Starting phenix.real_space_refine on Tue Feb 3 17:35:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k0c_61943/02_2026/9k0c_61943.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k0c_61943/02_2026/9k0c_61943.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k0c_61943/02_2026/9k0c_61943.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k0c_61943/02_2026/9k0c_61943.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k0c_61943/02_2026/9k0c_61943.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k0c_61943/02_2026/9k0c_61943.map" } resolution = 3.06 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= -0.003 sd= 0.104 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 S 39 5.16 5 Cl 1 4.86 5 C 3696 2.51 5 N 882 2.21 5 O 970 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5588 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 852 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 3, 'ASP:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 48 Chain: "L" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 726 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "A" Number of atoms: 4009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4009 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 27, 'TRANS': 501} Chain breaks: 1 Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 8, 'ASN:plan1': 5, 'ARG:plan': 4, 'TYR:plan': 6, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 140 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.54, per 1000 atoms: 0.28 Number of scatterers: 5588 At special positions: 0 Unit cell: (88.976, 84.688, 103.984, 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) Cl 1 17.00 S 39 16.00 O 970 8.00 N 882 7.00 C 3696 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 171 " distance=2.03 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: 0.46 Conformation dependent library (CDL) restraints added in 474.4 milliseconds 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1368 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 6 sheets defined 59.8% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.703A pdb=" N THR H 65 " --> pdb=" O ASP H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.089A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.727A pdb=" N ALA L 84 " --> pdb=" O ALA L 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 58 removed outlier: 3.539A pdb=" N GLY A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY A 57 " --> pdb=" O SER A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 65 through 74 removed outlier: 3.663A pdb=" N TYR A 69 " --> pdb=" O TRP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 106 removed outlier: 3.888A pdb=" N LEU A 80 " --> pdb=" O GLY A 76 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ILE A 81 " --> pdb=" O GLY A 77 " (cutoff:3.500A) Proline residue: A 82 - end of helix removed outlier: 5.704A pdb=" N LEU A 92 " --> pdb=" O PHE A 88 " (cutoff:3.500A) Proline residue: A 93 - end of helix Processing helix chain 'A' and resid 111 through 117 removed outlier: 3.654A pdb=" N LYS A 115 " --> pdb=" O THR A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 120 No H-bonds generated for 'chain 'A' and resid 118 through 120' Processing helix chain 'A' and resid 121 through 138 removed outlier: 3.831A pdb=" N TYR A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 153 removed outlier: 4.014A pdb=" N LEU A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 179 removed outlier: 3.987A pdb=" N LYS A 178 " --> pdb=" O THR A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 202 Processing helix chain 'A' and resid 217 through 238 Processing helix chain 'A' and resid 244 through 266 removed outlier: 4.357A pdb=" N PHE A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 269 through 279 removed outlier: 3.744A pdb=" N GLY A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 285 Processing helix chain 'A' and resid 287 through 302 removed outlier: 4.376A pdb=" N TRP A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE A 298 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE A 299 " --> pdb=" O GLY A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 314 removed outlier: 3.631A pdb=" N SER A 314 " --> pdb=" O THR A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 356 removed outlier: 3.519A pdb=" N SER A 337 " --> pdb=" O ASN A 333 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 removed outlier: 3.683A pdb=" N VAL A 362 " --> pdb=" O ILE A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 368 No H-bonds generated for 'chain 'A' and resid 366 through 368' Processing helix chain 'A' and resid 369 through 380 removed outlier: 3.660A pdb=" N TYR A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) Proline residue: A 375 - end of helix removed outlier: 3.736A pdb=" N MET A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 418 removed outlier: 3.669A pdb=" N TRP A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 444 removed outlier: 4.093A pdb=" N ILE A 430 " --> pdb=" O TYR A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 450 through 462 removed outlier: 3.824A pdb=" N VAL A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 482 removed outlier: 3.683A pdb=" N LEU A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 497 Processing helix chain 'A' and resid 501 through 510 Processing helix chain 'A' and resid 510 through 526 Processing helix chain 'A' and resid 539 through 555 removed outlier: 3.883A pdb=" N SER A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 567 Processing helix chain 'A' and resid 571 through 581 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.558A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.769A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N GLU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N MET H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 6 removed outlier: 5.960A pdb=" N THR L 70 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 10.426A pdb=" N SER L 27 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 9.963A pdb=" N SER L 68 " --> pdb=" O SER L 27 " (cutoff:3.500A) removed outlier: 11.815A pdb=" N VAL L 29 " --> pdb=" O SER L 66 " (cutoff:3.500A) removed outlier: 11.867A pdb=" N SER L 66 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 10 through 11 removed outlier: 4.012A pdb=" N MET L 11 " --> pdb=" O LYS L 104 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N TRP L 36 " --> pdb=" O TRP L 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 11 removed outlier: 4.012A pdb=" N MET L 11 " --> pdb=" O LYS L 104 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 531 through 532 330 hydrogen bonds defined for protein. 933 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: 0.99 Time building geometry restraints manager: 0.62 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: 1653 1.34 - 1.46: 1200 1.46 - 1.58: 2845 1.58 - 1.70: 0 1.70 - 1.82: 56 Bond restraints: 5754 Sorted by residual: bond pdb=" CA VAL A 557 " pdb=" CB VAL A 557 " ideal model delta sigma weight residual 1.539 1.549 -0.010 5.40e-03 3.43e+04 3.74e+00 bond pdb=" N PRO A 82 " pdb=" CA PRO A 82 " ideal model delta sigma weight residual 1.471 1.446 0.025 1.32e-02 5.74e+03 3.63e+00 bond pdb=" CZ2 TRP A 291 " pdb=" CH2 TRP A 291 " ideal model delta sigma weight residual 1.368 1.404 -0.036 1.90e-02 2.77e+03 3.54e+00 bond pdb=" CA GLU A 286 " pdb=" C GLU A 286 " ideal model delta sigma weight residual 1.523 1.545 -0.023 1.41e-02 5.03e+03 2.58e+00 bond pdb=" CA ASP A 287 " pdb=" C ASP A 287 " ideal model delta sigma weight residual 1.519 1.539 -0.020 1.28e-02 6.10e+03 2.33e+00 ... (remaining 5749 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 7596 1.43 - 2.85: 223 2.85 - 4.28: 45 4.28 - 5.71: 14 5.71 - 7.14: 2 Bond angle restraints: 7880 Sorted by residual: angle pdb=" C SER L 51 " pdb=" N THR L 52 " pdb=" CA THR L 52 " ideal model delta sigma weight residual 121.54 128.68 -7.14 1.91e+00 2.74e-01 1.40e+01 angle pdb=" CA PHE A 79 " pdb=" CB PHE A 79 " pdb=" CG PHE A 79 " ideal model delta sigma weight residual 113.80 117.33 -3.53 1.00e+00 1.00e+00 1.25e+01 angle pdb=" C ASP A 287 " pdb=" N PRO A 288 " pdb=" CA PRO A 288 " ideal model delta sigma weight residual 119.56 122.67 -3.11 1.02e+00 9.61e-01 9.32e+00 angle pdb=" C GLY A 57 " pdb=" N PHE A 58 " pdb=" CA PHE A 58 " ideal model delta sigma weight residual 122.65 118.15 4.50 1.60e+00 3.91e-01 7.90e+00 angle pdb=" C PRO A 288 " pdb=" CA PRO A 288 " pdb=" CB PRO A 288 " ideal model delta sigma weight residual 111.85 107.87 3.98 1.42e+00 4.96e-01 7.87e+00 ... (remaining 7875 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 2968 17.96 - 35.92: 208 35.92 - 53.88: 52 53.88 - 71.84: 5 71.84 - 89.80: 2 Dihedral angle restraints: 3235 sinusoidal: 1079 harmonic: 2156 Sorted by residual: dihedral pdb=" CA VAL A 510 " pdb=" C VAL A 510 " pdb=" N ILE A 511 " pdb=" CA ILE A 511 " ideal model delta harmonic sigma weight residual -180.00 -159.10 -20.90 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 89 " pdb=" CB CYS L 89 " ideal model delta sinusoidal sigma weight residual 93.00 61.95 31.05 1 1.00e+01 1.00e-02 1.38e+01 dihedral pdb=" CA PRO A 280 " pdb=" C PRO A 280 " pdb=" N ASP A 281 " pdb=" CA ASP A 281 " ideal model delta harmonic sigma weight residual 180.00 162.77 17.23 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 3232 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 737 0.052 - 0.103: 138 0.103 - 0.155: 24 0.155 - 0.207: 0 0.207 - 0.258: 1 Chirality restraints: 900 Sorted by residual: chirality pdb=" CA PRO A 82 " pdb=" N PRO A 82 " pdb=" C PRO A 82 " pdb=" CB PRO A 82 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA PRO A 288 " pdb=" N PRO A 288 " pdb=" C PRO A 288 " pdb=" CB PRO A 288 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.72e-01 chirality pdb=" CA PRO A 280 " pdb=" N PRO A 280 " pdb=" C PRO A 280 " pdb=" CB PRO A 280 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.13e-01 ... (remaining 897 not shown) Planarity restraints: 977 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 79 " -0.054 2.00e-02 2.50e+03 3.29e-02 1.89e+01 pdb=" CG PHE A 79 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE A 79 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 PHE A 79 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 PHE A 79 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 79 " -0.012 2.00e-02 2.50e+03 pdb=" CZ PHE A 79 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 291 " 0.043 2.00e-02 2.50e+03 2.49e-02 1.55e+01 pdb=" CG TRP A 291 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TRP A 291 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP A 291 " -0.024 2.00e-02 2.50e+03 pdb=" NE1 TRP A 291 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TRP A 291 " -0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP A 291 " -0.040 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 291 " 0.019 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 291 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 291 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 522 " 0.037 2.00e-02 2.50e+03 2.30e-02 9.26e+00 pdb=" CG PHE A 522 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE A 522 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE A 522 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE A 522 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 522 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 522 " 0.023 2.00e-02 2.50e+03 ... (remaining 974 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 32 2.64 - 3.20: 5131 3.20 - 3.77: 8954 3.77 - 4.33: 12332 4.33 - 4.90: 20746 Nonbonded interactions: 47195 Sorted by model distance: nonbonded pdb=" OH TYR A 69 " pdb=" OD2 ASP A 459 " model vdw 2.072 3.040 nonbonded pdb=" OG1 THR A 168 " pdb=" OE1 GLU A 197 " model vdw 2.078 3.040 nonbonded pdb=" OH TYR H 57 " pdb=" OD1 ASP A 491 " model vdw 2.093 3.040 nonbonded pdb=" OE2 GLU H 50 " pdb=" OH TYR L 95 " model vdw 2.334 3.040 nonbonded pdb=" O GLY A 307 " pdb=" OG1 THR A 310 " model vdw 2.414 3.040 ... (remaining 47190 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.630 Find NCS groups from input model: 0.030 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 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 0.036 5757 Z= 0.170 Angle : 0.611 7.135 7886 Z= 0.345 Chirality : 0.041 0.258 900 Planarity : 0.005 0.043 977 Dihedral : 13.372 89.796 1858 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.55 % Allowed : 11.76 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.43 (0.32), residues: 746 helix: 1.82 (0.27), residues: 381 sheet: 1.36 (0.57), residues: 92 loop : -0.42 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 66 TYR 0.016 0.001 TYR A 69 PHE 0.054 0.003 PHE A 79 TRP 0.043 0.003 TRP A 291 HIS 0.002 0.001 HIS L 35 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 5754) covalent geometry : angle 0.61041 ( 7880) SS BOND : bond 0.00158 ( 3) SS BOND : angle 0.79392 ( 6) hydrogen bonds : bond 0.14022 ( 328) hydrogen bonds : angle 5.81224 ( 933) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 98 time to evaluate : 0.216 Fit side-chains REVERT: A 275 LYS cc_start: 0.8234 (ttpt) cc_final: 0.7422 (tptt) REVERT: A 554 MET cc_start: 0.8848 (mtp) cc_final: 0.8606 (mtm) outliers start: 3 outliers final: 2 residues processed: 99 average time/residue: 0.0758 time to fit residues: 9.9945 Evaluate side-chains 84 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 82 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain A residue 353 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.2980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN H 39 GLN A 164 HIS A 321 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.136299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.109465 restraints weight = 6734.268| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.70 r_work: 0.3006 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5757 Z= 0.157 Angle : 0.559 5.967 7886 Z= 0.291 Chirality : 0.041 0.167 900 Planarity : 0.004 0.044 977 Dihedral : 4.513 38.572 812 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.57 % Allowed : 10.66 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.29 (0.31), residues: 746 helix: 1.73 (0.27), residues: 373 sheet: 1.01 (0.56), residues: 88 loop : -0.32 (0.38), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 324 TYR 0.021 0.002 TYR A 69 PHE 0.017 0.002 PHE A 79 TRP 0.016 0.002 TRP A 113 HIS 0.001 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 5754) covalent geometry : angle 0.55835 ( 7880) SS BOND : bond 0.00261 ( 3) SS BOND : angle 1.19602 ( 6) hydrogen bonds : bond 0.04149 ( 328) hydrogen bonds : angle 4.87388 ( 933) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.191 Fit side-chains REVERT: H 60 TYR cc_start: 0.8962 (m-80) cc_final: 0.8729 (m-80) REVERT: L 92 PHE cc_start: 0.8802 (OUTLIER) cc_final: 0.7432 (m-80) REVERT: A 69 TYR cc_start: 0.9005 (OUTLIER) cc_final: 0.8076 (p90) REVERT: A 334 SER cc_start: 0.8244 (OUTLIER) cc_final: 0.7888 (m) REVERT: A 495 MET cc_start: 0.8604 (mtp) cc_final: 0.8329 (mtm) outliers start: 14 outliers final: 9 residues processed: 96 average time/residue: 0.0644 time to fit residues: 8.4163 Evaluate side-chains 96 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 92 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain A residue 479 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 38 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 33 optimal weight: 0.0970 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 ASN ** 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 = 0.3421 r_free = 0.3421 target = 0.133872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.107382 restraints weight = 6681.055| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.68 r_work: 0.2971 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5757 Z= 0.159 Angle : 0.542 6.045 7886 Z= 0.282 Chirality : 0.041 0.145 900 Planarity : 0.004 0.040 977 Dihedral : 4.655 38.404 812 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.12 % Allowed : 10.85 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.01 (0.31), residues: 746 helix: 1.55 (0.26), residues: 374 sheet: 0.85 (0.55), residues: 86 loop : -0.54 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 324 TYR 0.023 0.002 TYR A 69 PHE 0.017 0.002 PHE A 79 TRP 0.016 0.001 TRP A 470 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 5754) covalent geometry : angle 0.54093 ( 7880) SS BOND : bond 0.00209 ( 3) SS BOND : angle 1.14161 ( 6) hydrogen bonds : bond 0.03929 ( 328) hydrogen bonds : angle 4.76327 ( 933) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.205 Fit side-chains REVERT: H 60 TYR cc_start: 0.8999 (m-80) cc_final: 0.8798 (m-80) REVERT: L 92 PHE cc_start: 0.8853 (OUTLIER) cc_final: 0.7241 (m-80) REVERT: A 69 TYR cc_start: 0.9023 (OUTLIER) cc_final: 0.8052 (p90) REVERT: A 334 SER cc_start: 0.8209 (OUTLIER) cc_final: 0.7881 (m) REVERT: A 495 MET cc_start: 0.8580 (mtp) cc_final: 0.8313 (mtm) REVERT: A 523 SER cc_start: 0.8595 (t) cc_final: 0.8218 (m) REVERT: A 554 MET cc_start: 0.8822 (mtp) cc_final: 0.8523 (mtm) outliers start: 17 outliers final: 11 residues processed: 97 average time/residue: 0.0710 time to fit residues: 9.4298 Evaluate side-chains 98 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 92 PHE Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain A residue 479 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 62 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 11 optimal weight: 0.1980 chunk 6 optimal weight: 0.0070 chunk 52 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 31 optimal weight: 0.0770 chunk 30 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.3356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** 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 = 0.3460 r_free = 0.3460 target = 0.137131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.111060 restraints weight = 6606.238| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.66 r_work: 0.3022 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5757 Z= 0.106 Angle : 0.487 5.821 7886 Z= 0.251 Chirality : 0.039 0.143 900 Planarity : 0.004 0.034 977 Dihedral : 4.398 38.162 812 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.31 % Allowed : 11.03 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.18 (0.31), residues: 746 helix: 1.82 (0.27), residues: 373 sheet: 0.77 (0.54), residues: 86 loop : -0.59 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 324 TYR 0.018 0.001 TYR A 69 PHE 0.015 0.001 PHE A 350 TRP 0.016 0.001 TRP A 470 HIS 0.001 0.000 HIS L 35 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 5754) covalent geometry : angle 0.48649 ( 7880) SS BOND : bond 0.00261 ( 3) SS BOND : angle 0.89902 ( 6) hydrogen bonds : bond 0.03303 ( 328) hydrogen bonds : angle 4.52414 ( 933) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.205 Fit side-chains REVERT: L 92 PHE cc_start: 0.8851 (OUTLIER) cc_final: 0.7613 (m-80) REVERT: A 69 TYR cc_start: 0.8884 (OUTLIER) cc_final: 0.7842 (p90) REVERT: A 167 ASN cc_start: 0.8245 (m-40) cc_final: 0.7960 (m-40) REVERT: A 441 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8570 (mm) REVERT: A 495 MET cc_start: 0.8594 (mtp) cc_final: 0.8331 (mtm) REVERT: A 523 SER cc_start: 0.8565 (t) cc_final: 0.8236 (m) REVERT: A 554 MET cc_start: 0.8804 (mtp) cc_final: 0.8523 (mtm) REVERT: A 578 TYR cc_start: 0.7762 (t80) cc_final: 0.7520 (t80) outliers start: 18 outliers final: 12 residues processed: 100 average time/residue: 0.0699 time to fit residues: 9.5068 Evaluate side-chains 100 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 92 PHE Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 479 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 72 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 5 optimal weight: 0.2980 chunk 36 optimal weight: 0.0670 chunk 7 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.130871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.104669 restraints weight = 6820.843| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.66 r_work: 0.2950 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 5757 Z= 0.187 Angle : 0.561 6.943 7886 Z= 0.289 Chirality : 0.041 0.140 900 Planarity : 0.004 0.036 977 Dihedral : 4.719 37.326 812 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.04 % Allowed : 11.40 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.81 (0.30), residues: 746 helix: 1.48 (0.26), residues: 374 sheet: 0.48 (0.54), residues: 86 loop : -0.67 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 324 TYR 0.024 0.002 TYR A 69 PHE 0.017 0.002 PHE A 392 TRP 0.013 0.001 TRP A 470 HIS 0.003 0.001 HIS H 80 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 5754) covalent geometry : angle 0.55973 ( 7880) SS BOND : bond 0.00219 ( 3) SS BOND : angle 1.20821 ( 6) hydrogen bonds : bond 0.03921 ( 328) hydrogen bonds : angle 4.73489 ( 933) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.197 Fit side-chains REVERT: H 57 TYR cc_start: 0.8793 (m-80) cc_final: 0.8294 (m-80) REVERT: L 48 TRP cc_start: 0.8731 (OUTLIER) cc_final: 0.6750 (m-90) REVERT: L 92 PHE cc_start: 0.8864 (OUTLIER) cc_final: 0.7272 (m-80) REVERT: A 69 TYR cc_start: 0.9016 (OUTLIER) cc_final: 0.8077 (p90) REVERT: A 334 SER cc_start: 0.8271 (OUTLIER) cc_final: 0.7987 (m) REVERT: A 441 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8635 (mm) REVERT: A 495 MET cc_start: 0.8617 (mtp) cc_final: 0.8359 (mtm) REVERT: A 523 SER cc_start: 0.8656 (t) cc_final: 0.8295 (m) outliers start: 22 outliers final: 15 residues processed: 104 average time/residue: 0.0568 time to fit residues: 8.1883 Evaluate side-chains 107 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 48 TRP Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 92 PHE Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 479 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.0770 chunk 16 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 72 optimal weight: 0.0030 chunk 64 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 21 optimal weight: 0.1980 overall best weight: 0.3348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** 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 = 0.3439 r_free = 0.3439 target = 0.135479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.109539 restraints weight = 6668.922| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 1.67 r_work: 0.3010 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5757 Z= 0.106 Angle : 0.493 7.697 7886 Z= 0.252 Chirality : 0.039 0.138 900 Planarity : 0.004 0.034 977 Dihedral : 4.419 37.079 812 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.31 % Allowed : 13.05 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.08 (0.31), residues: 746 helix: 1.77 (0.27), residues: 374 sheet: 0.55 (0.55), residues: 86 loop : -0.63 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 324 TYR 0.018 0.001 TYR A 69 PHE 0.016 0.001 PHE A 350 TRP 0.017 0.001 TRP A 470 HIS 0.002 0.001 HIS H 80 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 5754) covalent geometry : angle 0.49199 ( 7880) SS BOND : bond 0.00357 ( 3) SS BOND : angle 0.96573 ( 6) hydrogen bonds : bond 0.03222 ( 328) hydrogen bonds : angle 4.50165 ( 933) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.130 Fit side-chains REVERT: H 31 SER cc_start: 0.8990 (t) cc_final: 0.8650 (t) REVERT: L 92 PHE cc_start: 0.8865 (OUTLIER) cc_final: 0.7208 (m-80) REVERT: A 69 TYR cc_start: 0.8862 (OUTLIER) cc_final: 0.7823 (p90) REVERT: A 172 MET cc_start: 0.8150 (mmm) cc_final: 0.7884 (tpt) REVERT: A 441 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8483 (mm) REVERT: A 495 MET cc_start: 0.8553 (mtp) cc_final: 0.8316 (mtm) REVERT: A 523 SER cc_start: 0.8545 (t) cc_final: 0.8236 (m) REVERT: A 578 TYR cc_start: 0.7765 (t80) cc_final: 0.7463 (t80) outliers start: 18 outliers final: 15 residues processed: 101 average time/residue: 0.0571 time to fit residues: 7.9846 Evaluate side-chains 103 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 92 PHE Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 479 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 45 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.131728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.105627 restraints weight = 6755.501| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.66 r_work: 0.2968 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5757 Z= 0.174 Angle : 0.547 8.495 7886 Z= 0.280 Chirality : 0.041 0.161 900 Planarity : 0.004 0.035 977 Dihedral : 4.633 36.432 812 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.60 % Allowed : 12.50 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.83 (0.31), residues: 746 helix: 1.57 (0.26), residues: 374 sheet: 0.27 (0.57), residues: 82 loop : -0.68 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 324 TYR 0.024 0.002 TYR A 69 PHE 0.015 0.002 PHE A 392 TRP 0.013 0.001 TRP A 470 HIS 0.003 0.001 HIS H 80 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 5754) covalent geometry : angle 0.54589 ( 7880) SS BOND : bond 0.00224 ( 3) SS BOND : angle 1.21708 ( 6) hydrogen bonds : bond 0.03711 ( 328) hydrogen bonds : angle 4.66107 ( 933) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.204 Fit side-chains REVERT: L 48 TRP cc_start: 0.8697 (OUTLIER) cc_final: 0.6758 (m-90) REVERT: L 92 PHE cc_start: 0.8897 (OUTLIER) cc_final: 0.7215 (m-80) REVERT: A 69 TYR cc_start: 0.9003 (OUTLIER) cc_final: 0.8048 (p90) REVERT: A 334 SER cc_start: 0.8143 (OUTLIER) cc_final: 0.7909 (m) REVERT: A 441 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8607 (mm) REVERT: A 495 MET cc_start: 0.8594 (mtp) cc_final: 0.8345 (mtm) REVERT: A 523 SER cc_start: 0.8633 (t) cc_final: 0.8293 (m) outliers start: 25 outliers final: 18 residues processed: 104 average time/residue: 0.0592 time to fit residues: 8.4909 Evaluate side-chains 107 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 48 TRP Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 92 PHE Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 479 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 chunk 32 optimal weight: 0.4980 chunk 46 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 34 optimal weight: 0.0980 chunk 22 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** 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 = 0.3413 r_free = 0.3413 target = 0.133207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.107254 restraints weight = 6627.899| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.65 r_work: 0.2982 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5757 Z= 0.134 Angle : 0.519 9.003 7886 Z= 0.266 Chirality : 0.040 0.142 900 Planarity : 0.004 0.035 977 Dihedral : 4.556 36.292 812 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 4.23 % Allowed : 13.05 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.90 (0.31), residues: 746 helix: 1.66 (0.26), residues: 373 sheet: 0.23 (0.56), residues: 82 loop : -0.66 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 324 TYR 0.022 0.001 TYR A 69 PHE 0.015 0.001 PHE A 350 TRP 0.015 0.001 TRP A 470 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 5754) covalent geometry : angle 0.51846 ( 7880) SS BOND : bond 0.00239 ( 3) SS BOND : angle 1.10929 ( 6) hydrogen bonds : bond 0.03468 ( 328) hydrogen bonds : angle 4.57454 ( 933) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.208 Fit side-chains REVERT: L 48 TRP cc_start: 0.8634 (OUTLIER) cc_final: 0.6814 (m-90) REVERT: L 92 PHE cc_start: 0.8887 (OUTLIER) cc_final: 0.7211 (m-80) REVERT: A 69 TYR cc_start: 0.8943 (OUTLIER) cc_final: 0.7960 (p90) REVERT: A 441 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8572 (mm) REVERT: A 495 MET cc_start: 0.8554 (mtp) cc_final: 0.8316 (mtm) REVERT: A 523 SER cc_start: 0.8591 (t) cc_final: 0.8284 (m) outliers start: 23 outliers final: 17 residues processed: 104 average time/residue: 0.0588 time to fit residues: 8.3856 Evaluate side-chains 106 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 48 TRP Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 92 PHE Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 479 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 58 optimal weight: 0.0370 chunk 61 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 4 optimal weight: 0.0980 chunk 21 optimal weight: 10.0000 chunk 12 optimal weight: 0.0770 chunk 28 optimal weight: 0.8980 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.135561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.110064 restraints weight = 6648.119| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.62 r_work: 0.3027 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5757 Z= 0.108 Angle : 0.498 9.101 7886 Z= 0.253 Chirality : 0.039 0.136 900 Planarity : 0.004 0.035 977 Dihedral : 4.375 35.815 812 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.86 % Allowed : 13.60 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.07 (0.31), residues: 746 helix: 1.83 (0.27), residues: 373 sheet: 0.33 (0.56), residues: 82 loop : -0.63 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 324 TYR 0.019 0.001 TYR A 69 PHE 0.015 0.001 PHE A 350 TRP 0.016 0.001 TRP A 470 HIS 0.001 0.000 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 5754) covalent geometry : angle 0.49770 ( 7880) SS BOND : bond 0.00250 ( 3) SS BOND : angle 1.00955 ( 6) hydrogen bonds : bond 0.03193 ( 328) hydrogen bonds : angle 4.43585 ( 933) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.147 Fit side-chains REVERT: L 48 TRP cc_start: 0.8586 (OUTLIER) cc_final: 0.6834 (m-90) REVERT: L 92 PHE cc_start: 0.8871 (OUTLIER) cc_final: 0.7568 (m-80) REVERT: A 69 TYR cc_start: 0.8909 (OUTLIER) cc_final: 0.7865 (p90) REVERT: A 172 MET cc_start: 0.8132 (mmm) cc_final: 0.7865 (tpt) REVERT: A 441 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8560 (mm) REVERT: A 495 MET cc_start: 0.8544 (mtp) cc_final: 0.8329 (mtm) REVERT: A 523 SER cc_start: 0.8568 (t) cc_final: 0.8292 (m) outliers start: 21 outliers final: 15 residues processed: 99 average time/residue: 0.0534 time to fit residues: 7.2151 Evaluate side-chains 101 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 48 TRP Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 92 PHE Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 479 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 2 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 4 optimal weight: 0.0070 chunk 12 optimal weight: 0.0570 chunk 26 optimal weight: 1.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** 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 = 0.3423 r_free = 0.3423 target = 0.133957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.108145 restraints weight = 6714.623| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.65 r_work: 0.2996 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5757 Z= 0.129 Angle : 0.517 9.595 7886 Z= 0.262 Chirality : 0.040 0.139 900 Planarity : 0.004 0.035 977 Dihedral : 4.025 22.286 809 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 4.23 % Allowed : 13.60 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.01 (0.31), residues: 746 helix: 1.77 (0.27), residues: 373 sheet: 0.33 (0.57), residues: 82 loop : -0.65 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 324 TYR 0.022 0.001 TYR A 69 PHE 0.013 0.001 PHE A 350 TRP 0.014 0.001 TRP A 470 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 5754) covalent geometry : angle 0.51673 ( 7880) SS BOND : bond 0.00232 ( 3) SS BOND : angle 1.12255 ( 6) hydrogen bonds : bond 0.03348 ( 328) hydrogen bonds : angle 4.47430 ( 933) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.206 Fit side-chains REVERT: L 48 TRP cc_start: 0.8622 (OUTLIER) cc_final: 0.6837 (m-90) REVERT: L 92 PHE cc_start: 0.8872 (OUTLIER) cc_final: 0.7432 (m-80) REVERT: A 69 TYR cc_start: 0.8956 (OUTLIER) cc_final: 0.7975 (p90) REVERT: A 172 MET cc_start: 0.8130 (mmm) cc_final: 0.7871 (tpt) REVERT: A 197 GLU cc_start: 0.8581 (pt0) cc_final: 0.8319 (pt0) REVERT: A 441 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8566 (mm) REVERT: A 495 MET cc_start: 0.8538 (mtp) cc_final: 0.8318 (mtm) REVERT: A 523 SER cc_start: 0.8570 (t) cc_final: 0.8268 (m) outliers start: 23 outliers final: 17 residues processed: 102 average time/residue: 0.0510 time to fit residues: 7.3272 Evaluate side-chains 104 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 48 TRP Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 92 PHE Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 479 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 27 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 6 optimal weight: 0.0170 chunk 52 optimal weight: 0.9980 chunk 53 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** 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 = 0.3419 r_free = 0.3419 target = 0.133658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.107828 restraints weight = 6617.881| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.65 r_work: 0.2995 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5757 Z= 0.135 Angle : 0.518 7.679 7886 Z= 0.264 Chirality : 0.040 0.145 900 Planarity : 0.004 0.035 977 Dihedral : 4.071 22.271 809 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.04 % Allowed : 13.42 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.98 (0.31), residues: 746 helix: 1.73 (0.26), residues: 373 sheet: 0.29 (0.57), residues: 82 loop : -0.65 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 324 TYR 0.022 0.001 TYR A 69 PHE 0.013 0.001 PHE A 350 TRP 0.014 0.001 TRP A 470 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 5754) covalent geometry : angle 0.51733 ( 7880) SS BOND : bond 0.00238 ( 3) SS BOND : angle 1.21402 ( 6) hydrogen bonds : bond 0.03405 ( 328) hydrogen bonds : angle 4.49741 ( 933) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1550.01 seconds wall clock time: 27 minutes 10.62 seconds (1630.62 seconds total)