Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 9 23:36:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq5_32086/08_2023/7vq5_32086_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq5_32086/08_2023/7vq5_32086.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq5_32086/08_2023/7vq5_32086.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq5_32086/08_2023/7vq5_32086.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq5_32086/08_2023/7vq5_32086_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq5_32086/08_2023/7vq5_32086_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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 34 5.16 5 C 4074 2.51 5 N 1052 2.21 5 O 1155 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 5": "NH1" <-> "NH2" Residue "A ARG 9": "NH1" <-> "NH2" Residue "A ARG 13": "NH1" <-> "NH2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A GLU 364": "OE1" <-> "OE2" Residue "A GLU 386": "OE1" <-> "OE2" Residue "A GLU 390": "OE1" <-> "OE2" Residue "B ARG 5": "NH1" <-> "NH2" Residue "B GLU 6": "OE1" <-> "OE2" Residue "B ARG 9": "NH1" <-> "NH2" Residue "B ARG 13": "NH1" <-> "NH2" Residue "B ARG 20": "NH1" <-> "NH2" Residue "B GLU 106": "OE1" <-> "OE2" Residue "B ARG 229": "NH1" <-> "NH2" Residue "B GLU 234": "OE1" <-> "OE2" Residue "B ARG 265": "NH1" <-> "NH2" Residue "B GLU 364": "OE1" <-> "OE2" Residue "B GLU 386": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 6315 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3153 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 12, 'TRANS': 387} Chain breaks: 1 Chain: "B" Number of atoms: 3162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3162 Unusual residues: {'LMR': 1} Classifications: {'peptide': 400, 'undetermined': 1} Link IDs: {'PTRANS': 12, 'TRANS': 387, None: 1} Not linked: pdbres="MET B 405 " pdbres="LMR B 601 " Chain breaks: 1 Time building chain proxies: 3.73, per 1000 atoms: 0.59 Number of scatterers: 6315 At special positions: 0 Unit cell: (83.148, 90.246, 112.554, 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 34 16.00 O 1155 8.00 N 1052 7.00 C 4074 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.45 Conformation dependent library (CDL) restraints added in 1.0 seconds 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1504 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 33 helices and 0 sheets defined 79.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 2 through 17 Processing helix chain 'A' and resid 20 through 40 removed outlier: 3.942A pdb=" N GLY A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 65 Processing helix chain 'A' and resid 70 through 101 Processing helix chain 'A' and resid 105 through 126 removed outlier: 4.213A pdb=" N PHE A 126 " --> pdb=" O THR A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 132 Processing helix chain 'A' and resid 135 through 150 Processing helix chain 'A' and resid 155 through 182 Processing helix chain 'A' and resid 188 through 213 Processing helix chain 'A' and resid 224 through 240 removed outlier: 5.024A pdb=" N ARG A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N TYR A 236 " --> pdb=" O ASN A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 255 removed outlier: 3.568A pdb=" N ASN A 251 " --> pdb=" O GLU A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 292 Processing helix chain 'A' and resid 300 through 304 Processing helix chain 'A' and resid 307 through 329 Processing helix chain 'A' and resid 336 through 356 removed outlier: 3.800A pdb=" N SER A 344 " --> pdb=" O HIS A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'A' and resid 365 through 398 Processing helix chain 'B' and resid 2 through 17 removed outlier: 3.518A pdb=" N ILE B 7 " --> pdb=" O LYS B 3 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU B 10 " --> pdb=" O GLU B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 40 removed outlier: 3.560A pdb=" N ILE B 23 " --> pdb=" O ARG B 20 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N HIS B 24 " --> pdb=" O ARG B 21 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE B 26 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL B 28 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY B 29 " --> pdb=" O PHE B 26 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B 32 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL B 33 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER B 36 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR B 39 " --> pdb=" O SER B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 65 removed outlier: 3.523A pdb=" N VAL B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 63 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL B 64 " --> pdb=" O MET B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 101 removed outlier: 3.844A pdb=" N LEU B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG B 99 " --> pdb=" O HIS B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 126 removed outlier: 4.046A pdb=" N VAL B 111 " --> pdb=" O PRO B 107 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE B 123 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE B 126 " --> pdb=" O THR B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 132 removed outlier: 4.026A pdb=" N THR B 132 " --> pdb=" O PRO B 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 128 through 132' Processing helix chain 'B' and resid 135 through 148 removed outlier: 3.631A pdb=" N PHE B 145 " --> pdb=" O PHE B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 182 removed outlier: 3.715A pdb=" N MET B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU B 163 " --> pdb=" O MET B 159 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE B 171 " --> pdb=" O SER B 167 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY B 172 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N CYS B 176 " --> pdb=" O GLY B 172 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE B 179 " --> pdb=" O SER B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 214 removed outlier: 3.812A pdb=" N ASP B 201 " --> pdb=" O ALA B 197 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE B 206 " --> pdb=" O THR B 202 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY B 211 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASP B 212 " --> pdb=" O GLN B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 240 removed outlier: 4.884A pdb=" N ARG B 235 " --> pdb=" O LYS B 231 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR B 236 " --> pdb=" O ASN B 232 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N SER B 238 " --> pdb=" O GLU B 234 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N VAL B 239 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU B 240 " --> pdb=" O TYR B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 255 removed outlier: 3.601A pdb=" N GLU B 254 " --> pdb=" O ALA B 250 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N TRP B 255 " --> pdb=" O ASN B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 290 removed outlier: 3.512A pdb=" N GLN B 280 " --> pdb=" O ALA B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 329 removed outlier: 3.724A pdb=" N LYS B 305 " --> pdb=" O ASP B 301 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LEU B 306 " --> pdb=" O ILE B 302 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU B 307 " --> pdb=" O LYS B 303 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N THR B 308 " --> pdb=" O LYS B 304 " (cutoff:3.500A) Proline residue: B 309 - end of helix removed outlier: 3.881A pdb=" N GLU B 323 " --> pdb=" O ASN B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 356 removed outlier: 3.524A pdb=" N ASN B 343 " --> pdb=" O ILE B 339 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER B 344 " --> pdb=" O HIS B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 362 No H-bonds generated for 'chain 'B' and resid 360 through 362' Processing helix chain 'B' and resid 365 through 398 removed outlier: 4.667A pdb=" N SER B 370 " --> pdb=" O LEU B 366 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS B 387 " --> pdb=" O ASN B 383 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER B 397 " --> pdb=" O HIS B 393 " (cutoff:3.500A) 444 hydrogen bonds defined for protein. 1302 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: 1.74 Time building geometry restraints manager: 2.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1586 1.33 - 1.45: 1178 1.45 - 1.57: 3618 1.57 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 6442 Sorted by residual: bond pdb=" C1 LMR B 601 " pdb=" C2 LMR B 601 " ideal model delta sigma weight residual 1.543 1.495 0.048 2.00e-02 2.50e+03 5.70e+00 bond pdb=" C ILE B 53 " pdb=" O ILE B 53 " ideal model delta sigma weight residual 1.236 1.212 0.025 1.19e-02 7.06e+03 4.27e+00 bond pdb=" C ILE A 53 " pdb=" O ILE A 53 " ideal model delta sigma weight residual 1.236 1.212 0.024 1.19e-02 7.06e+03 4.09e+00 bond pdb=" CB THR A 168 " pdb=" CG2 THR A 168 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.09e+00 bond pdb=" C3 LMR B 601 " pdb=" C4 LMR B 601 " ideal model delta sigma weight residual 1.538 1.503 0.035 2.00e-02 2.50e+03 3.07e+00 ... (remaining 6437 not shown) Histogram of bond angle deviations from ideal: 99.26 - 106.23: 125 106.23 - 113.19: 3618 113.19 - 120.16: 2582 120.16 - 127.12: 2317 127.12 - 134.09: 60 Bond angle restraints: 8702 Sorted by residual: angle pdb=" C GLU A 307 " pdb=" N THR A 308 " pdb=" CA THR A 308 " ideal model delta sigma weight residual 119.83 116.03 3.80 1.11e+00 8.12e-01 1.17e+01 angle pdb=" N TYR A 39 " pdb=" CA TYR A 39 " pdb=" C TYR A 39 " ideal model delta sigma weight residual 111.36 114.89 -3.53 1.09e+00 8.42e-01 1.05e+01 angle pdb=" C GLU B 6 " pdb=" N ILE B 7 " pdb=" CA ILE B 7 " ideal model delta sigma weight residual 122.35 118.75 3.60 1.18e+00 7.18e-01 9.31e+00 angle pdb=" C THR A 132 " pdb=" N LYS A 133 " pdb=" CA LYS A 133 " ideal model delta sigma weight residual 122.42 118.05 4.37 1.55e+00 4.16e-01 7.96e+00 angle pdb=" C GLY B 260 " pdb=" N GLN B 261 " pdb=" CA GLN B 261 " ideal model delta sigma weight residual 124.31 128.72 -4.41 1.67e+00 3.59e-01 6.98e+00 ... (remaining 8697 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 3382 17.98 - 35.95: 405 35.95 - 53.93: 64 53.93 - 71.91: 5 71.91 - 89.89: 1 Dihedral angle restraints: 3857 sinusoidal: 1533 harmonic: 2324 Sorted by residual: dihedral pdb=" CA PRO A 299 " pdb=" C PRO A 299 " pdb=" N VAL A 300 " pdb=" CA VAL A 300 " ideal model delta harmonic sigma weight residual 180.00 -156.85 -23.15 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA TRP A 255 " pdb=" C TRP A 255 " pdb=" N GLU A 256 " pdb=" CA GLU A 256 " ideal model delta harmonic sigma weight residual -180.00 -161.40 -18.60 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA LEU A 233 " pdb=" C LEU A 233 " pdb=" N GLU A 234 " pdb=" CA GLU A 234 " ideal model delta harmonic sigma weight residual 180.00 -163.11 -16.89 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 3854 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 783 0.054 - 0.108: 197 0.108 - 0.163: 15 0.163 - 0.217: 1 0.217 - 0.271: 1 Chirality restraints: 997 Sorted by residual: chirality pdb=" CA TYR A 39 " pdb=" N TYR A 39 " pdb=" C TYR A 39 " pdb=" CB TYR A 39 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA TYR A 40 " pdb=" N TYR A 40 " pdb=" C TYR A 40 " pdb=" CB TYR A 40 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.09e-01 chirality pdb=" CA PRO B 258 " pdb=" N PRO B 258 " pdb=" C PRO B 258 " pdb=" CB PRO B 258 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.97e-01 ... (remaining 994 not shown) Planarity restraints: 1092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 257 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.90e+00 pdb=" N PRO B 258 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 258 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 258 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 18 " 0.028 5.00e-02 4.00e+02 4.17e-02 2.79e+00 pdb=" N PRO A 19 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 19 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 19 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 200 " -0.013 2.00e-02 2.50e+03 1.02e-02 1.81e+00 pdb=" CG PHE B 200 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE B 200 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE B 200 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 200 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 200 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 200 " -0.003 2.00e-02 2.50e+03 ... (remaining 1089 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 97 2.67 - 3.23: 6486 3.23 - 3.78: 9477 3.78 - 4.34: 12885 4.34 - 4.90: 21474 Nonbonded interactions: 50419 Sorted by model distance: nonbonded pdb=" OH TYR B 236 " pdb=" OD1 ASP B 286 " model vdw 2.110 2.440 nonbonded pdb=" OE1 GLU B 246 " pdb=" NH2 ARG B 279 " model vdw 2.185 2.520 nonbonded pdb=" O ILE B 369 " pdb=" OG1 THR B 373 " model vdw 2.210 2.440 nonbonded pdb=" NH2 ARG B 80 " pdb=" O4A LMR B 601 " model vdw 2.242 2.520 nonbonded pdb=" NZ LYS B 133 " pdb=" OE1 GLU B 254 " model vdw 2.247 2.520 ... (remaining 50414 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 1 through 405) } 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: 0.240 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: 1.850 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 19.800 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.067 6442 Z= 0.591 Angle : 0.766 7.360 8702 Z= 0.446 Chirality : 0.046 0.271 997 Planarity : 0.004 0.043 1092 Dihedral : 14.724 89.886 2353 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer Outliers : 0.14 % 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: -3.56 (0.25), residues: 792 helix: -1.79 (0.17), residues: 664 sheet: None (None), residues: 0 loop : -4.38 (0.42), residues: 128 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 0.727 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 94 average time/residue: 0.2115 time to fit residues: 25.8747 Evaluate side-chains 76 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.751 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 95 HIS A 266 HIS A 289 ASN A 293 ASN A 340 HIS B 266 HIS ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 6442 Z= 0.203 Angle : 0.495 5.297 8702 Z= 0.274 Chirality : 0.037 0.141 997 Planarity : 0.004 0.035 1092 Dihedral : 4.453 19.745 859 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer Outliers : 1.87 % 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: -0.71 (0.29), residues: 792 helix: 0.13 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -3.30 (0.51), residues: 126 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 0.732 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 93 average time/residue: 0.2013 time to fit residues: 25.4922 Evaluate side-chains 93 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 85 time to evaluate : 0.772 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0646 time to fit residues: 1.9985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 78 optimal weight: 0.0070 chunk 64 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 58 optimal weight: 0.0170 chunk 71 optimal weight: 0.9980 overall best weight: 1.2040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 ASN A 393 HIS B 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 6442 Z= 0.183 Angle : 0.467 5.263 8702 Z= 0.251 Chirality : 0.036 0.145 997 Planarity : 0.003 0.035 1092 Dihedral : 4.142 19.674 859 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer Outliers : 1.15 % 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: 0.51 (0.31), residues: 792 helix: 0.97 (0.20), residues: 670 sheet: None (None), residues: 0 loop : -3.03 (0.53), residues: 122 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 92 time to evaluate : 0.778 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 97 average time/residue: 0.1671 time to fit residues: 22.5387 Evaluate side-chains 89 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 86 time to evaluate : 0.744 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0656 time to fit residues: 1.4061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 0.0870 chunk 20 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 6442 Z= 0.143 Angle : 0.423 5.162 8702 Z= 0.227 Chirality : 0.035 0.146 997 Planarity : 0.003 0.035 1092 Dihedral : 3.923 20.343 859 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer Outliers : 1.29 % 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: 1.25 (0.31), residues: 792 helix: 1.44 (0.21), residues: 668 sheet: None (None), residues: 0 loop : -2.55 (0.54), residues: 124 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 102 time to evaluate : 0.721 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 104 average time/residue: 0.1732 time to fit residues: 24.3245 Evaluate side-chains 93 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 89 time to evaluate : 0.721 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0600 time to fit residues: 1.4474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 39 optimal weight: 0.0170 chunk 69 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.9620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 HIS B 289 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 6442 Z= 0.160 Angle : 0.440 5.331 8702 Z= 0.234 Chirality : 0.036 0.144 997 Planarity : 0.003 0.035 1092 Dihedral : 3.863 19.640 859 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer Outliers : 1.29 % 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: 1.56 (0.31), residues: 792 helix: 1.64 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -2.36 (0.54), residues: 124 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 92 time to evaluate : 0.783 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 95 average time/residue: 0.1694 time to fit residues: 22.1737 Evaluate side-chains 93 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 90 time to evaluate : 0.726 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0614 time to fit residues: 1.3394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 35 optimal weight: 0.2980 chunk 6 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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: 0.7987 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 6442 Z= 0.144 Angle : 0.426 5.311 8702 Z= 0.227 Chirality : 0.036 0.144 997 Planarity : 0.003 0.035 1092 Dihedral : 3.831 19.272 859 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer Outliers : 0.86 % 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: 1.83 (0.31), residues: 792 helix: 1.84 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -2.51 (0.52), residues: 120 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 94 time to evaluate : 0.738 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 95 average time/residue: 0.1694 time to fit residues: 22.0669 Evaluate side-chains 91 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 88 time to evaluate : 0.738 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0683 time to fit residues: 1.3833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 65 optimal weight: 0.3980 chunk 77 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 46 optimal weight: 0.4980 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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: 0.8033 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 6442 Z= 0.202 Angle : 0.461 5.511 8702 Z= 0.244 Chirality : 0.036 0.141 997 Planarity : 0.003 0.035 1092 Dihedral : 3.911 19.208 859 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer Outliers : 0.72 % 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: 1.88 (0.31), residues: 792 helix: 1.93 (0.21), residues: 660 sheet: None (None), residues: 0 loop : -2.36 (0.52), residues: 132 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 93 time to evaluate : 0.728 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 96 average time/residue: 0.1713 time to fit residues: 22.6645 Evaluate side-chains 92 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 90 time to evaluate : 0.785 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0610 time to fit residues: 1.2519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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: 0.8010 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 6442 Z= 0.171 Angle : 0.455 6.006 8702 Z= 0.239 Chirality : 0.036 0.151 997 Planarity : 0.003 0.035 1092 Dihedral : 3.901 19.351 859 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer Outliers : 0.57 % 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: 1.99 (0.31), residues: 792 helix: 1.99 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -2.23 (0.51), residues: 132 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 0.670 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 95 average time/residue: 0.1688 time to fit residues: 22.0858 Evaluate side-chains 90 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 88 time to evaluate : 0.697 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0565 time to fit residues: 1.1448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 31 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 46 optimal weight: 0.2980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 6442 Z= 0.179 Angle : 0.457 6.046 8702 Z= 0.241 Chirality : 0.036 0.143 997 Planarity : 0.003 0.033 1092 Dihedral : 3.906 19.846 859 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer Outliers : 0.29 % 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: 2.04 (0.31), residues: 792 helix: 2.01 (0.21), residues: 660 sheet: None (None), residues: 0 loop : -2.17 (0.51), residues: 132 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 90 time to evaluate : 0.741 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 91 average time/residue: 0.1560 time to fit residues: 20.2092 Evaluate side-chains 86 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.742 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 0.9990 chunk 52 optimal weight: 0.0970 chunk 79 optimal weight: 5.9990 chunk 73 optimal weight: 0.0770 chunk 63 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.5736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 HIS ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 6442 Z= 0.136 Angle : 0.428 6.224 8702 Z= 0.227 Chirality : 0.036 0.144 997 Planarity : 0.003 0.035 1092 Dihedral : 3.830 19.819 859 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer Outliers : 0.29 % 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: 2.16 (0.31), residues: 792 helix: 2.08 (0.20), residues: 674 sheet: None (None), residues: 0 loop : -2.57 (0.50), residues: 118 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 93 time to evaluate : 0.734 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 94 average time/residue: 0.1553 time to fit residues: 20.7854 Evaluate side-chains 91 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 90 time to evaluate : 0.737 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0629 time to fit residues: 1.1412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 HIS B 95 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.138717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.101416 restraints weight = 8420.988| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.20 r_work: 0.3124 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 6442 Z= 0.201 Angle : 0.462 6.110 8702 Z= 0.244 Chirality : 0.037 0.141 997 Planarity : 0.003 0.035 1092 Dihedral : 3.921 19.788 859 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer Outliers : 0.29 % 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: 2.13 (0.31), residues: 792 helix: 2.04 (0.21), residues: 666 sheet: None (None), residues: 0 loop : -2.14 (0.53), residues: 126 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1432.68 seconds wall clock time: 26 minutes 47.92 seconds (1607.92 seconds total)