Starting phenix.real_space_refine on Thu Jul 2 02:07:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k0o_61949/07_2026/9k0o_61949.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k0o_61949/07_2026/9k0o_61949.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k0o_61949/07_2026/9k0o_61949.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k0o_61949/07_2026/9k0o_61949.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k0o_61949/07_2026/9k0o_61949.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k0o_61949/07_2026/9k0o_61949.map" } resolution = 2.95 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= 0.093 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 38 5.16 5 Cl 1 4.86 5 C 3658 2.51 5 N 870 2.21 5 O 967 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5534 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 854 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 57 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: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 732 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 4 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: 3939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3939 Classifications: {'peptide': 521} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 27, 'TRANS': 493} Chain breaks: 1 Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 264 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 5, 'ARG:plan': 6, 'TYR:plan': 5, 'ASP:plan': 2, 'GLN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 135 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 8 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'NMG': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Time building chain proxies: 1.28, per 1000 atoms: 0.23 Number of scatterers: 5534 At special positions: 0 Unit cell: (76.112, 81.472, 110.416, 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 38 16.00 O 967 8.00 N 870 7.00 C 3658 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.40 Conformation dependent library (CDL) restraints added in 224.7 milliseconds 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1352 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 6 sheets defined 60.1% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.816A 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: 4.121A 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: 3.754A pdb=" N ALA L 84 " --> pdb=" O ALA L 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 65 through 74 removed outlier: 3.837A pdb=" N TYR A 69 " --> pdb=" O TRP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 90 removed outlier: 3.992A pdb=" N LEU A 80 " --> pdb=" O GLY A 76 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE A 81 " --> pdb=" O GLY A 77 " (cutoff:3.500A) Proline residue: A 82 - end of helix Processing helix chain 'A' and resid 90 through 106 Processing helix chain 'A' and resid 111 through 116 Processing helix chain 'A' and resid 117 through 120 Processing helix chain 'A' and resid 121 through 153 removed outlier: 3.649A pdb=" N TYR A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE A 139 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.933A pdb=" N HIS A 161 " --> pdb=" O PRO A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 178 removed outlier: 4.064A pdb=" N LYS A 178 " --> pdb=" O ASP A 174 " (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 267 removed outlier: 4.167A 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: 3.856A pdb=" N GLY A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 287 removed outlier: 3.546A pdb=" N GLU A 286 " --> pdb=" O THR A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 302 removed outlier: 3.618A pdb=" N PHE A 299 " --> pdb=" O GLY A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 316 removed outlier: 3.921A pdb=" N ASN A 316 " --> pdb=" O LEU A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 356 removed outlier: 3.677A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA A 343 " --> pdb=" O VAL A 339 " (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 379 removed outlier: 3.749A pdb=" N TYR A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) Proline residue: A 375 - end of helix Processing helix chain 'A' and resid 383 through 418 removed outlier: 3.694A pdb=" N TRP A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU A 397 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 417 " --> pdb=" O SER A 413 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 444 removed outlier: 3.940A 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: 3.823A pdb=" N VAL A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 481 removed outlier: 3.567A 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: 3.909A 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: 3.546A 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: 6.761A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.836A 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: 6.084A pdb=" N THR L 70 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 10.452A pdb=" N SER L 27 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 9.940A pdb=" N SER L 68 " --> pdb=" O SER L 27 " (cutoff:3.500A) removed outlier: 12.035A pdb=" N VAL L 29 " --> pdb=" O SER L 66 " (cutoff:3.500A) removed outlier: 12.066A 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: 7.179A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.437A 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: 3.547A pdb=" N GLN L 91 " --> pdb=" O THR L 98 " (cutoff:3.500A) removed outlier: 4.417A 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 532 335 hydrogen bonds defined for protein. 930 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: 0.93 Time building geometry restraints manager: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 839 1.29 - 1.42: 1668 1.42 - 1.55: 3137 1.55 - 1.69: 1 1.69 - 1.82: 54 Bond restraints: 5699 Sorted by residual: bond pdb=" C GLU A 406 " pdb=" O GLU A 406 " ideal model delta sigma weight residual 1.236 1.160 0.076 1.29e-02 6.01e+03 3.48e+01 bond pdb=" CA GLU A 406 " pdb=" CB GLU A 406 " ideal model delta sigma weight residual 1.529 1.444 0.086 1.63e-02 3.76e+03 2.76e+01 bond pdb=" C HIS A 170 " pdb=" O HIS A 170 " ideal model delta sigma weight residual 1.236 1.167 0.069 1.35e-02 5.49e+03 2.60e+01 bond pdb=" CZ NMG A 702 " pdb=" NH1 NMG A 702 " ideal model delta sigma weight residual 1.343 1.251 0.092 2.00e-02 2.50e+03 2.13e+01 bond pdb=" NE NMG A 702 " pdb=" CZ NMG A 702 " ideal model delta sigma weight residual 1.362 1.451 -0.089 2.00e-02 2.50e+03 1.99e+01 ... (remaining 5694 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 7530 2.13 - 4.26: 250 4.26 - 6.40: 23 6.40 - 8.53: 2 8.53 - 10.66: 2 Bond angle restraints: 7807 Sorted by residual: angle pdb=" C HIS A 170 " pdb=" CA HIS A 170 " pdb=" CB HIS A 170 " ideal model delta sigma weight residual 110.11 99.46 10.65 1.90e+00 2.77e-01 3.14e+01 angle pdb=" CG1 VAL H 37 " pdb=" CB VAL H 37 " pdb=" CG2 VAL H 37 " ideal model delta sigma weight residual 110.80 121.46 -10.66 2.20e+00 2.07e-01 2.35e+01 angle pdb=" CA LEU A 396 " pdb=" C LEU A 396 " pdb=" N LEU A 397 " ideal model delta sigma weight residual 117.02 122.01 -4.99 1.17e+00 7.31e-01 1.82e+01 angle pdb=" N GLY A 76 " pdb=" CA GLY A 76 " pdb=" C GLY A 76 " ideal model delta sigma weight residual 111.67 115.57 -3.90 9.20e-01 1.18e+00 1.80e+01 angle pdb=" CA VAL H 37 " pdb=" CB VAL H 37 " pdb=" CG2 VAL H 37 " ideal model delta sigma weight residual 110.40 116.92 -6.52 1.70e+00 3.46e-01 1.47e+01 ... (remaining 7802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 2917 17.44 - 34.88: 208 34.88 - 52.32: 57 52.32 - 69.75: 9 69.75 - 87.19: 5 Dihedral angle restraints: 3196 sinusoidal: 1063 harmonic: 2133 Sorted by residual: dihedral pdb=" CA PHE A 58 " pdb=" C PHE A 58 " pdb=" N VAL A 59 " pdb=" CA VAL A 59 " ideal model delta harmonic sigma weight residual 180.00 151.92 28.08 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" C HIS A 170 " pdb=" N HIS A 170 " pdb=" CA HIS A 170 " pdb=" CB HIS A 170 " ideal model delta harmonic sigma weight residual -122.60 -111.79 -10.81 0 2.50e+00 1.60e-01 1.87e+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 180.00 158.92 21.08 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 3193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.276: 886 0.276 - 0.553: 2 0.553 - 0.829: 0 0.829 - 1.105: 0 1.105 - 1.382: 1 Chirality restraints: 889 Sorted by residual: chirality pdb=" CB VAL H 37 " pdb=" CA VAL H 37 " pdb=" CG1 VAL H 37 " pdb=" CG2 VAL H 37 " both_signs ideal model delta sigma weight residual False -2.63 -1.25 -1.38 2.00e-01 2.50e+01 4.77e+01 chirality pdb=" CA ARG A 66 " pdb=" N ARG A 66 " pdb=" C ARG A 66 " pdb=" CB ARG A 66 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CA PHE A 58 " pdb=" N PHE A 58 " pdb=" C PHE A 58 " pdb=" CB PHE A 58 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.67e+00 ... (remaining 886 not shown) Planarity restraints: 970 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 65 " 0.175 2.00e-02 2.50e+03 9.26e-02 2.14e+02 pdb=" CG TRP A 65 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TRP A 65 " -0.080 2.00e-02 2.50e+03 pdb=" CD2 TRP A 65 " -0.058 2.00e-02 2.50e+03 pdb=" NE1 TRP A 65 " -0.068 2.00e-02 2.50e+03 pdb=" CE2 TRP A 65 " 0.016 2.00e-02 2.50e+03 pdb=" CE3 TRP A 65 " -0.108 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 65 " 0.134 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 65 " -0.067 2.00e-02 2.50e+03 pdb=" CH2 TRP A 65 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 138 " 0.172 2.00e-02 2.50e+03 9.65e-02 1.86e+02 pdb=" CG TYR A 138 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR A 138 " -0.082 2.00e-02 2.50e+03 pdb=" CD2 TYR A 138 " -0.070 2.00e-02 2.50e+03 pdb=" CE1 TYR A 138 " -0.055 2.00e-02 2.50e+03 pdb=" CE2 TYR A 138 " -0.064 2.00e-02 2.50e+03 pdb=" CZ TYR A 138 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR A 138 " 0.156 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 291 " -0.061 2.00e-02 2.50e+03 3.37e-02 2.84e+01 pdb=" CG TRP A 291 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TRP A 291 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP A 291 " 0.021 2.00e-02 2.50e+03 pdb=" NE1 TRP A 291 " 0.029 2.00e-02 2.50e+03 pdb=" CE2 TRP A 291 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 291 " 0.058 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 291 " -0.025 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 291 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 291 " -0.047 2.00e-02 2.50e+03 ... (remaining 967 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 45 2.61 - 3.18: 5036 3.18 - 3.76: 8776 3.76 - 4.33: 12459 4.33 - 4.90: 20930 Nonbonded interactions: 47246 Sorted by model distance: nonbonded pdb=" OG SER H 52 " pdb=" OE2 GLU A 490 " model vdw 2.040 3.040 nonbonded pdb=" NH2 ARG H 56 " pdb=" OD1 ASP A 491 " model vdw 2.101 3.120 nonbonded pdb=" N GLU A 114 " pdb=" OE1 GLU A 114 " model vdw 2.144 3.120 nonbonded pdb=" OG1 THR A 168 " pdb=" OE1 GLU A 197 " model vdw 2.222 3.040 nonbonded pdb=" O SER A 548 " pdb=" OG SER A 552 " model vdw 2.303 3.040 ... (remaining 47241 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: 1.630 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: 6.420 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:6.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 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 : 0.013 0.864 5703 Z= 1.189 Angle : 0.771 10.659 7813 Z= 0.487 Chirality : 0.067 1.382 889 Planarity : 0.007 0.097 970 Dihedral : 13.973 87.193 1835 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.93 % Allowed : 15.08 % Favored : 83.99 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % 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: 0.59 (0.31), residues: 738 helix: 1.06 (0.27), residues: 369 sheet: 0.91 (0.55), residues: 99 loop : -0.66 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG H 104 TYR 0.172 0.004 TYR A 138 PHE 0.052 0.003 PHE A 79 TRP 0.175 0.005 TRP A 65 HIS 0.004 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.32 ( 5699) covalent geometry : angle 0.77119 / 0.49 ( 7807) SS BOND : bond 0.00056 / 0.03 ( 3) SS BOND : angle 0.42105 / 0.24 ( 6) hydrogen bonds : bond 0.21847 / 14.75 ( 332) hydrogen bonds : angle 7.41984 / 5.22 ( 930) Misc. bond : bond 0.86408 / 45.48 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 108 time to evaluate : 0.171 Fit side-chains REVERT: H 59 TYR cc_start: 0.6981 (m-80) cc_final: 0.6690 (m-80) REVERT: A 69 TYR cc_start: 0.8561 (OUTLIER) cc_final: 0.7913 (t80) REVERT: A 284 ARG cc_start: 0.8143 (tpp-160) cc_final: 0.7650 (tpt90) REVERT: A 309 MET cc_start: 0.7340 (mmp) cc_final: 0.6855 (mmp) REVERT: A 459 ASP cc_start: 0.8409 (t0) cc_final: 0.8152 (t0) REVERT: A 494 ASP cc_start: 0.8545 (t0) cc_final: 0.8174 (t70) outliers start: 5 outliers final: 2 residues processed: 113 average time/residue: 0.3588 time to fit residues: 43.1973 Evaluate side-chains 97 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 94 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR 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: 1.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.0970 chunk 62 optimal weight: 0.2980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 GLN A 164 HIS ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.155666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.134827 restraints weight = 6664.172| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 1.78 r_work: 0.3517 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5703 Z= 0.144 Angle : 0.583 10.386 7813 Z= 0.304 Chirality : 0.042 0.217 889 Planarity : 0.004 0.042 970 Dihedral : 5.895 59.625 809 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.47 % Allowed : 13.41 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.17 (0.32), residues: 738 helix: 1.78 (0.27), residues: 369 sheet: 0.83 (0.57), residues: 87 loop : -0.57 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 104 TYR 0.018 0.002 TYR A 137 PHE 0.012 0.002 PHE A 276 TRP 0.013 0.001 TRP H 47 HIS 0.002 0.001 HIS L 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 5699) covalent geometry : angle 0.58225 / 0.30 ( 7807) SS BOND : bond 0.00338 / 0.17 ( 3) SS BOND : angle 1.19445 / 0.66 ( 6) hydrogen bonds : bond 0.04460 / 3.08 ( 332) hydrogen bonds : angle 5.05687 / 3.49 ( 930) Misc. bond : bond 0.00300 / 0.16 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.213 Fit side-chains REVERT: H 59 TYR cc_start: 0.7703 (m-80) cc_final: 0.7424 (m-80) REVERT: L 95 TYR cc_start: 0.5359 (OUTLIER) cc_final: 0.5029 (t80) REVERT: A 69 TYR cc_start: 0.8940 (OUTLIER) cc_final: 0.7768 (t80) REVERT: A 267 LEU cc_start: 0.7181 (OUTLIER) cc_final: 0.6548 (mm) REVERT: A 284 ARG cc_start: 0.8351 (tpp-160) cc_final: 0.7686 (tpt90) REVERT: A 309 MET cc_start: 0.7203 (mmp) cc_final: 0.6791 (mmp) REVERT: A 333 ASN cc_start: 0.7995 (t0) cc_final: 0.7711 (t0) REVERT: A 506 TYR cc_start: 0.8110 (m-80) cc_final: 0.7863 (m-80) outliers start: 24 outliers final: 9 residues processed: 114 average time/residue: 0.3325 time to fit residues: 40.6970 Evaluate side-chains 102 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 95 TYR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 447 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 167 ASN ** 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 = 0.3794 r_free = 0.3794 target = 0.147695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.127027 restraints weight = 6776.445| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.76 r_work: 0.3404 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 5703 Z= 0.223 Angle : 0.652 9.172 7813 Z= 0.336 Chirality : 0.045 0.250 889 Planarity : 0.005 0.044 970 Dihedral : 6.283 58.695 806 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 5.21 % Allowed : 13.41 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.68 (0.31), residues: 738 helix: 1.35 (0.27), residues: 371 sheet: 0.34 (0.56), residues: 88 loop : -0.67 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 98 TYR 0.023 0.002 TYR L 95 PHE 0.015 0.002 PHE A 276 TRP 0.014 0.002 TRP A 113 HIS 0.005 0.002 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.22 ( 5699) covalent geometry : angle 0.64894 / 0.33 ( 7807) SS BOND : bond 0.00253 / 0.13 ( 3) SS BOND : angle 2.34910 / 1.42 ( 6) hydrogen bonds : bond 0.04673 / 3.25 ( 332) hydrogen bonds : angle 4.94106 / 3.38 ( 930) Misc. bond : bond 0.00150 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 0.144 Fit side-chains REVERT: H 59 TYR cc_start: 0.8754 (m-80) cc_final: 0.8402 (m-80) REVERT: L 95 TYR cc_start: 0.5955 (OUTLIER) cc_final: 0.5437 (t80) REVERT: A 66 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.8901 (ttt-90) REVERT: A 114 GLU cc_start: 0.8060 (mp0) cc_final: 0.7731 (mp0) REVERT: A 284 ARG cc_start: 0.8396 (tpp-160) cc_final: 0.7753 (tpt90) REVERT: A 380 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8119 (mtp) REVERT: A 430 ILE cc_start: 0.7011 (mm) cc_final: 0.6799 (mp) REVERT: A 441 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8208 (mm) REVERT: A 506 TYR cc_start: 0.8394 (m-80) cc_final: 0.8157 (m-80) REVERT: A 521 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8292 (mm) outliers start: 28 outliers final: 15 residues processed: 116 average time/residue: 0.3228 time to fit residues: 40.2140 Evaluate side-chains 103 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 95 TYR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 548 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 24 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.149422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.128585 restraints weight = 6657.612| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.77 r_work: 0.3434 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5703 Z= 0.145 Angle : 0.562 7.467 7813 Z= 0.290 Chirality : 0.042 0.208 889 Planarity : 0.004 0.038 970 Dihedral : 5.789 58.321 806 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.28 % Allowed : 16.57 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.79 (0.31), residues: 738 helix: 1.47 (0.27), residues: 372 sheet: 0.25 (0.56), residues: 88 loop : -0.63 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 98 TYR 0.019 0.002 TYR A 69 PHE 0.012 0.001 PHE A 276 TRP 0.016 0.001 TRP A 470 HIS 0.003 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.14 ( 5699) covalent geometry : angle 0.55983 / 0.29 ( 7807) SS BOND : bond 0.00295 / 0.15 ( 3) SS BOND : angle 1.78560 / 1.06 ( 6) hydrogen bonds : bond 0.03925 / 2.72 ( 332) hydrogen bonds : angle 4.75327 / 3.25 ( 930) Misc. bond : bond 0.00103 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 0.202 Fit side-chains REVERT: H 59 TYR cc_start: 0.8717 (m-80) cc_final: 0.8184 (m-80) REVERT: L 95 TYR cc_start: 0.5689 (OUTLIER) cc_final: 0.5414 (t80) REVERT: A 114 GLU cc_start: 0.7966 (mp0) cc_final: 0.7644 (mp0) REVERT: A 284 ARG cc_start: 0.8397 (tpp-160) cc_final: 0.7763 (tpt90) REVERT: A 441 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8201 (mm) outliers start: 23 outliers final: 13 residues processed: 105 average time/residue: 0.2871 time to fit residues: 32.4690 Evaluate side-chains 99 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 95 TYR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 566 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 39 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.149845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.129180 restraints weight = 6795.608| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.76 r_work: 0.3439 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5703 Z= 0.158 Angle : 0.570 7.854 7813 Z= 0.293 Chirality : 0.042 0.223 889 Planarity : 0.004 0.045 970 Dihedral : 5.719 58.356 806 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 5.59 % Allowed : 15.83 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.75 (0.31), residues: 738 helix: 1.49 (0.27), residues: 371 sheet: 0.13 (0.56), residues: 88 loop : -0.69 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 66 TYR 0.020 0.002 TYR A 69 PHE 0.012 0.002 PHE A 276 TRP 0.015 0.001 TRP A 113 HIS 0.003 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 ( 5699) covalent geometry : angle 0.56787 / 0.29 ( 7807) SS BOND : bond 0.00338 / 0.17 ( 3) SS BOND : angle 1.90149 / 1.14 ( 6) hydrogen bonds : bond 0.03937 / 2.73 ( 332) hydrogen bonds : angle 4.71479 / 3.22 ( 930) Misc. bond : bond 0.00116 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 90 time to evaluate : 0.223 Fit side-chains REVERT: H 59 TYR cc_start: 0.8812 (m-80) cc_final: 0.8111 (m-80) REVERT: L 95 TYR cc_start: 0.5862 (OUTLIER) cc_final: 0.5571 (t80) REVERT: A 114 GLU cc_start: 0.7875 (mp0) cc_final: 0.7526 (mp0) REVERT: A 284 ARG cc_start: 0.8376 (tpp-160) cc_final: 0.7735 (tpt90) REVERT: A 441 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8162 (mm) outliers start: 30 outliers final: 18 residues processed: 111 average time/residue: 0.2932 time to fit residues: 35.1699 Evaluate side-chains 106 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 95 TYR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 131 VAL 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 258 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 566 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 18 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 53 optimal weight: 0.0570 chunk 4 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 overall best weight: 0.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.149588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.129059 restraints weight = 6793.595| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.75 r_work: 0.3433 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5703 Z= 0.154 Angle : 0.565 7.658 7813 Z= 0.289 Chirality : 0.042 0.218 889 Planarity : 0.004 0.045 970 Dihedral : 5.672 58.319 806 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 5.03 % Allowed : 16.76 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.75 (0.31), residues: 738 helix: 1.53 (0.26), residues: 371 sheet: 0.08 (0.57), residues: 88 loop : -0.73 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 66 TYR 0.020 0.002 TYR A 69 PHE 0.012 0.002 PHE A 276 TRP 0.015 0.001 TRP A 470 HIS 0.003 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.15 ( 5699) covalent geometry : angle 0.56236 / 0.29 ( 7807) SS BOND : bond 0.00325 / 0.16 ( 3) SS BOND : angle 1.86168 / 1.11 ( 6) hydrogen bonds : bond 0.03825 / 2.67 ( 332) hydrogen bonds : angle 4.68929 / 3.20 ( 930) Misc. bond : bond 0.00118 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 0.207 Fit side-chains REVERT: H 59 TYR cc_start: 0.8838 (m-80) cc_final: 0.8173 (m-80) REVERT: L 95 TYR cc_start: 0.5864 (OUTLIER) cc_final: 0.5630 (t80) REVERT: A 114 GLU cc_start: 0.7875 (mp0) cc_final: 0.7566 (mp0) REVERT: A 284 ARG cc_start: 0.8373 (tpp-160) cc_final: 0.7725 (tpt90) REVERT: A 394 MET cc_start: 0.8312 (tmm) cc_final: 0.8096 (ttt) REVERT: A 441 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8034 (mm) outliers start: 27 outliers final: 17 residues processed: 108 average time/residue: 0.3216 time to fit residues: 37.2258 Evaluate side-chains 101 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 95 TYR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 131 VAL 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 245 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 566 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 44 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.148998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.128451 restraints weight = 6851.403| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.76 r_work: 0.3425 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5703 Z= 0.164 Angle : 0.589 8.315 7813 Z= 0.299 Chirality : 0.042 0.227 889 Planarity : 0.004 0.048 970 Dihedral : 5.358 58.231 804 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 5.21 % Allowed : 16.95 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.73 (0.31), residues: 738 helix: 1.56 (0.27), residues: 369 sheet: -0.03 (0.56), residues: 88 loop : -0.76 (0.38), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 66 TYR 0.020 0.002 TYR A 69 PHE 0.012 0.002 PHE A 392 TRP 0.014 0.001 TRP A 470 HIS 0.003 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.16 ( 5699) covalent geometry : angle 0.58672 / 0.30 ( 7807) SS BOND : bond 0.00295 / 0.15 ( 3) SS BOND : angle 1.90010 / 1.13 ( 6) hydrogen bonds : bond 0.03896 / 2.72 ( 332) hydrogen bonds : angle 4.71008 / 3.21 ( 930) Misc. bond : bond 0.00124 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 81 time to evaluate : 0.217 Fit side-chains REVERT: H 59 TYR cc_start: 0.8827 (m-80) cc_final: 0.8170 (m-80) REVERT: L 95 TYR cc_start: 0.5885 (OUTLIER) cc_final: 0.5516 (t80) REVERT: A 114 GLU cc_start: 0.7900 (mp0) cc_final: 0.7496 (mp0) REVERT: A 284 ARG cc_start: 0.8391 (tpp-160) cc_final: 0.7765 (tpt90) REVERT: A 292 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8374 (mp) REVERT: A 394 MET cc_start: 0.8428 (tmm) cc_final: 0.8206 (ttt) REVERT: A 441 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8130 (mm) outliers start: 28 outliers final: 19 residues processed: 102 average time/residue: 0.2544 time to fit residues: 28.0154 Evaluate side-chains 104 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.194 ------------------------------------------------------------------------------- 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 114 THR Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 95 TYR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 131 VAL 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 245 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 566 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 52 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.146411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.126149 restraints weight = 6778.777| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.71 r_work: 0.3396 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 5703 Z= 0.225 Angle : 0.658 11.644 7813 Z= 0.328 Chirality : 0.045 0.245 889 Planarity : 0.005 0.049 970 Dihedral : 5.709 57.297 804 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 5.59 % Allowed : 16.39 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.47 (0.31), residues: 738 helix: 1.35 (0.26), residues: 370 sheet: -0.13 (0.56), residues: 88 loop : -0.90 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 102 TYR 0.022 0.002 TYR A 69 PHE 0.015 0.002 PHE A 392 TRP 0.012 0.002 TRP A 113 HIS 0.004 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.22 ( 5699) covalent geometry : angle 0.65548 / 0.33 ( 7807) SS BOND : bond 0.00295 / 0.15 ( 3) SS BOND : angle 2.28070 / 1.36 ( 6) hydrogen bonds : bond 0.04329 / 3.02 ( 332) hydrogen bonds : angle 4.88281 / 3.32 ( 930) Misc. bond : bond 0.00150 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 81 time to evaluate : 0.143 Fit side-chains REVERT: H 59 TYR cc_start: 0.8899 (m-80) cc_final: 0.8110 (m-80) REVERT: L 95 TYR cc_start: 0.6125 (OUTLIER) cc_final: 0.5649 (t80) REVERT: A 114 GLU cc_start: 0.8001 (mp0) cc_final: 0.7609 (mp0) REVERT: A 284 ARG cc_start: 0.8400 (tpp-160) cc_final: 0.7778 (tpt90) REVERT: A 292 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8369 (mp) REVERT: A 441 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8131 (mm) outliers start: 30 outliers final: 24 residues processed: 103 average time/residue: 0.2671 time to fit residues: 29.6422 Evaluate side-chains 108 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 81 time to evaluate : 0.203 ------------------------------------------------------------------------------- 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 114 THR Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 95 TYR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 131 VAL 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 245 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 566 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 34 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 39 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 61 optimal weight: 0.2980 chunk 36 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.149945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.129718 restraints weight = 6744.605| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.73 r_work: 0.3439 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5703 Z= 0.132 Angle : 0.589 10.505 7813 Z= 0.292 Chirality : 0.041 0.199 889 Planarity : 0.004 0.046 970 Dihedral : 5.246 57.872 804 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.66 % Allowed : 18.06 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.73 (0.31), residues: 738 helix: 1.60 (0.27), residues: 369 sheet: -0.10 (0.56), residues: 88 loop : -0.79 (0.38), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 102 TYR 0.018 0.001 TYR A 69 PHE 0.011 0.001 PHE A 338 TRP 0.018 0.001 TRP A 470 HIS 0.004 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 5699) covalent geometry : angle 0.58745 / 0.29 ( 7807) SS BOND : bond 0.00301 / 0.15 ( 3) SS BOND : angle 1.76635 / 1.03 ( 6) hydrogen bonds : bond 0.03655 / 2.55 ( 332) hydrogen bonds : angle 4.70467 / 3.21 ( 930) Misc. bond : bond 0.00128 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 0.140 Fit side-chains REVERT: H 59 TYR cc_start: 0.8788 (m-80) cc_final: 0.8100 (m-80) REVERT: L 95 TYR cc_start: 0.5722 (OUTLIER) cc_final: 0.5409 (t80) REVERT: A 114 GLU cc_start: 0.7958 (mp0) cc_final: 0.7531 (mp0) REVERT: A 207 SER cc_start: 0.8529 (OUTLIER) cc_final: 0.8300 (m) REVERT: A 284 ARG cc_start: 0.8376 (tpp-160) cc_final: 0.7754 (tpt90) REVERT: A 292 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8273 (mp) REVERT: A 441 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8114 (mm) outliers start: 25 outliers final: 17 residues processed: 105 average time/residue: 0.2789 time to fit residues: 31.4426 Evaluate side-chains 101 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.189 ------------------------------------------------------------------------------- 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 114 THR Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 95 TYR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 131 VAL 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 245 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 566 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 37 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 20 optimal weight: 0.0670 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.149771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.129314 restraints weight = 6775.446| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.76 r_work: 0.3437 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5703 Z= 0.141 Angle : 0.589 10.327 7813 Z= 0.294 Chirality : 0.042 0.214 889 Planarity : 0.004 0.047 970 Dihedral : 5.241 58.361 804 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 4.47 % Allowed : 18.62 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.72 (0.31), residues: 738 helix: 1.60 (0.27), residues: 369 sheet: -0.17 (0.56), residues: 88 loop : -0.80 (0.38), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 102 TYR 0.018 0.001 TYR A 69 PHE 0.017 0.002 PHE A 150 TRP 0.016 0.001 TRP A 470 HIS 0.004 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 ( 5699) covalent geometry : angle 0.58694 / 0.29 ( 7807) SS BOND : bond 0.00286 / 0.14 ( 3) SS BOND : angle 1.74463 / 1.02 ( 6) hydrogen bonds : bond 0.03706 / 2.59 ( 332) hydrogen bonds : angle 4.69073 / 3.20 ( 930) Misc. bond : bond 0.00122 / 0.06 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.240 Fit side-chains REVERT: H 59 TYR cc_start: 0.8795 (m-80) cc_final: 0.8118 (m-80) REVERT: L 95 TYR cc_start: 0.5790 (OUTLIER) cc_final: 0.5503 (t80) REVERT: A 114 GLU cc_start: 0.7988 (mp0) cc_final: 0.7565 (mp0) REVERT: A 207 SER cc_start: 0.8558 (OUTLIER) cc_final: 0.8342 (m) REVERT: A 284 ARG cc_start: 0.8383 (tpp-160) cc_final: 0.7766 (tpt90) REVERT: A 292 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.8289 (mp) REVERT: A 441 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8103 (mm) outliers start: 24 outliers final: 19 residues processed: 102 average time/residue: 0.3264 time to fit residues: 35.8367 Evaluate side-chains 109 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.208 ------------------------------------------------------------------------------- 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 114 THR Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 95 TYR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 131 VAL 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 245 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 566 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 9 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 19 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.148910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.128605 restraints weight = 6815.149| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.76 r_work: 0.3428 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5703 Z= 0.159 Angle : 0.610 10.205 7813 Z= 0.302 Chirality : 0.043 0.226 889 Planarity : 0.004 0.048 970 Dihedral : 5.334 58.608 804 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.66 % Allowed : 18.62 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.65 (0.31), residues: 738 helix: 1.54 (0.27), residues: 369 sheet: -0.18 (0.57), residues: 88 loop : -0.83 (0.38), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 102 TYR 0.020 0.002 TYR A 69 PHE 0.012 0.002 PHE A 392 TRP 0.015 0.001 TRP A 470 HIS 0.004 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 ( 5699) covalent geometry : angle 0.60845 / 0.30 ( 7807) SS BOND : bond 0.00290 / 0.15 ( 3) SS BOND : angle 1.86680 / 1.10 ( 6) hydrogen bonds : bond 0.03806 / 2.65 ( 332) hydrogen bonds : angle 4.71896 / 3.22 ( 930) Misc. bond : bond 0.00130 / 0.07 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1586.80 seconds wall clock time: 27 minutes 49.22 seconds (1669.22 seconds total)