Starting phenix.real_space_refine on Sat Apr 6 01:56:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ge4_29955/04_2024/8ge4_29955_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ge4_29955/04_2024/8ge4_29955.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ge4_29955/04_2024/8ge4_29955.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ge4_29955/04_2024/8ge4_29955.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ge4_29955/04_2024/8ge4_29955_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ge4_29955/04_2024/8ge4_29955_updated.pdb" } resolution = 3.3 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= 0.036 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 45 5.16 5 C 4285 2.51 5 N 1140 2.21 5 O 1176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 6646 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1746 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 208 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 12, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 123 Chain: "B" Number of atoms: 2359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2359 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 5, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 6, 'ARG:plan': 9, 'ASN:plan1': 4, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 141 Chain: "G" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 344 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "R" Number of atoms: 2181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2181 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 75 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.24, per 1000 atoms: 0.64 Number of scatterers: 6646 At special positions: 0 Unit cell: (68.9, 97.52, 127.2, 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 45 16.00 O 1176 8.00 N 1140 7.00 C 4285 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " 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=0, symmetry=0 Time building additional restraints: 2.58 Conformation dependent library (CDL) restraints added in 1.4 seconds 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1706 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 8 sheets defined 44.2% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.736A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 233 through 238 removed outlier: 3.786A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 332 through 351 removed outlier: 3.775A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'B' and resid 7 through 24 Processing helix chain 'B' and resid 30 through 36 removed outlier: 4.675A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'R' and resid 31 through 60 Processing helix chain 'R' and resid 62 through 64 No H-bonds generated for 'chain 'R' and resid 62 through 64' Processing helix chain 'R' and resid 67 through 96 removed outlier: 3.842A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 103 through 136 Processing helix chain 'R' and resid 138 through 144 removed outlier: 4.468A pdb=" N GLN R 142 " --> pdb=" O PRO R 138 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N SER R 143 " --> pdb=" O PHE R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 170 removed outlier: 3.609A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE R 153 " --> pdb=" O LYS R 149 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 179 through 186 Processing helix chain 'R' and resid 197 through 207 Processing helix chain 'R' and resid 209 through 236 Processing helix chain 'R' and resid 269 through 298 removed outlier: 4.185A pdb=" N THR R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.645A pdb=" N VAL R 292 " --> pdb=" O PRO R 288 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 326 removed outlier: 4.063A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 330 through 340 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 362 removed outlier: 7.258A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 49 through 51 Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.859A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.727A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 148 through 151 removed outlier: 6.638A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 208 through 212 removed outlier: 3.575A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 262 through 265 removed outlier: 3.618A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.518A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 358 hydrogen bonds defined for protein. 1044 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: 2.23 Time building geometry restraints manager: 2.67 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: 2136 1.34 - 1.46: 1611 1.46 - 1.58: 2983 1.58 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 6792 Sorted by residual: bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.449 -0.052 2.00e-02 2.50e+03 6.82e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.564 -0.044 2.00e-02 2.50e+03 4.85e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.437 -0.043 2.00e-02 2.50e+03 4.63e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.566 -0.043 2.00e-02 2.50e+03 4.60e+00 bond pdb=" CAD G1I R 501 " pdb=" OAK G1I R 501 " ideal model delta sigma weight residual 1.353 1.323 0.030 2.00e-02 2.50e+03 2.31e+00 ... (remaining 6787 not shown) Histogram of bond angle deviations from ideal: 99.52 - 106.41: 135 106.41 - 113.31: 3767 113.31 - 120.20: 2274 120.20 - 127.10: 3023 127.10 - 133.99: 77 Bond angle restraints: 9276 Sorted by residual: angle pdb=" N GLY A 329 " pdb=" CA GLY A 329 " pdb=" C GLY A 329 " ideal model delta sigma weight residual 113.18 107.44 5.74 2.37e+00 1.78e-01 5.87e+00 angle pdb=" CA GLU A 50 " pdb=" CB GLU A 50 " pdb=" CG GLU A 50 " ideal model delta sigma weight residual 114.10 118.52 -4.42 2.00e+00 2.50e-01 4.88e+00 angle pdb=" C THR B 86 " pdb=" N THR B 87 " pdb=" CA THR B 87 " ideal model delta sigma weight residual 122.46 125.55 -3.09 1.41e+00 5.03e-01 4.80e+00 angle pdb=" C VAL R 87 " pdb=" CA VAL R 87 " pdb=" CB VAL R 87 " ideal model delta sigma weight residual 114.00 111.22 2.78 1.31e+00 5.83e-01 4.51e+00 angle pdb=" C TYR A 391 " pdb=" N GLU A 392 " pdb=" CA GLU A 392 " ideal model delta sigma weight residual 122.21 119.08 3.13 1.48e+00 4.57e-01 4.47e+00 ... (remaining 9271 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 3585 16.94 - 33.88: 301 33.88 - 50.81: 42 50.81 - 67.75: 5 67.75 - 84.69: 2 Dihedral angle restraints: 3935 sinusoidal: 1308 harmonic: 2627 Sorted by residual: dihedral pdb=" CA TRP B 332 " pdb=" C TRP B 332 " pdb=" N ASP B 333 " pdb=" CA ASP B 333 " ideal model delta harmonic sigma weight residual 180.00 161.69 18.31 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA ASP B 76 " pdb=" C ASP B 76 " pdb=" N GLY B 77 " pdb=" CA GLY B 77 " ideal model delta harmonic sigma weight residual -180.00 -162.88 -17.12 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA ASP B 333 " pdb=" C ASP B 333 " pdb=" N SER B 334 " pdb=" CA SER B 334 " ideal model delta harmonic sigma weight residual -180.00 -164.35 -15.65 0 5.00e+00 4.00e-02 9.79e+00 ... (remaining 3932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 731 0.030 - 0.060: 242 0.060 - 0.091: 88 0.091 - 0.121: 40 0.121 - 0.151: 3 Chirality restraints: 1104 Sorted by residual: chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.55 -0.15 2.00e-01 2.50e+01 5.71e-01 chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.08e-01 chirality pdb=" CA ILE A 288 " pdb=" N ILE A 288 " pdb=" C ILE A 288 " pdb=" CB ILE A 288 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.81e-01 ... (remaining 1101 not shown) Planarity restraints: 1164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 38 " 0.020 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO B 39 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 39 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 39 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " -0.009 2.00e-02 2.50e+03 8.45e-03 1.43e+00 pdb=" CG TYR B 59 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 50 " 0.006 2.00e-02 2.50e+03 1.17e-02 1.37e+00 pdb=" C GLU A 50 " -0.020 2.00e-02 2.50e+03 pdb=" O GLU A 50 " 0.008 2.00e-02 2.50e+03 pdb=" N SER A 51 " 0.007 2.00e-02 2.50e+03 ... (remaining 1161 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1431 2.78 - 3.31: 6352 3.31 - 3.84: 11171 3.84 - 4.37: 12582 4.37 - 4.90: 22885 Nonbonded interactions: 54421 Sorted by model distance: nonbonded pdb=" O GLU A 392 " pdb=" OG1 THR R 274 " model vdw 2.248 2.440 nonbonded pdb=" NE2 GLN B 75 " pdb=" O VAL B 100 " model vdw 2.270 2.520 nonbonded pdb=" OE1 GLN A 19 " pdb=" OG1 THR B 86 " model vdw 2.288 2.440 nonbonded pdb=" NE2 HIS B 311 " pdb=" OG1 THR B 329 " model vdw 2.311 2.520 nonbonded pdb=" OH TYR R 185 " pdb=" O PHE R 194 " model vdw 2.341 2.440 ... (remaining 54416 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 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: 1.380 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: 5.930 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 22.270 Find NCS groups from input model: 0.210 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: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 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 : 0.003 0.052 6792 Z= 0.199 Angle : 0.453 5.742 9276 Z= 0.242 Chirality : 0.038 0.151 1104 Planarity : 0.003 0.031 1164 Dihedral : 12.450 84.690 2226 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.63 (0.29), residues: 885 helix: 2.49 (0.26), residues: 404 sheet: 0.01 (0.40), residues: 168 loop : -0.12 (0.37), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 82 HIS 0.006 0.001 HIS B 183 PHE 0.016 0.001 PHE B 234 TYR 0.021 0.001 TYR B 59 ARG 0.002 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.825 Fit side-chains revert: symmetry clash REVERT: A 215 ASP cc_start: 0.8400 (t0) cc_final: 0.8032 (t0) REVERT: A 339 TYR cc_start: 0.8312 (m-80) cc_final: 0.7722 (m-80) REVERT: B 274 THR cc_start: 0.9326 (m) cc_final: 0.9033 (p) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.2080 time to fit residues: 34.6952 Evaluate side-chains 100 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 23 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN B 266 HIS R 178 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.0825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6792 Z= 0.209 Angle : 0.472 6.716 9276 Z= 0.252 Chirality : 0.040 0.141 1104 Planarity : 0.003 0.027 1164 Dihedral : 4.723 70.281 972 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.90 % Allowed : 8.10 % Favored : 90.00 % 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: 1.62 (0.30), residues: 885 helix: 2.47 (0.26), residues: 402 sheet: -0.31 (0.38), residues: 187 loop : 0.17 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 339 HIS 0.006 0.001 HIS R 178 PHE 0.012 0.001 PHE B 241 TYR 0.021 0.001 TYR B 59 ARG 0.003 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 105 time to evaluate : 0.778 Fit side-chains revert: symmetry clash REVERT: A 215 ASP cc_start: 0.8411 (t0) cc_final: 0.8049 (t0) REVERT: A 339 TYR cc_start: 0.8369 (m-80) cc_final: 0.7713 (m-80) outliers start: 12 outliers final: 8 residues processed: 113 average time/residue: 0.2012 time to fit residues: 30.1139 Evaluate side-chains 104 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 96 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 192 ASP Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN B 266 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6792 Z= 0.218 Angle : 0.465 6.084 9276 Z= 0.248 Chirality : 0.040 0.132 1104 Planarity : 0.003 0.028 1164 Dihedral : 4.761 71.585 972 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.90 % Allowed : 10.95 % Favored : 87.14 % 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: 1.57 (0.29), residues: 885 helix: 2.45 (0.26), residues: 401 sheet: -0.28 (0.38), residues: 187 loop : 0.05 (0.38), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.006 0.001 HIS B 183 PHE 0.011 0.001 PHE B 241 TYR 0.021 0.001 TYR B 59 ARG 0.004 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 101 time to evaluate : 0.749 Fit side-chains revert: symmetry clash REVERT: A 215 ASP cc_start: 0.8461 (t0) cc_final: 0.8078 (t0) REVERT: A 339 TYR cc_start: 0.8402 (m-80) cc_final: 0.7674 (m-80) REVERT: B 301 LYS cc_start: 0.9135 (mtpp) cc_final: 0.8732 (mttp) outliers start: 12 outliers final: 11 residues processed: 111 average time/residue: 0.2098 time to fit residues: 30.5515 Evaluate side-chains 107 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 192 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 2.9990 chunk 42 optimal weight: 0.2980 chunk 8 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 54 optimal weight: 0.0020 chunk 81 optimal weight: 0.0670 chunk 86 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 23 optimal weight: 9.9990 chunk 71 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 overall best weight: 0.3926 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN B 239 ASN B 266 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6792 Z= 0.133 Angle : 0.424 5.290 9276 Z= 0.227 Chirality : 0.038 0.136 1104 Planarity : 0.003 0.028 1164 Dihedral : 4.540 71.179 972 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.43 % Allowed : 13.02 % Favored : 85.56 % 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: 1.74 (0.30), residues: 885 helix: 2.54 (0.26), residues: 403 sheet: -0.11 (0.38), residues: 186 loop : 0.14 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS B 183 PHE 0.008 0.001 PHE A 212 TYR 0.013 0.001 TYR B 59 ARG 0.003 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 105 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: A 215 ASP cc_start: 0.8472 (t0) cc_final: 0.8084 (t0) REVERT: A 339 TYR cc_start: 0.8298 (m-80) cc_final: 0.7673 (m-80) REVERT: B 301 LYS cc_start: 0.9093 (mtpp) cc_final: 0.8643 (mttp) outliers start: 9 outliers final: 5 residues processed: 114 average time/residue: 0.1999 time to fit residues: 29.8635 Evaluate side-chains 100 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 95 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 192 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 43 optimal weight: 0.2980 chunk 77 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN B 266 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6792 Z= 0.204 Angle : 0.450 5.476 9276 Z= 0.240 Chirality : 0.039 0.133 1104 Planarity : 0.003 0.027 1164 Dihedral : 4.636 72.008 972 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.90 % Allowed : 13.17 % Favored : 84.92 % 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: 1.66 (0.29), residues: 885 helix: 2.50 (0.26), residues: 402 sheet: -0.08 (0.38), residues: 186 loop : 0.02 (0.38), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS B 183 PHE 0.009 0.001 PHE A 212 TYR 0.015 0.001 TYR B 59 ARG 0.004 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 0.816 Fit side-chains revert: symmetry clash REVERT: A 215 ASP cc_start: 0.8499 (t0) cc_final: 0.8117 (t0) REVERT: A 339 TYR cc_start: 0.8353 (m-80) cc_final: 0.7736 (m-80) REVERT: B 301 LYS cc_start: 0.9121 (mtpp) cc_final: 0.8745 (mttp) outliers start: 12 outliers final: 11 residues processed: 106 average time/residue: 0.2042 time to fit residues: 28.5256 Evaluate side-chains 104 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 93 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 192 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 71 optimal weight: 0.1980 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 9 optimal weight: 0.3980 chunk 49 optimal weight: 0.1980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN B 266 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6792 Z= 0.138 Angle : 0.426 5.348 9276 Z= 0.228 Chirality : 0.038 0.133 1104 Planarity : 0.003 0.027 1164 Dihedral : 4.557 72.222 972 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.90 % Allowed : 14.13 % Favored : 83.97 % 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: 1.76 (0.29), residues: 885 helix: 2.58 (0.26), residues: 402 sheet: -0.05 (0.38), residues: 186 loop : 0.07 (0.38), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS B 183 PHE 0.008 0.001 PHE A 212 TYR 0.011 0.001 TYR B 59 ARG 0.003 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 0.792 Fit side-chains revert: symmetry clash REVERT: A 215 ASP cc_start: 0.8492 (t0) cc_final: 0.8114 (t0) REVERT: A 339 TYR cc_start: 0.8281 (m-80) cc_final: 0.7678 (m-80) REVERT: B 43 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8483 (mt) REVERT: B 301 LYS cc_start: 0.9104 (mtpp) cc_final: 0.8710 (mttp) outliers start: 12 outliers final: 10 residues processed: 109 average time/residue: 0.2258 time to fit residues: 32.9868 Evaluate side-chains 105 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 94 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 192 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 52 optimal weight: 0.0370 chunk 39 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 chunk 16 optimal weight: 0.0970 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN B 266 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6792 Z= 0.138 Angle : 0.424 5.364 9276 Z= 0.226 Chirality : 0.038 0.133 1104 Planarity : 0.003 0.028 1164 Dihedral : 4.521 72.304 972 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.90 % Allowed : 13.97 % Favored : 84.13 % 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: 1.84 (0.29), residues: 885 helix: 2.59 (0.26), residues: 403 sheet: 0.19 (0.39), residues: 175 loop : 0.03 (0.37), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS B 183 PHE 0.008 0.001 PHE A 212 TYR 0.011 0.001 TYR B 59 ARG 0.003 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 0.802 Fit side-chains revert: symmetry clash REVERT: A 215 ASP cc_start: 0.8501 (t0) cc_final: 0.8123 (t0) REVERT: A 339 TYR cc_start: 0.8265 (m-80) cc_final: 0.7670 (m-80) REVERT: B 43 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8493 (mt) REVERT: B 301 LYS cc_start: 0.9126 (mtpp) cc_final: 0.8749 (mttp) outliers start: 12 outliers final: 9 residues processed: 107 average time/residue: 0.1994 time to fit residues: 28.3474 Evaluate side-chains 105 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 95 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 192 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 82 optimal weight: 0.0170 chunk 74 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 HIS R 69 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 6792 Z= 0.311 Angle : 0.501 6.120 9276 Z= 0.267 Chirality : 0.040 0.131 1104 Planarity : 0.003 0.027 1164 Dihedral : 4.938 75.024 972 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.54 % Allowed : 13.33 % Favored : 84.13 % 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: 1.49 (0.29), residues: 885 helix: 2.34 (0.26), residues: 402 sheet: -0.14 (0.38), residues: 185 loop : -0.06 (0.38), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 339 HIS 0.009 0.001 HIS B 183 PHE 0.012 0.001 PHE R 289 TYR 0.019 0.002 TYR B 59 ARG 0.004 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 97 time to evaluate : 0.782 Fit side-chains revert: symmetry clash REVERT: A 215 ASP cc_start: 0.8544 (t0) cc_final: 0.8190 (t0) REVERT: A 339 TYR cc_start: 0.8567 (m-80) cc_final: 0.7712 (m-80) REVERT: B 301 LYS cc_start: 0.9109 (mtpp) cc_final: 0.8903 (mtmm) REVERT: R 318 ASN cc_start: 0.8807 (t0) cc_final: 0.8532 (t0) outliers start: 16 outliers final: 13 residues processed: 110 average time/residue: 0.1982 time to fit residues: 28.8570 Evaluate side-chains 105 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 92 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 140 LYS Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 192 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 24 optimal weight: 7.9990 chunk 72 optimal weight: 0.0040 chunk 75 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 84 optimal weight: 0.4980 chunk 51 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 HIS R 312 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6792 Z= 0.166 Angle : 0.444 5.299 9276 Z= 0.237 Chirality : 0.039 0.134 1104 Planarity : 0.003 0.032 1164 Dihedral : 4.677 73.518 972 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.54 % Allowed : 13.65 % Favored : 83.81 % 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: 1.60 (0.29), residues: 885 helix: 2.44 (0.26), residues: 402 sheet: -0.10 (0.38), residues: 186 loop : -0.02 (0.38), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.005 0.001 HIS B 183 PHE 0.009 0.001 PHE B 241 TYR 0.013 0.001 TYR B 59 ARG 0.002 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 0.812 Fit side-chains revert: symmetry clash REVERT: A 215 ASP cc_start: 0.8542 (t0) cc_final: 0.8178 (t0) REVERT: A 339 TYR cc_start: 0.8468 (m-80) cc_final: 0.7671 (m-80) outliers start: 16 outliers final: 10 residues processed: 116 average time/residue: 0.1869 time to fit residues: 29.0361 Evaluate side-chains 105 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 95 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 192 ASP Chi-restraints excluded: chain R residue 196 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 0.3980 chunk 81 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 HIS R 312 ASN ** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6792 Z= 0.192 Angle : 0.461 5.371 9276 Z= 0.244 Chirality : 0.039 0.134 1104 Planarity : 0.003 0.032 1164 Dihedral : 4.694 73.593 972 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.75 % Allowed : 14.76 % Favored : 83.49 % 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: 1.57 (0.29), residues: 885 helix: 2.43 (0.26), residues: 398 sheet: -0.09 (0.38), residues: 186 loop : -0.04 (0.37), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS B 183 PHE 0.009 0.001 PHE B 241 TYR 0.015 0.001 TYR B 59 ARG 0.002 0.000 ARG R 239 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 0.756 Fit side-chains revert: symmetry clash REVERT: A 215 ASP cc_start: 0.8542 (t0) cc_final: 0.8186 (t0) REVERT: A 339 TYR cc_start: 0.8471 (m-80) cc_final: 0.7660 (m-80) outliers start: 11 outliers final: 9 residues processed: 108 average time/residue: 0.1917 time to fit residues: 27.3929 Evaluate side-chains 104 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 95 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 192 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 72 optimal weight: 0.0570 chunk 8 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 4 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 HIS B 266 HIS R 69 ASN R 312 ASN ** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.138897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.120569 restraints weight = 9718.804| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.99 r_work: 0.3416 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3316 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3316 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6792 Z= 0.161 Angle : 0.442 5.309 9276 Z= 0.236 Chirality : 0.039 0.134 1104 Planarity : 0.003 0.033 1164 Dihedral : 4.611 73.226 972 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.75 % Allowed : 14.60 % Favored : 83.65 % 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: 1.62 (0.29), residues: 885 helix: 2.50 (0.26), residues: 398 sheet: -0.06 (0.38), residues: 184 loop : -0.05 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS B 183 PHE 0.008 0.001 PHE B 241 TYR 0.013 0.001 TYR B 59 ARG 0.002 0.000 ARG R 239 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1799.45 seconds wall clock time: 33 minutes 20.25 seconds (2000.25 seconds total)