Starting phenix.real_space_refine on Thu Jul 2 02:14:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k1i_61976/07_2026/9k1i_61976.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k1i_61976/07_2026/9k1i_61976.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k1i_61976/07_2026/9k1i_61976.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k1i_61976/07_2026/9k1i_61976.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k1i_61976/07_2026/9k1i_61976.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k1i_61976/07_2026/9k1i_61976.map" } resolution = 2.92 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= 0.105 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 3710 2.51 5 N 881 2.21 5 O 976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s 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: 5607 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4007 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 27, 'TRANS': 501} Chain breaks: 1 Unresolved non-hydrogen bonds: 209 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 177 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 7, 'ASN:plan1': 4, 'ARG:plan': 6, 'TYR:plan': 3, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 128 Chain: "H" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 859 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 3, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 45 Chain: "L" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 730 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 53 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: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 10 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'IZC': 1} Classifications: {'undetermined': 1, 'water': 1} Chain breaks: 1 Time building chain proxies: 1.37, per 1000 atoms: 0.24 Number of scatterers: 5607 At special positions: 0 Unit cell: (83.616, 80.4, 107.2, 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 976 8.00 N 881 7.00 C 3710 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 171 " distance=2.03 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 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: 0.47 Conformation dependent library (CDL) restraints added in 218.5 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: 35 helices and 6 sheets defined 59.9% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 47 through 53 Processing helix chain 'A' and resid 54 through 59 Processing helix chain 'A' and resid 60 through 74 removed outlier: 3.785A pdb=" N VAL A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE A 67 " --> pdb=" O ASN A 63 " (cutoff:3.500A) Proline residue: A 68 - end of helix Processing helix chain 'A' and resid 76 through 90 removed outlier: 4.095A pdb=" N LEU A 80 " --> pdb=" O GLY A 76 " (cutoff:3.500A) removed outlier: 4.199A 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 107 through 112 removed outlier: 3.684A pdb=" N THR A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N CYS A 112 " --> pdb=" O GLY A 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 107 through 112' Processing helix chain 'A' and resid 113 through 116 Processing helix chain 'A' and resid 117 through 120 Processing helix chain 'A' and resid 121 through 152 removed outlier: 3.845A pdb=" N TYR A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE A 139 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ILE A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 178 removed outlier: 4.535A 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: 4.457A pdb=" N PHE A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) Proline residue: A 253 - end of helix removed outlier: 3.557A pdb=" N LEU A 267 " --> pdb=" O ARG A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 279 Processing helix chain 'A' and resid 287 through 302 removed outlier: 3.786A pdb=" N TRP A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A 298 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE A 299 " --> pdb=" O GLY A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 315 removed outlier: 3.742A pdb=" N TYR A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 356 removed outlier: 3.752A pdb=" N ASP A 325 " --> pdb=" O ASN A 321 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 removed outlier: 3.524A pdb=" N VAL A 362 " --> pdb=" O ILE A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 380 Proline residue: A 375 - end of helix Processing helix chain 'A' and resid 383 through 416 removed outlier: 3.726A pdb=" N TRP A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 423 Processing helix chain 'A' and resid 426 through 444 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: 3.856A pdb=" N VAL A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 482 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: 3.837A pdb=" N SER A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 568 Processing helix chain 'A' and resid 571 through 581 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.783A 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 Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 532 Processing sheet with id=AA2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.877A pdb=" N MET H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 11 removed outlier: 7.198A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N TRP L 36 " --> pdb=" O TRP L 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 11 removed outlier: 4.240A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) 347 hydrogen bonds defined for protein. 978 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: 0.90 Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 849 1.31 - 1.44: 1752 1.44 - 1.57: 3118 1.57 - 1.69: 0 1.69 - 1.82: 56 Bond restraints: 5775 Sorted by residual: bond pdb=" C2 IZC A 701 " pdb=" N1 IZC A 701 " ideal model delta sigma weight residual 1.441 1.312 0.129 2.00e-02 2.50e+03 4.18e+01 bond pdb=" C2 IZC A 701 " pdb=" N3 IZC A 701 " ideal model delta sigma weight residual 1.437 1.308 0.129 2.00e-02 2.50e+03 4.16e+01 bond pdb=" C4 IZC A 701 " pdb=" C5 IZC A 701 " ideal model delta sigma weight residual 1.482 1.379 0.103 2.00e-02 2.50e+03 2.68e+01 bond pdb=" CA LYS H 19 " pdb=" C LYS H 19 " ideal model delta sigma weight residual 1.522 1.464 0.059 1.18e-02 7.18e+03 2.47e+01 bond pdb=" C GLU A 354 " pdb=" O GLU A 354 " ideal model delta sigma weight residual 1.237 1.184 0.053 1.16e-02 7.43e+03 2.05e+01 ... (remaining 5770 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 7665 2.32 - 4.63: 221 4.63 - 6.95: 18 6.95 - 9.27: 3 9.27 - 11.59: 1 Bond angle restraints: 7908 Sorted by residual: angle pdb=" C LYS H 19 " pdb=" CA LYS H 19 " pdb=" CB LYS H 19 " ideal model delta sigma weight residual 110.62 103.00 7.62 1.51e+00 4.39e-01 2.55e+01 angle pdb=" C4 IZC A 701 " pdb=" C6 IZC A 701 " pdb=" C7 IZC A 701 " ideal model delta sigma weight residual 121.54 109.95 11.59 3.00e+00 1.11e-01 1.49e+01 angle pdb=" CA PHE A 299 " pdb=" CB PHE A 299 " pdb=" CG PHE A 299 " ideal model delta sigma weight residual 113.80 117.64 -3.84 1.00e+00 1.00e+00 1.47e+01 angle pdb=" C LEU A 92 " pdb=" N PRO A 93 " pdb=" CA PRO A 93 " ideal model delta sigma weight residual 119.05 123.19 -4.14 1.11e+00 8.12e-01 1.39e+01 angle pdb=" N VAL H 64 " pdb=" CA VAL H 64 " pdb=" C VAL H 64 " ideal model delta sigma weight residual 113.20 109.69 3.51 9.60e-01 1.09e+00 1.34e+01 ... (remaining 7903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.86: 2980 16.86 - 33.72: 190 33.72 - 50.59: 56 50.59 - 67.45: 13 67.45 - 84.31: 4 Dihedral angle restraints: 3243 sinusoidal: 1084 harmonic: 2159 Sorted by residual: dihedral pdb=" CA VAL H 2 " pdb=" C VAL H 2 " pdb=" N GLN H 3 " pdb=" CA GLN H 3 " ideal model delta harmonic sigma weight residual -180.00 -157.26 -22.74 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA TYR A 461 " pdb=" C TYR A 461 " pdb=" N ALA A 462 " pdb=" CA ALA A 462 " ideal model delta harmonic sigma weight residual 180.00 -163.20 -16.80 0 5.00e+00 4.00e-02 1.13e+01 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 -163.33 -16.67 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 3240 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 724 0.055 - 0.111: 149 0.111 - 0.166: 18 0.166 - 0.221: 2 0.221 - 0.276: 4 Chirality restraints: 897 Sorted by residual: chirality pdb=" CA PRO A 93 " pdb=" N PRO A 93 " pdb=" C PRO A 93 " pdb=" CB PRO A 93 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA PHE A 345 " pdb=" N PHE A 345 " pdb=" C PHE A 345 " pdb=" CB PHE A 345 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 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 2.48 0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 894 not shown) Planarity restraints: 980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 291 " -0.085 2.00e-02 2.50e+03 4.66e-02 5.43e+01 pdb=" CG TRP A 291 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 TRP A 291 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP A 291 " 0.029 2.00e-02 2.50e+03 pdb=" NE1 TRP A 291 " 0.035 2.00e-02 2.50e+03 pdb=" CE2 TRP A 291 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 291 " 0.074 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 291 " -0.050 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 291 " 0.022 2.00e-02 2.50e+03 pdb=" CH2 TRP A 291 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 302 " 0.049 2.00e-02 2.50e+03 2.90e-02 1.68e+01 pdb=" CG TYR A 302 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR A 302 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 302 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR A 302 " -0.027 2.00e-02 2.50e+03 pdb=" CE2 TYR A 302 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR A 302 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 302 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 79 " 0.046 2.00e-02 2.50e+03 2.92e-02 1.49e+01 pdb=" CG PHE A 79 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE A 79 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 PHE A 79 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE A 79 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE A 79 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 79 " 0.031 2.00e-02 2.50e+03 ... (remaining 977 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 838 2.76 - 3.30: 5594 3.30 - 3.83: 9525 3.83 - 4.37: 11593 4.37 - 4.90: 20137 Nonbonded interactions: 47687 Sorted by model distance: nonbonded pdb=" O SER L 31 " pdb=" OG1 THR L 52 " model vdw 2.226 3.040 nonbonded pdb=" ND2 ASN A 63 " pdb=" OG SER A 337 " model vdw 2.233 3.120 nonbonded pdb=" OD1 ASP A 491 " pdb=" OH TYR H 57 " model vdw 2.252 3.040 nonbonded pdb=" O SER A 311 " pdb=" OG SER A 314 " model vdw 2.262 3.040 nonbonded pdb=" N GLU H 1 " pdb=" O GLY H 26 " model vdw 2.326 3.120 ... (remaining 47682 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: 1.070 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: 0.010 Process input model: 7.220 Find NCS groups from input model: 0.040 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:8.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 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 : 0.006 0.129 5778 Z= 0.319 Angle : 0.834 11.586 7914 Z= 0.515 Chirality : 0.048 0.276 897 Planarity : 0.008 0.118 980 Dihedral : 13.419 84.309 1866 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.29 % Allowed : 11.40 % Favored : 87.32 % 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: 0.28 (0.30), residues: 746 helix: 0.47 (0.25), residues: 376 sheet: 0.50 (0.54), residues: 96 loop : -0.12 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 66 TYR 0.049 0.003 TYR A 302 PHE 0.046 0.005 PHE A 299 TRP 0.085 0.004 TRP A 291 HIS 0.003 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.32 ( 5775) covalent geometry : angle 0.83388 / 0.52 ( 7908) SS BOND : bond 0.00144 / 0.07 ( 3) SS BOND : angle 1.06436 / 0.58 ( 6) hydrogen bonds : bond 0.14589 / 9.64 ( 344) hydrogen bonds : angle 6.45837 / 4.68 ( 978) *********************** 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 111 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 0.210 Fit side-chains REVERT: A 103 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7604 (mt0) REVERT: A 275 LYS cc_start: 0.7806 (ttpt) cc_final: 0.7402 (mtmt) REVERT: A 494 ASP cc_start: 0.8621 (t70) cc_final: 0.8273 (t70) REVERT: H 34 MET cc_start: 0.9052 (mmm) cc_final: 0.8810 (mmm) REVERT: H 95 TYR cc_start: 0.8543 (m-80) cc_final: 0.8224 (m-80) outliers start: 7 outliers final: 2 residues processed: 110 average time/residue: 0.4794 time to fit residues: 55.4753 Evaluate side-chains 84 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain L residue 40 LYS 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: 6.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 167 ASN A 333 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.153775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.131596 restraints weight = 6674.204| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.66 r_work: 0.3422 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5778 Z= 0.137 Angle : 0.576 6.163 7914 Z= 0.302 Chirality : 0.042 0.147 897 Planarity : 0.005 0.039 980 Dihedral : 6.114 59.955 825 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.68 % Allowed : 10.85 % Favored : 85.48 % 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: 0.93 (0.31), residues: 746 helix: 1.19 (0.25), residues: 381 sheet: 0.39 (0.56), residues: 95 loop : 0.05 (0.40), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 564 TYR 0.019 0.001 TYR A 69 PHE 0.019 0.002 PHE A 232 TRP 0.020 0.002 TRP A 470 HIS 0.004 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 5775) covalent geometry : angle 0.57518 / 0.30 ( 7908) SS BOND : bond 0.00464 / 0.23 ( 3) SS BOND : angle 1.45903 / 0.73 ( 6) hydrogen bonds : bond 0.04147 / 2.70 ( 344) hydrogen bonds : angle 5.02483 / 3.66 ( 978) *********************** 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 112 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.203 Fit side-chains REVERT: A 275 LYS cc_start: 0.7940 (ttpt) cc_final: 0.7660 (ttmm) REVERT: A 494 ASP cc_start: 0.8657 (t70) cc_final: 0.8352 (t70) REVERT: H 34 MET cc_start: 0.9190 (mmm) cc_final: 0.8974 (mmm) outliers start: 20 outliers final: 15 residues processed: 104 average time/residue: 0.4451 time to fit residues: 48.9592 Evaluate side-chains 94 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 103 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 39 optimal weight: 0.1980 chunk 41 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 167 ASN A 567 GLN H 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.154127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.132019 restraints weight = 6604.942| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.64 r_work: 0.3425 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5778 Z= 0.124 Angle : 0.530 5.571 7914 Z= 0.278 Chirality : 0.040 0.142 897 Planarity : 0.005 0.041 980 Dihedral : 4.954 52.042 818 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.78 % Allowed : 10.85 % Favored : 84.38 % 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: 1.22 (0.31), residues: 746 helix: 1.60 (0.26), residues: 375 sheet: 0.28 (0.56), residues: 95 loop : 0.02 (0.40), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 564 TYR 0.019 0.001 TYR A 69 PHE 0.015 0.002 PHE A 474 TRP 0.016 0.001 TRP A 470 HIS 0.005 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 ( 5775) covalent geometry : angle 0.52890 / 0.28 ( 7908) SS BOND : bond 0.00368 / 0.18 ( 3) SS BOND : angle 1.25813 / 0.65 ( 6) hydrogen bonds : bond 0.03746 / 2.46 ( 344) hydrogen bonds : angle 4.72816 / 3.46 ( 978) *********************** 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 116 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.208 Fit side-chains REVERT: A 219 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.7846 (p0) REVERT: A 258 LEU cc_start: 0.8310 (tp) cc_final: 0.8032 (tp) REVERT: A 275 LYS cc_start: 0.8021 (ttpt) cc_final: 0.7690 (ttmm) REVERT: H 34 MET cc_start: 0.9165 (mmm) cc_final: 0.8878 (mmm) REVERT: L 44 SER cc_start: 0.8918 (p) cc_final: 0.8546 (m) outliers start: 26 outliers final: 15 residues processed: 103 average time/residue: 0.4424 time to fit residues: 48.2491 Evaluate side-chains 102 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 103 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 53 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 2 optimal weight: 0.4980 chunk 22 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 167 ASN A 567 GLN H 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.152863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.130900 restraints weight = 6564.828| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.62 r_work: 0.3408 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5778 Z= 0.135 Angle : 0.536 5.803 7914 Z= 0.279 Chirality : 0.040 0.138 897 Planarity : 0.004 0.042 980 Dihedral : 4.870 52.080 818 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 4.04 % Allowed : 12.68 % Favored : 83.27 % 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: 1.28 (0.31), residues: 746 helix: 1.74 (0.26), residues: 375 sheet: 0.25 (0.55), residues: 95 loop : -0.08 (0.40), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 583 TYR 0.019 0.001 TYR A 69 PHE 0.014 0.002 PHE A 474 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 0.00322 / 0.14 ( 5775) covalent geometry : angle 0.53467 / 0.28 ( 7908) SS BOND : bond 0.00357 / 0.18 ( 3) SS BOND : angle 1.24856 / 0.63 ( 6) hydrogen bonds : bond 0.03749 / 2.47 ( 344) hydrogen bonds : angle 4.71804 / 3.46 ( 978) *********************** 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 111 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.213 Fit side-chains REVERT: A 219 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.7862 (p0) REVERT: A 258 LEU cc_start: 0.8327 (tp) cc_final: 0.8057 (tp) REVERT: A 344 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.8015 (mm) REVERT: H 34 MET cc_start: 0.9201 (mmm) cc_final: 0.8938 (mmm) REVERT: L 44 SER cc_start: 0.8928 (p) cc_final: 0.8580 (m) outliers start: 22 outliers final: 17 residues processed: 102 average time/residue: 0.3882 time to fit residues: 41.9143 Evaluate side-chains 104 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 103 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 14 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 64 optimal weight: 0.0980 chunk 62 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 167 ASN A 567 GLN H 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.153838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.131691 restraints weight = 6689.865| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.63 r_work: 0.3426 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5778 Z= 0.123 Angle : 0.519 5.583 7914 Z= 0.269 Chirality : 0.040 0.136 897 Planarity : 0.004 0.043 980 Dihedral : 4.733 52.014 818 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.78 % Allowed : 13.05 % 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: 1.38 (0.32), residues: 746 helix: 1.86 (0.26), residues: 376 sheet: 0.31 (0.55), residues: 95 loop : -0.11 (0.40), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 564 TYR 0.018 0.001 TYR A 69 PHE 0.013 0.001 PHE A 474 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 0.00287 / 0.12 ( 5775) covalent geometry : angle 0.51829 / 0.27 ( 7908) SS BOND : bond 0.00322 / 0.16 ( 3) SS BOND : angle 1.21345 / 0.62 ( 6) hydrogen bonds : bond 0.03567 / 2.35 ( 344) hydrogen bonds : angle 4.63327 / 3.40 ( 978) *********************** 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 118 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.146 Fit side-chains REVERT: A 219 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.7818 (p0) REVERT: A 258 LEU cc_start: 0.8294 (tp) cc_final: 0.8020 (tp) REVERT: A 344 ILE cc_start: 0.8197 (OUTLIER) cc_final: 0.7977 (mm) REVERT: H 34 MET cc_start: 0.9185 (mmm) cc_final: 0.8979 (mmm) REVERT: L 44 SER cc_start: 0.8981 (p) cc_final: 0.8689 (m) outliers start: 26 outliers final: 17 residues processed: 108 average time/residue: 0.3833 time to fit residues: 44.0268 Evaluate side-chains 104 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 103 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 45 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 52 optimal weight: 0.2980 chunk 5 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 7 optimal weight: 0.3980 chunk 40 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 17 optimal weight: 0.3980 chunk 6 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 GLN A 167 ASN A 316 ASN A 567 GLN H 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.154674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.132596 restraints weight = 6627.221| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.63 r_work: 0.3435 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5778 Z= 0.111 Angle : 0.505 5.549 7914 Z= 0.260 Chirality : 0.039 0.135 897 Planarity : 0.004 0.042 980 Dihedral : 4.612 51.991 818 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.86 % Allowed : 14.15 % Favored : 81.99 % 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: 1.96 (0.26), residues: 377 sheet: 0.26 (0.56), residues: 95 loop : -0.16 (0.40), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 564 TYR 0.017 0.001 TYR A 69 PHE 0.013 0.001 PHE A 404 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 0.00255 / 0.11 ( 5775) covalent geometry : angle 0.50477 / 0.26 ( 7908) SS BOND : bond 0.00334 / 0.17 ( 3) SS BOND : angle 1.10396 / 0.56 ( 6) hydrogen bonds : bond 0.03400 / 2.24 ( 344) hydrogen bonds : angle 4.54761 / 3.34 ( 978) *********************** 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 115 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.184 Fit side-chains REVERT: A 258 LEU cc_start: 0.8215 (tp) cc_final: 0.7939 (tp) REVERT: A 344 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7936 (mm) REVERT: H 34 MET cc_start: 0.9181 (mmm) cc_final: 0.8817 (mmm) REVERT: L 44 SER cc_start: 0.8974 (p) cc_final: 0.8708 (m) outliers start: 21 outliers final: 17 residues processed: 105 average time/residue: 0.3529 time to fit residues: 39.2897 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 : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 103 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 36 optimal weight: 0.0010 chunk 19 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 0.3980 chunk 47 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 65 optimal weight: 0.0770 chunk 63 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 overall best weight: 0.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 167 ASN A 567 GLN H 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.156066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.133968 restraints weight = 6693.865| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.65 r_work: 0.3449 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5778 Z= 0.101 Angle : 0.497 5.686 7914 Z= 0.255 Chirality : 0.039 0.136 897 Planarity : 0.004 0.041 980 Dihedral : 4.515 51.979 818 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.86 % Allowed : 14.71 % Favored : 81.43 % 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: 1.49 (0.32), residues: 746 helix: 2.07 (0.26), residues: 378 sheet: 0.27 (0.57), residues: 93 loop : -0.23 (0.39), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 564 TYR 0.016 0.001 TYR A 69 PHE 0.013 0.001 PHE A 404 TRP 0.015 0.001 TRP A 470 HIS 0.003 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 ( 5775) covalent geometry : angle 0.49652 / 0.25 ( 7908) SS BOND : bond 0.00357 / 0.18 ( 3) SS BOND : angle 0.91753 / 0.46 ( 6) hydrogen bonds : bond 0.03240 / 2.15 ( 344) hydrogen bonds : angle 4.47026 / 3.28 ( 978) *********************** 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 112 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.234 Fit side-chains REVERT: A 219 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.7881 (p0) REVERT: A 258 LEU cc_start: 0.8249 (tp) cc_final: 0.7968 (tp) REVERT: H 90 ASP cc_start: 0.8669 (m-30) cc_final: 0.8461 (m-30) REVERT: L 44 SER cc_start: 0.8936 (p) cc_final: 0.8685 (m) outliers start: 21 outliers final: 18 residues processed: 104 average time/residue: 0.3957 time to fit residues: 43.7783 Evaluate side-chains 109 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 103 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 69 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 65 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 2 optimal weight: 0.2980 chunk 54 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 167 ASN A 567 GLN H 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.153707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.131678 restraints weight = 6561.134| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.61 r_work: 0.3422 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5778 Z= 0.129 Angle : 0.532 6.037 7914 Z= 0.272 Chirality : 0.040 0.134 897 Planarity : 0.004 0.042 980 Dihedral : 4.661 51.892 818 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.86 % Allowed : 14.52 % Favored : 81.62 % 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: 1.35 (0.32), residues: 746 helix: 1.94 (0.26), residues: 377 sheet: 0.22 (0.57), residues: 93 loop : -0.27 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 564 TYR 0.019 0.001 TYR A 69 PHE 0.015 0.001 PHE A 404 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 0.00308 / 0.13 ( 5775) covalent geometry : angle 0.53066 / 0.27 ( 7908) SS BOND : bond 0.00308 / 0.15 ( 3) SS BOND : angle 1.26363 / 0.65 ( 6) hydrogen bonds : bond 0.03571 / 2.35 ( 344) hydrogen bonds : angle 4.58026 / 3.36 ( 978) *********************** 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 108 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.213 Fit side-chains REVERT: A 219 ASP cc_start: 0.8353 (OUTLIER) cc_final: 0.7893 (p0) REVERT: A 258 LEU cc_start: 0.8227 (tp) cc_final: 0.7951 (tp) REVERT: H 34 MET cc_start: 0.9128 (mmm) cc_final: 0.8890 (mmm) REVERT: H 90 ASP cc_start: 0.8720 (m-30) cc_final: 0.8488 (m-30) REVERT: L 44 SER cc_start: 0.8972 (p) cc_final: 0.8725 (m) outliers start: 21 outliers final: 19 residues processed: 101 average time/residue: 0.3959 time to fit residues: 42.5252 Evaluate side-chains 105 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 103 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 60 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 47 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 167 ASN H 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.150820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.128813 restraints weight = 6662.662| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.61 r_work: 0.3386 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5778 Z= 0.170 Angle : 0.576 6.175 7914 Z= 0.295 Chirality : 0.041 0.138 897 Planarity : 0.005 0.049 980 Dihedral : 4.968 53.115 818 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.78 % Allowed : 13.97 % Favored : 81.25 % 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: 1.16 (0.31), residues: 746 helix: 1.73 (0.26), residues: 376 sheet: 0.21 (0.57), residues: 93 loop : -0.29 (0.39), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 564 TYR 0.021 0.001 TYR A 69 PHE 0.015 0.002 PHE A 404 TRP 0.014 0.001 TRP A 470 HIS 0.005 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.17 ( 5775) covalent geometry : angle 0.57429 / 0.29 ( 7908) SS BOND : bond 0.00296 / 0.15 ( 3) SS BOND : angle 1.57038 / 0.81 ( 6) hydrogen bonds : bond 0.03958 / 2.58 ( 344) hydrogen bonds : angle 4.79267 / 3.51 ( 978) *********************** 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 109 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 83 time to evaluate : 0.216 Fit side-chains REVERT: A 219 ASP cc_start: 0.8396 (OUTLIER) cc_final: 0.7950 (p0) REVERT: A 258 LEU cc_start: 0.8311 (tp) cc_final: 0.8053 (tp) REVERT: A 564 ARG cc_start: 0.7337 (mtp180) cc_final: 0.7133 (mtp180) REVERT: H 34 MET cc_start: 0.9176 (mmm) cc_final: 0.8845 (mmm) REVERT: H 90 ASP cc_start: 0.8775 (m-30) cc_final: 0.8561 (m-30) REVERT: L 44 SER cc_start: 0.8929 (p) cc_final: 0.8686 (m) outliers start: 26 outliers final: 19 residues processed: 100 average time/residue: 0.3376 time to fit residues: 36.0802 Evaluate side-chains 104 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 103 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 46 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 3 GLN H 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.150696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.128787 restraints weight = 6720.090| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.62 r_work: 0.3386 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5778 Z= 0.168 Angle : 0.577 6.623 7914 Z= 0.294 Chirality : 0.041 0.135 897 Planarity : 0.005 0.051 980 Dihedral : 4.990 52.754 818 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.41 % Allowed : 14.52 % Favored : 81.07 % 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: 1.06 (0.31), residues: 746 helix: 1.64 (0.26), residues: 376 sheet: 0.33 (0.58), residues: 87 loop : -0.40 (0.38), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 564 TYR 0.020 0.001 TYR A 69 PHE 0.016 0.002 PHE A 404 TRP 0.014 0.001 TRP A 470 HIS 0.004 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 ( 5775) covalent geometry : angle 0.57526 / 0.29 ( 7908) SS BOND : bond 0.00310 / 0.15 ( 3) SS BOND : angle 1.61416 / 0.83 ( 6) hydrogen bonds : bond 0.03915 / 2.56 ( 344) hydrogen bonds : angle 4.82711 / 3.54 ( 978) ********************** 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 109 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.209 Fit side-chains REVERT: A 219 ASP cc_start: 0.8408 (OUTLIER) cc_final: 0.7955 (p0) REVERT: A 258 LEU cc_start: 0.8308 (tp) cc_final: 0.8040 (tp) REVERT: H 34 MET cc_start: 0.9184 (mmm) cc_final: 0.8855 (mmm) REVERT: L 44 SER cc_start: 0.8919 (p) cc_final: 0.8669 (m) outliers start: 24 outliers final: 21 residues processed: 99 average time/residue: 0.3575 time to fit residues: 37.7654 Evaluate side-chains 105 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 103 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 36 optimal weight: 0.6980 chunk 47 optimal weight: 0.0770 chunk 43 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 167 ASN H 3 GLN H 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.152063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.130034 restraints weight = 6618.377| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.63 r_work: 0.3403 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5778 Z= 0.134 Angle : 0.544 7.124 7914 Z= 0.277 Chirality : 0.040 0.134 897 Planarity : 0.004 0.047 980 Dihedral : 4.810 52.674 818 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.78 % Allowed : 14.15 % Favored : 81.07 % 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: 1.16 (0.31), residues: 746 helix: 1.77 (0.26), residues: 377 sheet: 0.17 (0.57), residues: 93 loop : -0.34 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 564 TYR 0.019 0.001 TYR A 69 PHE 0.016 0.001 PHE A 404 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 0.00320 / 0.13 ( 5775) covalent geometry : angle 0.54334 / 0.28 ( 7908) SS BOND : bond 0.00316 / 0.16 ( 3) SS BOND : angle 1.30439 / 0.67 ( 6) hydrogen bonds : bond 0.03611 / 2.36 ( 344) hydrogen bonds : angle 4.70825 / 3.45 ( 978) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1924.25 seconds wall clock time: 33 minutes 39.98 seconds (2019.98 seconds total)