Starting phenix.real_space_refine on Tue Aug 4 17:41:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21zh_68111/08_2026/21zh_68111.cif Found real_map, /net/cci-nas-00/data/ceres_data/21zh_68111/08_2026/21zh_68111.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/21zh_68111/08_2026/21zh_68111.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21zh_68111/08_2026/21zh_68111.map" model { file = "/net/cci-nas-00/data/ceres_data/21zh_68111/08_2026/21zh_68111.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21zh_68111/08_2026/21zh_68111.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.004 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: 5 Type Number sf(0) Gaussians P 39 5.49 5 S 29 5.16 5 C 3313 2.51 5 N 937 2.21 5 O 1104 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5422 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4567 Classifications: {'peptide': 579} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 538} Chain breaks: 2 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 99 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 3, 'GLN:plan1': 1, 'TRP:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 57 Chain: "B" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 828 Classifications: {'RNA': 39} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 3, 'rna3p_pur': 15, 'rna3p_pyr': 18} Link IDs: {'rna2p': 6, 'rna3p': 32} Chain breaks: 1 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} Time building chain proxies: 1.02, per 1000 atoms: 0.19 Number of scatterers: 5422 At special positions: 0 Unit cell: (87.42, 106.95, 71.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 29 16.00 P 39 15.00 O 1104 8.00 N 937 7.00 C 3313 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 - 3.00 Amino acid : True - 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: 0.30 Conformation dependent library (CDL) restraints added in 111.6 milliseconds 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1102 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 7 sheets defined 42.3% alpha, 14.0% beta 12 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 45 through 55 removed outlier: 3.585A pdb=" N LEU A 55 " --> pdb=" O TYR A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 70 Processing helix chain 'A' and resid 86 through 103 removed outlier: 4.595A pdb=" N PHE A 99 " --> pdb=" O LYS A 95 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N LYS A 100 " --> pdb=" O ASN A 96 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLU A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 102 " --> pdb=" O TYR A 98 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU A 103 " --> pdb=" O PHE A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 124 removed outlier: 3.858A pdb=" N GLU A 124 " --> pdb=" O TYR A 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 121 through 124' Processing helix chain 'A' and resid 132 through 138 removed outlier: 3.833A pdb=" N LEU A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 156 Processing helix chain 'A' and resid 166 through 172 removed outlier: 3.911A pdb=" N LEU A 170 " --> pdb=" O MET A 166 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 172 " --> pdb=" O PRO A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 199 removed outlier: 3.837A pdb=" N GLN A 193 " --> pdb=" O SER A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 229 removed outlier: 4.229A pdb=" N TYR A 222 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU A 223 " --> pdb=" O LYS A 219 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL A 225 " --> pdb=" O CYS A 221 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N HIS A 226 " --> pdb=" O TYR A 222 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'A' and resid 273 through 277 Processing helix chain 'A' and resid 280 through 286 removed outlier: 3.691A pdb=" N TRP A 284 " --> pdb=" O ILE A 281 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS A 285 " --> pdb=" O ASP A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 310 removed outlier: 3.510A pdb=" N LEU A 293 " --> pdb=" O THR A 289 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLY A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 340 removed outlier: 4.802A pdb=" N ALA A 330 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N VAL A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ILE A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 380 removed outlier: 3.875A pdb=" N VAL A 380 " --> pdb=" O TRP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 388 removed outlier: 4.533A pdb=" N THR A 386 " --> pdb=" O SER A 383 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN A 387 " --> pdb=" O ARG A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 4.010A pdb=" N MET A 392 " --> pdb=" O ARG A 389 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE A 393 " --> pdb=" O PRO A 390 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 389 through 393' Processing helix chain 'A' and resid 397 through 405 removed outlier: 3.500A pdb=" N HIS A 405 " --> pdb=" O LEU A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 409 removed outlier: 3.526A pdb=" N CYS A 409 " --> pdb=" O LEU A 406 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 406 through 409' Processing helix chain 'A' and resid 529 through 538 removed outlier: 4.083A pdb=" N ILE A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 546 No H-bonds generated for 'chain 'A' and resid 544 through 546' Processing helix chain 'A' and resid 564 through 574 Processing helix chain 'A' and resid 604 through 608 Processing helix chain 'A' and resid 611 through 615 removed outlier: 3.588A pdb=" N ILE A 615 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 631 Processing helix chain 'A' and resid 642 through 651 removed outlier: 4.185A pdb=" N ASP A 651 " --> pdb=" O SER A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 702 Processing sheet with id=AA1, first strand: chain 'A' and resid 126 through 127 Processing sheet with id=AA2, first strand: chain 'A' and resid 179 through 183 removed outlier: 4.768A pdb=" N LYS A 179 " --> pdb=" O PHE A 210 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ILE A 212 " --> pdb=" O LYS A 179 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU A 181 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASN A 214 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N MET A 183 " --> pdb=" O ASN A 214 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL A 211 " --> pdb=" O MET A 237 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N VAL A 239 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ALA A 213 " --> pdb=" O VAL A 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 250 through 251 Processing sheet with id=AA4, first strand: chain 'A' and resid 264 through 268 removed outlier: 6.785A pdb=" N ILE A 265 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N SER A 319 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N CYS A 267 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET A 316 " --> pdb=" O LEU A 427 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 264 through 268 removed outlier: 6.785A pdb=" N ILE A 265 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N SER A 319 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N CYS A 267 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET A 316 " --> pdb=" O LEU A 427 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 521 through 522 removed outlier: 3.630A pdb=" N LEU A 549 " --> pdb=" O TYR A 561 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU A 560 " --> pdb=" O VAL A 587 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 619 through 622 removed outlier: 3.751A pdb=" N GLY A 655 " --> pdb=" O ARG A 681 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY A 679 " --> pdb=" O ILE A 657 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 677 " --> pdb=" O LEU A 659 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE A 675 " --> pdb=" O TYR A 661 " (cutoff:3.500A) 153 hydrogen bonds defined for protein. 408 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 32 hydrogen bonds 60 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 0.88 Time building geometry restraints manager: 0.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1584 1.34 - 1.46: 1305 1.46 - 1.58: 2619 1.58 - 1.70: 76 1.70 - 1.82: 49 Bond restraints: 5633 Sorted by residual: bond pdb=" CA SER A 233 " pdb=" CB SER A 233 " ideal model delta sigma weight residual 1.532 1.504 0.028 1.69e-02 3.50e+03 2.83e+00 bond pdb=" N SER A 233 " pdb=" CA SER A 233 " ideal model delta sigma weight residual 1.453 1.489 -0.036 2.23e-02 2.01e+03 2.67e+00 bond pdb=" C PRO A 524 " pdb=" O PRO A 524 " ideal model delta sigma weight residual 1.235 1.215 0.020 1.30e-02 5.92e+03 2.32e+00 bond pdb=" CB PRO A 187 " pdb=" CG PRO A 187 " ideal model delta sigma weight residual 1.506 1.557 -0.051 3.90e-02 6.57e+02 1.71e+00 bond pdb=" CG GLU A 152 " pdb=" CD GLU A 152 " ideal model delta sigma weight residual 1.516 1.484 0.032 2.50e-02 1.60e+03 1.63e+00 ... (remaining 5628 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 7628 2.37 - 4.74: 179 4.74 - 7.11: 22 7.11 - 9.48: 6 9.48 - 11.86: 1 Bond angle restraints: 7836 Sorted by residual: angle pdb=" C VAL A 253 " pdb=" N ASP A 254 " pdb=" CA ASP A 254 " ideal model delta sigma weight residual 122.46 128.63 -6.17 1.41e+00 5.03e-01 1.91e+01 angle pdb=" CA ARG A 175 " pdb=" CB ARG A 175 " pdb=" CG ARG A 175 " ideal model delta sigma weight residual 114.10 122.09 -7.99 2.00e+00 2.50e-01 1.59e+01 angle pdb=" CA PRO A 234 " pdb=" C PRO A 234 " pdb=" O PRO A 234 " ideal model delta sigma weight residual 121.38 118.48 2.90 7.70e-01 1.69e+00 1.42e+01 angle pdb=" CG ARG A 256 " pdb=" CD ARG A 256 " pdb=" NE ARG A 256 " ideal model delta sigma weight residual 112.00 119.45 -7.45 2.20e+00 2.07e-01 1.15e+01 angle pdb=" O5' G B 65 " pdb=" C5' G B 65 " pdb=" C4' G B 65 " ideal model delta sigma weight residual 109.40 112.03 -2.63 8.00e-01 1.56e+00 1.08e+01 ... (remaining 7831 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.08: 2996 17.08 - 34.15: 339 34.15 - 51.23: 87 51.23 - 68.31: 52 68.31 - 85.38: 18 Dihedral angle restraints: 3492 sinusoidal: 1798 harmonic: 1694 Sorted by residual: dihedral pdb=" CA PRO A 176 " pdb=" C PRO A 176 " pdb=" N HIS A 177 " pdb=" CA HIS A 177 " ideal model delta harmonic sigma weight residual 180.00 157.07 22.93 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA CYS A 184 " pdb=" C CYS A 184 " pdb=" N ALA A 185 " pdb=" CA ALA A 185 " ideal model delta harmonic sigma weight residual 180.00 158.20 21.80 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA MET A 183 " pdb=" C MET A 183 " pdb=" N CYS A 184 " pdb=" CA CYS A 184 " ideal model delta harmonic sigma weight residual 180.00 161.62 18.38 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 3489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 737 0.067 - 0.133: 147 0.133 - 0.200: 24 0.200 - 0.266: 2 0.266 - 0.333: 1 Chirality restraints: 911 Sorted by residual: chirality pdb=" CB ILE A 412 " pdb=" CA ILE A 412 " pdb=" CG1 ILE A 412 " pdb=" CG2 ILE A 412 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CB ILE A 533 " pdb=" CA ILE A 533 " pdb=" CG1 ILE A 533 " pdb=" CG2 ILE A 533 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CA GLU A 152 " pdb=" N GLU A 152 " pdb=" C GLU A 152 " pdb=" CB GLU A 152 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 908 not shown) Planarity restraints: 858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 175 " -0.042 5.00e-02 4.00e+02 6.35e-02 6.44e+00 pdb=" N PRO A 176 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 176 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 176 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 588 " 0.012 2.00e-02 2.50e+03 1.34e-02 4.48e+00 pdb=" CG TRP A 588 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP A 588 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 588 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 588 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 588 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 588 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 588 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 588 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 588 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 540 " -0.034 5.00e-02 4.00e+02 5.12e-02 4.20e+00 pdb=" N PRO A 541 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 541 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 541 " -0.028 5.00e-02 4.00e+02 ... (remaining 855 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 2314 2.94 - 3.43: 5702 3.43 - 3.92: 9367 3.92 - 4.41: 10297 4.41 - 4.90: 15709 Nonbonded interactions: 43389 Sorted by model distance: nonbonded pdb=" O VAL A 253 " pdb=" OD1 ASP A 254 " model vdw 2.447 3.040 nonbonded pdb=" O PHE A 148 " pdb=" OE1 GLU A 152 " model vdw 2.486 3.040 nonbonded pdb=" O LEU A 194 " pdb=" CB LEU A 198 " model vdw 2.504 2.752 nonbonded pdb=" O LEU A 172 " pdb=" OD1 ASN A 173 " model vdw 2.543 3.040 nonbonded pdb=" O2' SAM A 801 " pdb=" O3' SAM A 801 " model vdw 2.575 2.432 ... (remaining 43384 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 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: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.240 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 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:0.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 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 0.051 5633 Z= 0.166 Angle : 0.828 11.856 7836 Z= 0.471 Chirality : 0.054 0.333 911 Planarity : 0.006 0.063 858 Dihedral : 17.370 85.383 2390 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.34), residues: 573 helix: -0.46 (0.38), residues: 172 sheet: -2.38 (0.56), residues: 76 loop : -1.48 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 568 TYR 0.016 0.002 TYR A 51 PHE 0.013 0.002 PHE A 66 TRP 0.036 0.002 TRP A 588 HIS 0.009 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.17 ( 5633) covalent geometry : angle 0.82789 / 0.47 ( 7836) hydrogen bonds : bond 0.19219 / 13.22 ( 180) hydrogen bonds : angle 7.66133 / 5.49 ( 468) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LEU cc_start: 0.8529 (tp) cc_final: 0.7775 (pt) REVERT: A 197 MET cc_start: 0.7040 (ppp) cc_final: 0.6775 (ppp) REVERT: A 202 MET cc_start: 0.6147 (mpp) cc_final: 0.5484 (mpp) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.0589 time to fit residues: 9.6119 Evaluate side-chains 87 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 56 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 58 optimal weight: 20.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 697 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.079596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.064894 restraints weight = 31718.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.066241 restraints weight = 22744.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.067017 restraints weight = 18145.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.067819 restraints weight = 15891.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.068298 restraints weight = 13961.007| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 5633 Z= 0.273 Angle : 0.874 11.548 7836 Z= 0.443 Chirality : 0.048 0.206 911 Planarity : 0.007 0.089 858 Dihedral : 17.739 74.198 1271 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 26.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 1.82 % Allowed : 14.55 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.34), residues: 573 helix: -0.34 (0.39), residues: 174 sheet: -2.53 (0.53), residues: 77 loop : -1.42 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 411 TYR 0.020 0.003 TYR A 318 PHE 0.020 0.002 PHE A 145 TRP 0.014 0.002 TRP A 588 HIS 0.007 0.002 HIS A 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.27 ( 5633) covalent geometry : angle 0.87428 / 0.44 ( 7836) hydrogen bonds : bond 0.05908 / 3.78 ( 180) hydrogen bonds : angle 6.00349 / 4.26 ( 468) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LEU cc_start: 0.9447 (tp) cc_final: 0.8653 (pp) REVERT: A 160 ARG cc_start: 0.8334 (mtt180) cc_final: 0.8085 (mtt180) REVERT: A 183 MET cc_start: 0.6462 (mmm) cc_final: 0.6205 (mmm) REVERT: A 201 ASP cc_start: 0.7641 (p0) cc_final: 0.7342 (p0) outliers start: 9 outliers final: 6 residues processed: 94 average time/residue: 0.0664 time to fit residues: 7.9860 Evaluate side-chains 80 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 697 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 1.9990 chunk 42 optimal weight: 0.0670 chunk 55 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 chunk 57 optimal weight: 20.0000 overall best weight: 1.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 697 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.080713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.064547 restraints weight = 31456.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.066021 restraints weight = 22493.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.067091 restraints weight = 17919.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.067853 restraints weight = 15223.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.068439 restraints weight = 13478.523| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5633 Z= 0.159 Angle : 0.788 11.537 7836 Z= 0.388 Chirality : 0.045 0.223 911 Planarity : 0.007 0.103 858 Dihedral : 17.676 74.128 1271 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 21.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 2.42 % Allowed : 14.95 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.34), residues: 573 helix: -0.23 (0.40), residues: 173 sheet: -2.50 (0.51), residues: 77 loop : -1.46 (0.34), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 411 TYR 0.016 0.002 TYR A 698 PHE 0.018 0.002 PHE A 145 TRP 0.014 0.002 TRP A 588 HIS 0.008 0.001 HIS A 697 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 ( 5633) covalent geometry : angle 0.78794 / 0.39 ( 7836) hydrogen bonds : bond 0.04790 / 3.06 ( 180) hydrogen bonds : angle 5.70668 / 4.09 ( 468) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LEU cc_start: 0.9455 (tp) cc_final: 0.8706 (pp) REVERT: A 183 MET cc_start: 0.6914 (mmm) cc_final: 0.6696 (mmm) REVERT: A 201 ASP cc_start: 0.7711 (p0) cc_final: 0.7206 (p0) REVERT: A 237 MET cc_start: 0.8689 (tpt) cc_final: 0.8384 (tpt) REVERT: A 241 HIS cc_start: 0.8718 (m170) cc_final: 0.8463 (m-70) REVERT: A 264 ARG cc_start: 0.8688 (mmt-90) cc_final: 0.8340 (mmm-85) REVERT: A 367 MET cc_start: 0.8606 (tpt) cc_final: 0.7465 (tpt) outliers start: 12 outliers final: 5 residues processed: 89 average time/residue: 0.0587 time to fit residues: 6.9897 Evaluate side-chains 83 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 427 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 26 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 57 optimal weight: 20.0000 chunk 9 optimal weight: 9.9990 chunk 58 optimal weight: 20.0000 chunk 48 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 HIS ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.079609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.063939 restraints weight = 32236.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.065339 restraints weight = 23408.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.066351 restraints weight = 18807.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.067053 restraints weight = 16132.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.067546 restraints weight = 14348.973| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 5633 Z= 0.158 Angle : 0.757 11.854 7836 Z= 0.367 Chirality : 0.044 0.197 911 Planarity : 0.007 0.101 858 Dihedral : 17.661 74.172 1271 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 20.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 2.83 % Allowed : 16.77 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.34), residues: 573 helix: -0.18 (0.40), residues: 173 sheet: -2.54 (0.49), residues: 77 loop : -1.43 (0.34), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 79 TYR 0.013 0.002 TYR A 318 PHE 0.020 0.002 PHE A 148 TRP 0.014 0.002 TRP A 588 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 ( 5633) covalent geometry : angle 0.75675 / 0.37 ( 7836) hydrogen bonds : bond 0.04501 / 2.80 ( 180) hydrogen bonds : angle 5.49979 / 3.94 ( 468) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LEU cc_start: 0.9461 (tp) cc_final: 0.8706 (pp) REVERT: A 145 PHE cc_start: 0.9643 (OUTLIER) cc_final: 0.9307 (m-80) REVERT: A 160 ARG cc_start: 0.9451 (mtp180) cc_final: 0.8752 (ptm160) REVERT: A 183 MET cc_start: 0.6868 (mmm) cc_final: 0.6611 (mmm) REVERT: A 201 ASP cc_start: 0.7677 (p0) cc_final: 0.7200 (p0) REVERT: A 237 MET cc_start: 0.8677 (tpt) cc_final: 0.8275 (tpt) REVERT: A 409 CYS cc_start: 0.8994 (m) cc_final: 0.8171 (t) REVERT: A 605 GLN cc_start: 0.9303 (tm-30) cc_final: 0.8654 (tp40) outliers start: 14 outliers final: 8 residues processed: 96 average time/residue: 0.0528 time to fit residues: 6.7800 Evaluate side-chains 90 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 427 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 33 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 9 optimal weight: 9.9990 chunk 21 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 chunk 38 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.079403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.064398 restraints weight = 32237.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.065801 restraints weight = 22936.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.066764 restraints weight = 18264.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.067496 restraints weight = 15659.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.068016 restraints weight = 13815.379| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5633 Z= 0.146 Angle : 0.767 12.807 7836 Z= 0.363 Chirality : 0.045 0.213 911 Planarity : 0.007 0.107 858 Dihedral : 17.638 74.158 1271 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 21.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 2.63 % Allowed : 21.01 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.34), residues: 573 helix: -0.32 (0.39), residues: 182 sheet: -2.66 (0.47), residues: 77 loop : -1.41 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 175 TYR 0.012 0.001 TYR A 318 PHE 0.021 0.002 PHE A 148 TRP 0.011 0.002 TRP A 588 HIS 0.009 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 ( 5633) covalent geometry : angle 0.76739 / 0.36 ( 7836) hydrogen bonds : bond 0.04201 / 2.63 ( 180) hydrogen bonds : angle 5.39679 / 3.88 ( 468) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LEU cc_start: 0.9459 (tp) cc_final: 0.8720 (pp) REVERT: A 160 ARG cc_start: 0.9468 (mtp180) cc_final: 0.8738 (ptm160) REVERT: A 183 MET cc_start: 0.6998 (mmm) cc_final: 0.6684 (mmm) REVERT: A 201 ASP cc_start: 0.7627 (p0) cc_final: 0.6410 (p0) REVERT: A 202 MET cc_start: 0.7364 (mpp) cc_final: 0.6700 (mpp) REVERT: A 237 MET cc_start: 0.8749 (tpt) cc_final: 0.8327 (tpt) REVERT: A 264 ARG cc_start: 0.8685 (mmt-90) cc_final: 0.8380 (mmt90) REVERT: A 367 MET cc_start: 0.8737 (tpt) cc_final: 0.8070 (tpt) REVERT: A 409 CYS cc_start: 0.8851 (m) cc_final: 0.8071 (t) REVERT: A 605 GLN cc_start: 0.9331 (tm-30) cc_final: 0.8648 (tp40) REVERT: A 606 GLU cc_start: 0.8795 (pm20) cc_final: 0.8582 (pm20) outliers start: 13 outliers final: 9 residues processed: 94 average time/residue: 0.0550 time to fit residues: 7.0642 Evaluate side-chains 95 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 427 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 24 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 chunk 57 optimal weight: 20.0000 chunk 21 optimal weight: 0.0370 overall best weight: 0.7262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.079850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.064262 restraints weight = 31324.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.065708 restraints weight = 22387.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 15)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.066479 restraints weight = 17901.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.067350 restraints weight = 15578.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.067710 restraints weight = 13915.667| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5633 Z= 0.123 Angle : 0.754 12.039 7836 Z= 0.356 Chirality : 0.045 0.193 911 Planarity : 0.007 0.106 858 Dihedral : 17.564 74.081 1271 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 3.03 % Allowed : 21.62 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.34), residues: 573 helix: -0.37 (0.39), residues: 182 sheet: -2.54 (0.49), residues: 76 loop : -1.30 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 79 TYR 0.011 0.001 TYR A 98 PHE 0.020 0.002 PHE A 148 TRP 0.011 0.001 TRP A 588 HIS 0.010 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 5633) covalent geometry : angle 0.75409 / 0.36 ( 7836) hydrogen bonds : bond 0.03851 / 2.39 ( 180) hydrogen bonds : angle 5.23774 / 3.76 ( 468) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LEU cc_start: 0.9453 (tp) cc_final: 0.8703 (pp) REVERT: A 160 ARG cc_start: 0.9417 (mtp180) cc_final: 0.8696 (ptm160) REVERT: A 183 MET cc_start: 0.7217 (mmm) cc_final: 0.6868 (mmm) REVERT: A 197 MET cc_start: 0.8591 (ptm) cc_final: 0.8239 (ptp) REVERT: A 201 ASP cc_start: 0.7703 (p0) cc_final: 0.6471 (p0) REVERT: A 202 MET cc_start: 0.7553 (mpp) cc_final: 0.6890 (mpp) REVERT: A 237 MET cc_start: 0.8736 (tpt) cc_final: 0.8439 (tpt) REVERT: A 409 CYS cc_start: 0.8791 (m) cc_final: 0.7914 (t) REVERT: A 423 PHE cc_start: 0.9048 (t80) cc_final: 0.8162 (t80) REVERT: A 578 MET cc_start: 0.7857 (tmm) cc_final: 0.7640 (tmm) REVERT: A 605 GLN cc_start: 0.9363 (tm-30) cc_final: 0.8665 (tp40) outliers start: 15 outliers final: 9 residues processed: 99 average time/residue: 0.0597 time to fit residues: 7.8003 Evaluate side-chains 94 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 427 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 10 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 19 optimal weight: 0.0370 chunk 3 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 50 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 overall best weight: 1.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.079608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.064572 restraints weight = 32656.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.066045 restraints weight = 23566.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.067030 restraints weight = 18778.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.067763 restraints weight = 15932.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.068281 restraints weight = 14085.428| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 5633 Z= 0.154 Angle : 0.771 11.933 7836 Z= 0.370 Chirality : 0.046 0.233 911 Planarity : 0.007 0.105 858 Dihedral : 17.617 74.147 1271 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 20.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 2.83 % Allowed : 23.84 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.35), residues: 573 helix: -0.12 (0.40), residues: 182 sheet: -2.39 (0.52), residues: 74 loop : -1.24 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 545 TYR 0.015 0.001 TYR A 318 PHE 0.021 0.002 PHE A 148 TRP 0.008 0.001 TRP A 364 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 5633) covalent geometry : angle 0.77100 / 0.37 ( 7836) hydrogen bonds : bond 0.04154 / 2.61 ( 180) hydrogen bonds : angle 5.28319 / 3.82 ( 468) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LEU cc_start: 0.9453 (tp) cc_final: 0.8691 (pp) REVERT: A 160 ARG cc_start: 0.9414 (mtp180) cc_final: 0.8630 (ptm160) REVERT: A 183 MET cc_start: 0.7403 (mmm) cc_final: 0.7028 (mmm) REVERT: A 201 ASP cc_start: 0.7684 (p0) cc_final: 0.6416 (p0) REVERT: A 202 MET cc_start: 0.7403 (mpp) cc_final: 0.6731 (mpp) REVERT: A 237 MET cc_start: 0.8662 (tpt) cc_final: 0.8329 (tpt) REVERT: A 409 CYS cc_start: 0.8728 (m) cc_final: 0.7898 (t) REVERT: A 423 PHE cc_start: 0.9072 (t80) cc_final: 0.8111 (t80) REVERT: A 602 ARG cc_start: 0.7861 (mtt180) cc_final: 0.7371 (mtm180) REVERT: A 605 GLN cc_start: 0.9376 (tm-30) cc_final: 0.8669 (tp40) REVERT: A 606 GLU cc_start: 0.8967 (pm20) cc_final: 0.8661 (pm20) outliers start: 14 outliers final: 13 residues processed: 94 average time/residue: 0.0632 time to fit residues: 8.0468 Evaluate side-chains 96 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 427 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 54 optimal weight: 0.4980 chunk 20 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.079239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.063598 restraints weight = 33041.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.065042 restraints weight = 24136.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.065846 restraints weight = 19255.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.066744 restraints weight = 16649.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.067314 restraints weight = 14692.618| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5633 Z= 0.146 Angle : 0.774 11.590 7836 Z= 0.369 Chirality : 0.045 0.186 911 Planarity : 0.007 0.107 858 Dihedral : 17.645 74.154 1271 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 21.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 3.03 % Allowed : 24.44 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.35), residues: 573 helix: -0.19 (0.39), residues: 183 sheet: -2.36 (0.51), residues: 73 loop : -1.32 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 315 TYR 0.015 0.001 TYR A 318 PHE 0.021 0.002 PHE A 148 TRP 0.009 0.001 TRP A 364 HIS 0.005 0.001 HIS A 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 ( 5633) covalent geometry : angle 0.77414 / 0.37 ( 7836) hydrogen bonds : bond 0.04071 / 2.55 ( 180) hydrogen bonds : angle 5.17822 / 3.71 ( 468) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LEU cc_start: 0.9472 (tp) cc_final: 0.8748 (pp) REVERT: A 160 ARG cc_start: 0.9382 (mtp180) cc_final: 0.8676 (ptm160) REVERT: A 183 MET cc_start: 0.7446 (mmm) cc_final: 0.7054 (mmm) REVERT: A 201 ASP cc_start: 0.7611 (p0) cc_final: 0.6331 (p0) REVERT: A 202 MET cc_start: 0.7486 (mpp) cc_final: 0.6825 (mpp) REVERT: A 237 MET cc_start: 0.8732 (tpt) cc_final: 0.8305 (tpt) REVERT: A 409 CYS cc_start: 0.8632 (m) cc_final: 0.7870 (t) REVERT: A 423 PHE cc_start: 0.9118 (t80) cc_final: 0.8169 (t80) REVERT: A 602 ARG cc_start: 0.7896 (mtt180) cc_final: 0.7375 (mtm180) REVERT: A 605 GLN cc_start: 0.9410 (tm-30) cc_final: 0.8724 (tp40) REVERT: A 606 GLU cc_start: 0.9055 (pm20) cc_final: 0.8789 (pm20) outliers start: 15 outliers final: 13 residues processed: 95 average time/residue: 0.0480 time to fit residues: 6.3649 Evaluate side-chains 96 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 427 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 20 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 2 optimal weight: 0.0010 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 30 optimal weight: 0.4980 chunk 13 optimal weight: 0.5980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.080528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.065767 restraints weight = 32090.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.067208 restraints weight = 22569.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.068214 restraints weight = 17976.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.068909 restraints weight = 15358.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.069321 restraints weight = 13574.595| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5633 Z= 0.128 Angle : 0.797 12.692 7836 Z= 0.374 Chirality : 0.045 0.172 911 Planarity : 0.007 0.104 858 Dihedral : 17.610 74.074 1271 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 3.23 % Allowed : 24.04 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.35), residues: 573 helix: -0.35 (0.39), residues: 183 sheet: -2.18 (0.52), residues: 73 loop : -1.23 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 568 TYR 0.013 0.001 TYR A 318 PHE 0.018 0.002 PHE A 148 TRP 0.010 0.001 TRP A 588 HIS 0.004 0.001 HIS A 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 5633) covalent geometry : angle 0.79693 / 0.37 ( 7836) hydrogen bonds : bond 0.03874 / 2.43 ( 180) hydrogen bonds : angle 5.12176 / 3.67 ( 468) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 LEU cc_start: 0.9467 (tp) cc_final: 0.8749 (pp) REVERT: A 160 ARG cc_start: 0.9348 (mtp180) cc_final: 0.8727 (ptm160) REVERT: A 183 MET cc_start: 0.7486 (mmm) cc_final: 0.7106 (mmm) REVERT: A 201 ASP cc_start: 0.7555 (p0) cc_final: 0.6231 (p0) REVERT: A 202 MET cc_start: 0.7499 (mpp) cc_final: 0.6856 (mpp) REVERT: A 237 MET cc_start: 0.8708 (tpt) cc_final: 0.8258 (tpt) REVERT: A 409 CYS cc_start: 0.8598 (m) cc_final: 0.7813 (t) REVERT: A 423 PHE cc_start: 0.9091 (t80) cc_final: 0.8180 (t80) REVERT: A 602 ARG cc_start: 0.7897 (mtt180) cc_final: 0.7383 (mtm180) REVERT: A 605 GLN cc_start: 0.9407 (tm-30) cc_final: 0.8697 (tp40) REVERT: A 606 GLU cc_start: 0.9076 (pm20) cc_final: 0.8826 (pm20) outliers start: 16 outliers final: 13 residues processed: 94 average time/residue: 0.0507 time to fit residues: 6.6776 Evaluate side-chains 95 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 427 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 0.7980 chunk 59 optimal weight: 20.0000 chunk 20 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 7 optimal weight: 0.0980 chunk 54 optimal weight: 0.2980 chunk 42 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.079485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.065010 restraints weight = 32153.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.066401 restraints weight = 22552.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.067169 restraints weight = 18019.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.067958 restraints weight = 15625.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.068464 restraints weight = 13928.836| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5633 Z= 0.126 Angle : 0.810 13.008 7836 Z= 0.380 Chirality : 0.045 0.185 911 Planarity : 0.007 0.105 858 Dihedral : 17.578 74.053 1271 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 3.23 % Allowed : 24.24 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.34), residues: 573 helix: -0.42 (0.39), residues: 183 sheet: -2.12 (0.52), residues: 73 loop : -1.26 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 301 TYR 0.014 0.001 TYR A 318 PHE 0.035 0.002 PHE A 614 TRP 0.009 0.001 TRP A 287 HIS 0.004 0.001 HIS A 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 5633) covalent geometry : angle 0.81033 / 0.38 ( 7836) hydrogen bonds : bond 0.03892 / 2.45 ( 180) hydrogen bonds : angle 5.07859 / 3.64 ( 468) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LEU cc_start: 0.9469 (tp) cc_final: 0.8759 (pp) REVERT: A 160 ARG cc_start: 0.9338 (mtp180) cc_final: 0.8752 (ptm160) REVERT: A 183 MET cc_start: 0.7584 (mmm) cc_final: 0.7209 (mmm) REVERT: A 201 ASP cc_start: 0.7611 (p0) cc_final: 0.7198 (p0) REVERT: A 237 MET cc_start: 0.8626 (tpt) cc_final: 0.8183 (tpt) REVERT: A 316 MET cc_start: 0.8460 (ttm) cc_final: 0.8034 (ttp) REVERT: A 409 CYS cc_start: 0.8575 (m) cc_final: 0.7882 (t) REVERT: A 423 PHE cc_start: 0.9100 (t80) cc_final: 0.8179 (t80) REVERT: A 602 ARG cc_start: 0.7982 (mtt180) cc_final: 0.7475 (mtm180) REVERT: A 605 GLN cc_start: 0.9448 (tm-30) cc_final: 0.8725 (tp40) REVERT: A 606 GLU cc_start: 0.9090 (pm20) cc_final: 0.8855 (pm20) outliers start: 16 outliers final: 14 residues processed: 93 average time/residue: 0.0446 time to fit residues: 5.8205 Evaluate side-chains 97 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 410 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 57 optimal weight: 20.0000 chunk 34 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 10 optimal weight: 0.0770 chunk 35 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 overall best weight: 1.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.078086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.062609 restraints weight = 31824.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.064038 restraints weight = 23167.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.064976 restraints weight = 18741.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.065665 restraints weight = 16055.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.066151 restraints weight = 14390.217| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5633 Z= 0.130 Angle : 0.795 12.087 7836 Z= 0.374 Chirality : 0.044 0.174 911 Planarity : 0.007 0.104 858 Dihedral : 17.574 74.088 1271 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 18.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 2.83 % Allowed : 24.65 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.35), residues: 573 helix: -0.40 (0.39), residues: 184 sheet: -2.13 (0.52), residues: 74 loop : -1.25 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 175 TYR 0.014 0.001 TYR A 318 PHE 0.020 0.002 PHE A 148 TRP 0.008 0.001 TRP A 680 HIS 0.004 0.001 HIS A 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 5633) covalent geometry : angle 0.79464 / 0.37 ( 7836) hydrogen bonds : bond 0.03962 / 2.45 ( 180) hydrogen bonds : angle 5.02368 / 3.60 ( 468) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 945.75 seconds wall clock time: 17 minutes 0.07 seconds (1020.07 seconds total)