e+01 angle pdb=" CD2 TRP C 474 " pdb=" CE2 TRP C 474 " pdb=" CZ2 TRP C 474 " ideal model delta sigma weight residual 122.40 118.15 4.25 1.00e+00 1.00e+00 1.80e+01 angle pdb=" O PCA C 26 " pdb=" C PCA C 26 " pdb=" N ASP C 27 " ideal model delta sigma weight residual 123.00 116.24 6.76 1.60e+00 3.91e-01 1.79e+01 ... (remaining 10288 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.86: 4250 14.86 - 29.72: 264 29.72 - 44.57: 84 44.57 - 59.43: 24 59.43 - 74.29: 3 Dihedral angle restraints: 4625 sinusoidal: 1912 harmonic: 2713 Sorted by residual: dihedral pdb=" CA PHE B 383 " pdb=" C PHE B 383 " pdb=" N TRP B 384 " pdb=" CA TRP B 384 " ideal model delta harmonic sigma weight residual 180.00 160.02 19.98 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" SG CYS C 193 " pdb=" CB CYS C 323 " pdb=" SG CYS C 323 " pdb=" CA CYS C 323 " ideal model delta sinusoidal sigma weight residual 79.00 22.61 56.39 1 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" N CYS B 352 " pdb=" CA CYS B 352 " pdb=" CB CYS B 352 " pdb=" SG CYS B 352 " ideal model delta sinusoidal sigma weight residual 60.00 116.92 -56.92 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 4622 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 745 0.028 - 0.055: 277 0.055 - 0.083: 75 0.083 - 0.110: 63 0.110 - 0.138: 7 Chirality restraints: 1167 Sorted by residual: chirality pdb=" CA PRO C 70 " pdb=" N PRO C 70 " pdb=" C PRO C 70 " pdb=" CB PRO C 70 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.75e-01 chirality pdb=" CA ILE B 330 " pdb=" N ILE B 330 " pdb=" C ILE B 330 " pdb=" CB ILE B 330 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.99e-01 chirality pdb=" CA ILE C 139 " pdb=" N ILE C 139 " pdb=" C ILE C 139 " pdb=" CB ILE C 139 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.83e-01 ... (remaining 1164 not shown) Planarity restraints: 1320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PCA C 26 " 0.048 2.00e-02 2.50e+03 9.22e-02 8.50e+01 pdb=" C PCA C 26 " -0.159 2.00e-02 2.50e+03 pdb=" O PCA C 26 " 0.060 2.00e-02 2.50e+03 pdb=" N ASP C 27 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PCA B 26 " 0.037 2.00e-02 2.50e+03 7.26e-02 5.28e+01 pdb=" C PCA B 26 " -0.126 2.00e-02 2.50e+03 pdb=" O PCA B 26 " 0.047 2.00e-02 2.50e+03 pdb=" N ASP B 27 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 103 " 0.025 5.00e-02 4.00e+02 3.78e-02 2.28e+00 pdb=" N PRO A 104 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 104 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 104 " 0.021 5.00e-02 4.00e+02 ... (remaining 1317 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1104 2.76 - 3.30: 6797 3.30 - 3.83: 11643 3.83 - 4.37: 12721 4.37 - 4.90: 22754 Nonbonded interactions: 55019 Sorted by model distance: nonbonded pdb=" ND1 HIS C 412 " pdb=" OH TYR C 423 " model vdw 2.229 2.520 nonbonded pdb=" O SER B 318 " pdb=" OG SER B 360 " model vdw 2.236 2.440 nonbonded pdb=" OE1 GLU C 156 " pdb=" OH TYR C 167 " model vdw 2.275 2.440 nonbonded pdb=" NE2 GLN C 302 " pdb=" O SER C 350 " model vdw 2.280 2.520 nonbonded pdb=" O SER C 318 " pdb=" OG SER C 360 " model vdw 2.308 2.440 ... (remaining 55014 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 'B' and (resid 26 through 148 or (resid 149 and (name N or name CA or nam \ e C or name O or name CB )) or resid 150 through 173 or (resid 174 through 175 a \ nd (name N or name CA or name C or name O or name CB )) or resid 176 or (resid 1 \ 77 through 178 and (name N or name CA or name C or name O or name CB )) or resid \ 179 or (resid 180 and (name N or name CA or name C or name O or name CB )) or r \ esid 181 through 246 or (resid 247 and (name N or name CA or name C or name O or \ name CB )) or resid 248 through 294 or (resid 295 and (name N or name CA or nam \ e C or name O or name CB )) or resid 296 through 325 or (resid 326 through 327 a \ nd (name N or name CA or name C or name O or name CB )) or resid 328 through 329 \ or (resid 330 and (name N or name CA or name C or name O or name CB )) or resid \ 331 through 400 or resid 405 through 428 or (resid 435 through 437 and (name N \ or name CA or name C or name O or name CB )) or resid 438 through 450 or (resid \ 456 through 458 and (name N or name CA or name C or name O or name CB )) or resi \ d 459 through 482 or resid 1001 through 1006)) selection = (chain 'C' and (resid 26 through 85 or (resid 86 and (name N or name CA or name \ C or name O or name CB )) or resid 87 through 97 or (resid 98 and (name N or nam \ e CA or name C or name O or name CB )) or resid 99 through 145 or (resid 146 and \ (name N or name CA or name C or name O or name CB )) or resid 147 through 326 o \ r (resid 327 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 28 through 334 or (resid 335 and (name N or name CA or name C or name O or name \ CB )) or resid 336 through 337 or (resid 348 through 349 and (name N or name CA \ or name C or name O or name CB )) or resid 350 through 397 or (resid 398 through \ 405 and (name N or name CA or name C or name O or name CB )) or resid 406 throu \ gh 482 or resid 1001 through 1006)) } 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=1.00 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: 1.360 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: 0.000 Extract box with map and model: 5.690 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 23.340 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.030 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 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 : 0.005 0.119 7524 Z= 0.319 Angle : 0.661 11.245 10293 Z= 0.355 Chirality : 0.037 0.138 1167 Planarity : 0.005 0.092 1314 Dihedral : 11.250 74.289 2827 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.28 % Allowed : 5.64 % Favored : 92.08 % 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: 0.42 (0.29), residues: 916 helix: 2.74 (0.55), residues: 105 sheet: 0.61 (0.28), residues: 364 loop : -0.59 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 272 HIS 0.002 0.000 HIS C 376 PHE 0.007 0.001 PHE A 162 TYR 0.006 0.001 TYR C 423 ARG 0.002 0.000 ARG C 464 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 111 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 ASP cc_start: 0.8820 (p0) cc_final: 0.8501 (p0) REVERT: B 49 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8220 (t) REVERT: B 140 LYS cc_start: 0.8682 (mmtm) cc_final: 0.8464 (mmtm) REVERT: B 315 PHE cc_start: 0.7963 (p90) cc_final: 0.7559 (p90) REVERT: B 424 GLN cc_start: 0.7737 (pt0) cc_final: 0.7440 (pt0) REVERT: C 421 THR cc_start: 0.8513 (m) cc_final: 0.8301 (p) outliers start: 17 outliers final: 7 residues processed: 127 average time/residue: 0.1852 time to fit residues: 32.2527 Evaluate side-chains 95 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 87 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 105 PHE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 302 GLN Chi-restraints excluded: chain C residue 368 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 28 optimal weight: 0.0970 chunk 44 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN B 304 GLN C 64 GLN C 151 GLN ** C 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 GLN C 312 GLN C 424 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7524 Z= 0.233 Angle : 0.611 12.957 10293 Z= 0.292 Chirality : 0.039 0.146 1167 Planarity : 0.005 0.049 1314 Dihedral : 6.250 56.991 1258 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.49 % Allowed : 9.80 % Favored : 86.71 % 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: 0.48 (0.29), residues: 916 helix: 2.72 (0.55), residues: 105 sheet: 0.62 (0.26), residues: 384 loop : -0.55 (0.32), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 410 HIS 0.004 0.001 HIS C 353 PHE 0.023 0.001 PHE C 354 TYR 0.018 0.001 TYR C 470 ARG 0.004 0.000 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 93 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 ASP cc_start: 0.8801 (p0) cc_final: 0.8500 (p0) REVERT: B 49 THR cc_start: 0.8684 (OUTLIER) cc_final: 0.8387 (t) REVERT: B 287 LEU cc_start: 0.7208 (pt) cc_final: 0.6818 (tt) REVERT: B 315 PHE cc_start: 0.8045 (p90) cc_final: 0.7554 (p90) REVERT: B 477 TRP cc_start: 0.7447 (m100) cc_final: 0.6815 (m100) REVERT: C 142 MET cc_start: 0.8098 (ptt) cc_final: 0.7727 (ptp) outliers start: 26 outliers final: 11 residues processed: 117 average time/residue: 0.1572 time to fit residues: 26.2937 Evaluate side-chains 100 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 88 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 368 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 424 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7524 Z= 0.245 Angle : 0.631 12.719 10293 Z= 0.297 Chirality : 0.043 0.558 1167 Planarity : 0.004 0.049 1314 Dihedral : 6.181 59.468 1253 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.36 % Allowed : 10.74 % Favored : 85.91 % 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: 0.41 (0.29), residues: 916 helix: 2.70 (0.54), residues: 105 sheet: 0.52 (0.26), residues: 384 loop : -0.54 (0.32), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 272 HIS 0.002 0.001 HIS A 142 PHE 0.016 0.001 PHE C 354 TYR 0.031 0.001 TYR B 316 ARG 0.004 0.000 ARG C 351 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 93 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 ASP cc_start: 0.8772 (p0) cc_final: 0.8461 (p0) REVERT: B 49 THR cc_start: 0.8725 (OUTLIER) cc_final: 0.8438 (t) REVERT: B 287 LEU cc_start: 0.7135 (pt) cc_final: 0.6810 (tt) REVERT: B 302 GLN cc_start: 0.8349 (tm-30) cc_final: 0.7914 (tm-30) REVERT: B 315 PHE cc_start: 0.8095 (p90) cc_final: 0.7788 (p90) REVERT: B 477 TRP cc_start: 0.7439 (m100) cc_final: 0.6778 (m100) REVERT: C 470 TYR cc_start: 0.8107 (m-80) cc_final: 0.7764 (m-80) outliers start: 25 outliers final: 19 residues processed: 116 average time/residue: 0.1529 time to fit residues: 25.5278 Evaluate side-chains 105 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 85 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 469 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 40 optimal weight: 0.0980 chunk 56 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 250 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7524 Z= 0.199 Angle : 0.606 12.008 10293 Z= 0.284 Chirality : 0.042 0.579 1167 Planarity : 0.004 0.050 1314 Dihedral : 5.948 59.355 1253 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.62 % Allowed : 13.29 % Favored : 83.09 % 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: 0.53 (0.29), residues: 916 helix: 2.75 (0.54), residues: 105 sheet: 0.63 (0.26), residues: 384 loop : -0.49 (0.32), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 477 HIS 0.002 0.000 HIS A 142 PHE 0.014 0.001 PHE C 354 TYR 0.019 0.001 TYR B 316 ARG 0.001 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 91 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 ASP cc_start: 0.8772 (p0) cc_final: 0.8462 (p0) REVERT: B 49 THR cc_start: 0.8718 (OUTLIER) cc_final: 0.8449 (t) REVERT: B 140 LYS cc_start: 0.8695 (mmtm) cc_final: 0.8367 (mmtm) REVERT: B 287 LEU cc_start: 0.7082 (pt) cc_final: 0.6782 (tt) REVERT: B 302 GLN cc_start: 0.8375 (tm-30) cc_final: 0.7878 (tm-30) REVERT: B 315 PHE cc_start: 0.8060 (p90) cc_final: 0.7784 (p90) REVERT: B 477 TRP cc_start: 0.7423 (m100) cc_final: 0.6752 (m100) outliers start: 27 outliers final: 19 residues processed: 114 average time/residue: 0.1629 time to fit residues: 26.3865 Evaluate side-chains 108 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 88 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 353 HIS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 464 ARG Chi-restraints excluded: chain C residue 469 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 80 optimal weight: 0.0000 chunk 22 optimal weight: 0.0970 overall best weight: 0.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7524 Z= 0.165 Angle : 0.598 12.210 10293 Z= 0.278 Chirality : 0.041 0.502 1167 Planarity : 0.004 0.049 1314 Dihedral : 5.836 58.819 1253 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.36 % Allowed : 13.69 % Favored : 82.95 % 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: 0.59 (0.29), residues: 916 helix: 2.84 (0.55), residues: 105 sheet: 0.63 (0.26), residues: 393 loop : -0.44 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 477 HIS 0.005 0.001 HIS C 412 PHE 0.021 0.001 PHE C 354 TYR 0.016 0.001 TYR C 423 ARG 0.004 0.000 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 94 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 ASP cc_start: 0.8756 (p0) cc_final: 0.8448 (p0) REVERT: B 49 THR cc_start: 0.8697 (OUTLIER) cc_final: 0.8436 (t) REVERT: B 140 LYS cc_start: 0.8688 (mmtm) cc_final: 0.8400 (mmtm) REVERT: B 287 LEU cc_start: 0.7074 (pt) cc_final: 0.6780 (tt) REVERT: B 302 GLN cc_start: 0.8398 (tm-30) cc_final: 0.7902 (tm-30) REVERT: B 315 PHE cc_start: 0.8097 (p90) cc_final: 0.7821 (p90) REVERT: B 477 TRP cc_start: 0.7436 (m100) cc_final: 0.6738 (m100) REVERT: C 128 ASP cc_start: 0.8883 (p0) cc_final: 0.8414 (p0) outliers start: 25 outliers final: 20 residues processed: 115 average time/residue: 0.1651 time to fit residues: 26.8435 Evaluate side-chains 106 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 85 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 353 HIS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 464 ARG Chi-restraints excluded: chain C residue 469 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 52 optimal weight: 10.0000 chunk 22 optimal weight: 0.4980 chunk 89 optimal weight: 0.0670 chunk 74 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 7 optimal weight: 0.3980 chunk 29 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7524 Z= 0.182 Angle : 0.612 11.245 10293 Z= 0.285 Chirality : 0.041 0.529 1167 Planarity : 0.004 0.049 1314 Dihedral : 5.711 56.300 1253 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.22 % Allowed : 14.36 % Favored : 82.42 % 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: 0.56 (0.29), residues: 916 helix: 2.82 (0.54), residues: 105 sheet: 0.63 (0.26), residues: 386 loop : -0.46 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 477 HIS 0.003 0.000 HIS C 412 PHE 0.018 0.001 PHE C 354 TYR 0.015 0.001 TYR B 316 ARG 0.002 0.000 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 86 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 ASP cc_start: 0.8756 (p0) cc_final: 0.8555 (p0) REVERT: B 49 THR cc_start: 0.8700 (OUTLIER) cc_final: 0.8445 (t) REVERT: B 140 LYS cc_start: 0.8691 (mmtm) cc_final: 0.8432 (mmtm) REVERT: B 287 LEU cc_start: 0.7064 (pt) cc_final: 0.6778 (tt) REVERT: B 302 GLN cc_start: 0.8411 (tm-30) cc_final: 0.7908 (tm-30) REVERT: B 315 PHE cc_start: 0.8035 (p90) cc_final: 0.7713 (p90) REVERT: B 477 TRP cc_start: 0.7428 (m100) cc_final: 0.6726 (m100) outliers start: 24 outliers final: 21 residues processed: 107 average time/residue: 0.1572 time to fit residues: 23.8246 Evaluate side-chains 109 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 87 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 353 HIS Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 464 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 50 optimal weight: 10.0000 chunk 75 optimal weight: 0.9990 chunk 89 optimal weight: 0.3980 chunk 56 optimal weight: 0.6980 chunk 54 optimal weight: 0.0010 chunk 41 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7524 Z= 0.179 Angle : 0.611 13.551 10293 Z= 0.282 Chirality : 0.040 0.436 1167 Planarity : 0.004 0.050 1314 Dihedral : 5.665 58.036 1253 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.49 % Allowed : 14.63 % Favored : 81.88 % 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: 0.59 (0.29), residues: 916 helix: 2.82 (0.55), residues: 105 sheet: 0.70 (0.26), residues: 385 loop : -0.49 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 477 HIS 0.002 0.000 HIS A 142 PHE 0.016 0.001 PHE C 354 TYR 0.014 0.001 TYR C 423 ARG 0.006 0.000 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 93 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 ASP cc_start: 0.8749 (p0) cc_final: 0.8447 (p0) REVERT: B 49 THR cc_start: 0.8722 (OUTLIER) cc_final: 0.8478 (t) REVERT: B 140 LYS cc_start: 0.8688 (mmtm) cc_final: 0.8465 (mmtm) REVERT: B 287 LEU cc_start: 0.7060 (pt) cc_final: 0.6775 (tt) REVERT: B 302 GLN cc_start: 0.8446 (tm-30) cc_final: 0.7880 (tm-30) REVERT: B 315 PHE cc_start: 0.8114 (p90) cc_final: 0.7716 (p90) REVERT: B 477 TRP cc_start: 0.7402 (m100) cc_final: 0.6694 (m100) REVERT: C 128 ASP cc_start: 0.8891 (p0) cc_final: 0.8441 (p0) outliers start: 26 outliers final: 22 residues processed: 116 average time/residue: 0.1691 time to fit residues: 27.7045 Evaluate side-chains 109 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 86 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 353 HIS Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 250 ASN Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 464 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 0.0770 chunk 53 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 61 optimal weight: 0.4980 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 70 optimal weight: 0.0870 chunk 81 optimal weight: 7.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7524 Z= 0.172 Angle : 0.620 13.825 10293 Z= 0.283 Chirality : 0.041 0.441 1167 Planarity : 0.004 0.051 1314 Dihedral : 5.604 55.677 1253 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.36 % Allowed : 15.03 % Favored : 81.61 % 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: 0.60 (0.29), residues: 916 helix: 2.87 (0.54), residues: 105 sheet: 0.69 (0.26), residues: 387 loop : -0.48 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 477 HIS 0.002 0.000 HIS A 142 PHE 0.014 0.001 PHE C 354 TYR 0.013 0.001 TYR C 423 ARG 0.004 0.000 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 86 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 ASP cc_start: 0.8746 (p0) cc_final: 0.8440 (p0) REVERT: B 49 THR cc_start: 0.8711 (OUTLIER) cc_final: 0.8473 (t) REVERT: B 140 LYS cc_start: 0.8623 (mmtm) cc_final: 0.8421 (mmtm) REVERT: B 287 LEU cc_start: 0.7040 (pt) cc_final: 0.6751 (tt) REVERT: B 302 GLN cc_start: 0.8433 (tm-30) cc_final: 0.7866 (tm-30) REVERT: B 315 PHE cc_start: 0.8104 (p90) cc_final: 0.7744 (p90) REVERT: B 477 TRP cc_start: 0.7398 (m100) cc_final: 0.6649 (m100) REVERT: C 464 ARG cc_start: 0.7453 (OUTLIER) cc_final: 0.6985 (ttm-80) outliers start: 25 outliers final: 21 residues processed: 108 average time/residue: 0.1672 time to fit residues: 25.4441 Evaluate side-chains 112 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 89 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 105 PHE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 353 HIS Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 250 ASN Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 464 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 50 optimal weight: 8.9990 chunk 36 optimal weight: 0.6980 chunk 65 optimal weight: 0.0270 chunk 25 optimal weight: 1.9990 chunk 75 optimal weight: 0.0980 chunk 79 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7524 Z= 0.196 Angle : 0.623 13.921 10293 Z= 0.285 Chirality : 0.040 0.431 1167 Planarity : 0.004 0.053 1314 Dihedral : 5.503 53.136 1253 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.36 % Allowed : 15.03 % Favored : 81.61 % 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: 0.60 (0.29), residues: 916 helix: 2.86 (0.55), residues: 105 sheet: 0.66 (0.26), residues: 387 loop : -0.45 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 272 HIS 0.003 0.001 HIS C 412 PHE 0.014 0.001 PHE C 354 TYR 0.011 0.001 TYR B 316 ARG 0.009 0.000 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 90 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 ASP cc_start: 0.8759 (p0) cc_final: 0.8456 (p0) REVERT: B 49 THR cc_start: 0.8732 (OUTLIER) cc_final: 0.8489 (t) REVERT: B 287 LEU cc_start: 0.7063 (pt) cc_final: 0.6776 (tt) REVERT: B 302 GLN cc_start: 0.8469 (tm-30) cc_final: 0.7862 (tm-30) REVERT: B 315 PHE cc_start: 0.8120 (p90) cc_final: 0.7730 (p90) REVERT: B 477 TRP cc_start: 0.7419 (m100) cc_final: 0.6767 (m100) REVERT: C 128 ASP cc_start: 0.8883 (p0) cc_final: 0.8427 (p0) outliers start: 25 outliers final: 23 residues processed: 111 average time/residue: 0.1745 time to fit residues: 27.5106 Evaluate side-chains 108 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 84 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 353 HIS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 250 ASN Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 464 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 61 optimal weight: 0.0170 chunk 92 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 58 optimal weight: 0.2980 chunk 78 optimal weight: 0.9990 overall best weight: 0.5820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7524 Z= 0.198 Angle : 0.633 15.344 10293 Z= 0.290 Chirality : 0.040 0.377 1167 Planarity : 0.004 0.054 1314 Dihedral : 5.344 53.317 1253 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.22 % Allowed : 15.44 % Favored : 81.34 % 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: 0.58 (0.29), residues: 916 helix: 2.87 (0.55), residues: 105 sheet: 0.62 (0.26), residues: 389 loop : -0.45 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 110 HIS 0.002 0.000 HIS C 412 PHE 0.013 0.001 PHE C 354 TYR 0.010 0.001 TYR B 316 ARG 0.009 0.000 ARG C 319 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 84 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 ASP cc_start: 0.8751 (p0) cc_final: 0.8449 (p0) REVERT: B 49 THR cc_start: 0.8729 (OUTLIER) cc_final: 0.8486 (t) REVERT: B 287 LEU cc_start: 0.7059 (pt) cc_final: 0.6776 (tt) REVERT: B 315 PHE cc_start: 0.8114 (p90) cc_final: 0.7728 (p90) REVERT: B 477 TRP cc_start: 0.7398 (m100) cc_final: 0.6678 (m100) REVERT: C 128 ASP cc_start: 0.8875 (p0) cc_final: 0.8416 (p0) outliers start: 24 outliers final: 23 residues processed: 104 average time/residue: 0.1676 time to fit residues: 24.7021 Evaluate side-chains 111 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 87 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 353 HIS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 250 ASN Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 464 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 0.9990 chunk 68 optimal weight: 0.2980 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 30 optimal weight: 0.0980 chunk 75 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.137749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.096591 restraints weight = 14281.732| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 3.60 r_work: 0.3133 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7524 Z= 0.176 Angle : 0.611 14.773 10293 Z= 0.282 Chirality : 0.040 0.379 1167 Planarity : 0.004 0.052 1314 Dihedral : 5.203 53.592 1253 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.22 % Allowed : 15.03 % Favored : 81.74 % 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 (0.29), residues: 916 helix: 2.88 (0.55), residues: 105 sheet: 0.66 (0.26), residues: 391 loop : -0.43 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 110 HIS 0.002 0.000 HIS C 412 PHE 0.013 0.001 PHE C 354 TYR 0.010 0.001 TYR B 316 ARG 0.009 0.000 ARG C 319 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1873.25 seconds wall clock time: 34 minutes 53.55 seconds (2093.55 seconds total)