Starting phenix.real_space_refine on Tue Feb 3 17:38:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k1i_61976/02_2026/9k1i_61976.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k1i_61976/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9k1i_61976/02_2026/9k1i_61976.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k1i_61976/02_2026/9k1i_61976.map" model { file = "/net/cci-nas-00/data/ceres_data/9k1i_61976/02_2026/9k1i_61976.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k1i_61976/02_2026/9k1i_61976.cif" } 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-2.0-5952/lib/python3.9/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, 11 Unusual residues: {' CL': 1, 'IZC': 1} Classifications: {'undetermined': 2, 'water': 1} Link IDs: {None: 2} Time building chain proxies: 1.46, per 1000 atoms: 0.26 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: 0.51 Conformation dependent library (CDL) restraints added in 399.8 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: 0.20 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: 0.69 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: 1.160 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: 0.020 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.400 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 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:7.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 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 covalent geometry : bond 0.00574 ( 5775) covalent geometry : angle 0.83388 ( 7908) SS BOND : bond 0.00144 ( 3) SS BOND : angle 1.06436 ( 6) hydrogen bonds : bond 0.14589 ( 344) hydrogen bonds : angle 6.45837 ( 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 : 0.163 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: 0.4030 time to fit residues: 46.5797 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 : 0.130 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.153713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.131587 restraints weight = 6672.037| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.66 r_work: 0.3424 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1583 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= 0.137 Angle : 0.578 6.274 7914 Z= 0.302 Chirality : 0.042 0.148 897 Planarity : 0.005 0.039 980 Dihedral : 6.082 59.399 825 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.33 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: 1.00 (0.31), residues: 746 helix: 1.29 (0.26), residues: 375 sheet: 0.38 (0.56), residues: 95 loop : 0.04 (0.41), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 564 TYR 0.018 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 covalent geometry : bond 0.00317 ( 5775) covalent geometry : angle 0.57639 ( 7908) SS BOND : bond 0.00470 ( 3) SS BOND : angle 1.47041 ( 6) hydrogen bonds : bond 0.04088 ( 344) hydrogen bonds : angle 4.98978 ( 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 114 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.209 Fit side-chains REVERT: A 275 LYS cc_start: 0.7884 (ttpt) cc_final: 0.7593 (ttmm) REVERT: A 494 ASP cc_start: 0.8653 (t70) cc_final: 0.8351 (t70) outliers start: 20 outliers final: 15 residues processed: 106 average time/residue: 0.3672 time to fit residues: 41.0771 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: 1.9990 chunk 65 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN A 333 ASN A 567 GLN H 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.151335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.129328 restraints weight = 6604.162| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.61 r_work: 0.3389 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1937 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= 0.159 Angle : 0.568 6.185 7914 Z= 0.297 Chirality : 0.041 0.142 897 Planarity : 0.005 0.044 980 Dihedral : 5.124 52.399 818 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 5.33 % Allowed : 11.76 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.31), residues: 746 helix: 1.44 (0.25), residues: 375 sheet: 0.27 (0.56), residues: 95 loop : -0.03 (0.40), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 564 TYR 0.021 0.001 TYR A 69 PHE 0.017 0.002 PHE A 474 TRP 0.016 0.002 TRP A 470 HIS 0.005 0.002 HIS H 80 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 5775) covalent geometry : angle 0.56638 ( 7908) SS BOND : bond 0.00398 ( 3) SS BOND : angle 1.50442 ( 6) hydrogen bonds : bond 0.04120 ( 344) hydrogen bonds : angle 4.90201 ( 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 115 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 86 time to evaluate : 0.261 Fit side-chains REVERT: A 219 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.7889 (p0) REVERT: A 344 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7970 (mm) REVERT: H 34 MET cc_start: 0.9177 (mmm) cc_final: 0.8767 (mmm) REVERT: L 44 SER cc_start: 0.8921 (p) cc_final: 0.8556 (m) outliers start: 29 outliers final: 16 residues processed: 102 average time/residue: 0.3597 time to fit residues: 39.2705 Evaluate side-chains 102 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.208 ------------------------------------------------------------------------------- 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 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 19 VAL 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: 0.9990 chunk 34 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 41 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 2 optimal weight: 0.1980 chunk 22 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN A 333 ASN A 567 GLN H 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.152222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.130359 restraints weight = 6579.778| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.61 r_work: 0.3402 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2103 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= 0.137 Angle : 0.538 5.732 7914 Z= 0.280 Chirality : 0.040 0.138 897 Planarity : 0.005 0.046 980 Dihedral : 4.923 52.616 818 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.23 % Allowed : 13.05 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.31), residues: 746 helix: 1.65 (0.26), residues: 375 sheet: 0.25 (0.56), residues: 95 loop : -0.06 (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 0.015 0.002 PHE A 474 TRP 0.015 0.001 TRP A 470 HIS 0.004 0.001 HIS H 80 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 5775) covalent geometry : angle 0.53712 ( 7908) SS BOND : bond 0.00357 ( 3) SS BOND : angle 1.32677 ( 6) hydrogen bonds : bond 0.03753 ( 344) hydrogen bonds : angle 4.76848 ( 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 109 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.218 Fit side-chains REVERT: A 219 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.7861 (p0) REVERT: A 258 LEU cc_start: 0.8300 (tp) cc_final: 0.8028 (tp) REVERT: H 34 MET cc_start: 0.9155 (mmm) cc_final: 0.8773 (mmm) REVERT: L 44 SER cc_start: 0.8922 (p) cc_final: 0.8590 (m) outliers start: 23 outliers final: 16 residues processed: 100 average time/residue: 0.3966 time to fit residues: 42.0772 Evaluate side-chains 99 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.145 ------------------------------------------------------------------------------- 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 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 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: 0.8980 chunk 20 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 68 optimal weight: 0.4980 chunk 30 optimal weight: 0.7980 chunk 64 optimal weight: 0.3980 chunk 62 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN A 333 ASN A 567 GLN H 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.152626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.130560 restraints weight = 6702.890| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.63 r_work: 0.3402 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2207 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= 0.129 Angle : 0.523 5.727 7914 Z= 0.271 Chirality : 0.040 0.136 897 Planarity : 0.004 0.045 980 Dihedral : 4.791 52.469 818 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 4.96 % Allowed : 13.42 % 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: 1.31 (0.31), residues: 746 helix: 1.79 (0.26), residues: 375 sheet: 0.25 (0.56), residues: 95 loop : -0.10 (0.40), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 583 TYR 0.019 0.001 TYR A 69 PHE 0.013 0.001 PHE A 474 TRP 0.015 0.001 TRP A 470 HIS 0.004 0.001 HIS H 80 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 5775) covalent geometry : angle 0.52159 ( 7908) SS BOND : bond 0.00352 ( 3) SS BOND : angle 1.27103 ( 6) hydrogen bonds : bond 0.03648 ( 344) hydrogen bonds : angle 4.68437 ( 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 117 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 0.214 Fit side-chains REVERT: A 219 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.7890 (p0) REVERT: A 258 LEU cc_start: 0.8322 (tp) cc_final: 0.8053 (tp) REVERT: A 344 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.8030 (mm) REVERT: H 34 MET cc_start: 0.9154 (mmm) cc_final: 0.8819 (mmm) REVERT: L 44 SER cc_start: 0.8937 (p) cc_final: 0.8651 (m) outliers start: 27 outliers final: 20 residues processed: 107 average time/residue: 0.3577 time to fit residues: 40.6394 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 : 0.209 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 45 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 7 optimal weight: 0.2980 chunk 40 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 17 optimal weight: 0.0970 chunk 6 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN A 316 ASN A 333 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 = 0.3802 r_free = 0.3802 target = 0.153660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.131630 restraints weight = 6632.670| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.63 r_work: 0.3423 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2251 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= 0.117 Angle : 0.507 5.564 7914 Z= 0.262 Chirality : 0.039 0.136 897 Planarity : 0.004 0.044 980 Dihedral : 4.674 52.405 818 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.96 % Allowed : 13.42 % 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 (0.31), residues: 746 helix: 1.88 (0.26), residues: 377 sheet: 0.19 (0.55), residues: 95 loop : -0.16 (0.40), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 583 TYR 0.018 0.001 TYR A 69 PHE 0.013 0.001 PHE A 474 TRP 0.015 0.001 TRP A 470 HIS 0.003 0.001 HIS H 80 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 5775) covalent geometry : angle 0.50604 ( 7908) SS BOND : bond 0.00329 ( 3) SS BOND : angle 1.15643 ( 6) hydrogen bonds : bond 0.03480 ( 344) hydrogen bonds : angle 4.59280 ( 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 119 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 0.193 Fit side-chains REVERT: A 219 ASP cc_start: 0.8339 (OUTLIER) cc_final: 0.7861 (p0) REVERT: A 258 LEU cc_start: 0.8324 (tp) cc_final: 0.8051 (tp) REVERT: H 34 MET cc_start: 0.9142 (mmm) cc_final: 0.8898 (mmm) REVERT: L 44 SER cc_start: 0.8978 (p) cc_final: 0.8706 (m) outliers start: 27 outliers final: 22 residues processed: 109 average time/residue: 0.3804 time to fit residues: 43.9368 Evaluate side-chains 110 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 0.167 ------------------------------------------------------------------------------- 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 535 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 36 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 0.4980 chunk 47 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 63 optimal weight: 0.0970 chunk 25 optimal weight: 3.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN A 333 ASN A 567 GLN H 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.153004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.130919 restraints weight = 6710.209| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.64 r_work: 0.3412 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5778 Z= 0.128 Angle : 0.520 5.626 7914 Z= 0.269 Chirality : 0.040 0.135 897 Planarity : 0.004 0.045 980 Dihedral : 4.738 52.141 818 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.60 % Allowed : 13.97 % 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: 1.32 (0.31), residues: 746 helix: 1.86 (0.26), residues: 377 sheet: 0.20 (0.57), residues: 93 loop : -0.19 (0.40), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 564 TYR 0.019 0.001 TYR A 69 PHE 0.014 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 covalent geometry : bond 0.00302 ( 5775) covalent geometry : angle 0.51940 ( 7908) SS BOND : bond 0.00320 ( 3) SS BOND : angle 1.18019 ( 6) hydrogen bonds : bond 0.03587 ( 344) hydrogen bonds : angle 4.63121 ( 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 113 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 0.156 Fit side-chains REVERT: A 219 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.7868 (p0) REVERT: A 258 LEU cc_start: 0.8327 (tp) cc_final: 0.8050 (tp) REVERT: H 34 MET cc_start: 0.9141 (mmm) cc_final: 0.8886 (mmm) REVERT: L 44 SER cc_start: 0.8935 (p) cc_final: 0.8668 (m) outliers start: 25 outliers final: 20 residues processed: 104 average time/residue: 0.3508 time to fit residues: 38.7005 Evaluate side-chains 106 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.129 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 69 optimal weight: 0.0970 chunk 19 optimal weight: 0.1980 chunk 65 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 2 optimal weight: 0.0270 chunk 54 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.3036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN A 333 ASN A 567 GLN H 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.156268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.134573 restraints weight = 6570.945| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.62 r_work: 0.3454 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5778 Z= 0.098 Angle : 0.488 5.492 7914 Z= 0.252 Chirality : 0.038 0.136 897 Planarity : 0.004 0.042 980 Dihedral : 4.502 52.242 818 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.86 % Allowed : 14.89 % 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: 1.48 (0.32), residues: 746 helix: 2.07 (0.26), residues: 378 sheet: 0.20 (0.57), residues: 93 loop : -0.23 (0.39), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 564 TYR 0.015 0.001 TYR A 69 PHE 0.013 0.001 PHE A 474 TRP 0.016 0.001 TRP A 470 HIS 0.003 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 5775) covalent geometry : angle 0.48713 ( 7908) SS BOND : bond 0.00311 ( 3) SS BOND : angle 0.91040 ( 6) hydrogen bonds : bond 0.03185 ( 344) hydrogen bonds : angle 4.44824 ( 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 112 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.204 Fit side-chains REVERT: A 258 LEU cc_start: 0.8291 (tp) cc_final: 0.8018 (tp) REVERT: H 34 MET cc_start: 0.9089 (mmm) cc_final: 0.8719 (mmm) REVERT: L 44 SER cc_start: 0.8928 (p) cc_final: 0.8685 (m) outliers start: 21 outliers final: 19 residues processed: 103 average time/residue: 0.3676 time to fit residues: 40.1337 Evaluate side-chains 105 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 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 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 537 VAL 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 60 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 47 optimal weight: 0.3980 chunk 24 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 69 optimal weight: 0.3980 chunk 45 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 ASN A 333 ASN H 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.154120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.132314 restraints weight = 6629.862| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.60 r_work: 0.3429 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5778 Z= 0.123 Angle : 0.525 5.595 7914 Z= 0.269 Chirality : 0.039 0.135 897 Planarity : 0.004 0.045 980 Dihedral : 4.624 52.185 818 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.86 % Allowed : 15.81 % Favored : 80.33 % 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: 1.97 (0.26), residues: 377 sheet: 0.20 (0.57), residues: 93 loop : -0.26 (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 covalent geometry : bond 0.00291 ( 5775) covalent geometry : angle 0.52467 ( 7908) SS BOND : bond 0.00295 ( 3) SS BOND : angle 1.12129 ( 6) hydrogen bonds : bond 0.03503 ( 344) hydrogen bonds : angle 4.53164 ( 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 107 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.218 Fit side-chains REVERT: A 258 LEU cc_start: 0.8293 (tp) cc_final: 0.8032 (tp) REVERT: H 34 MET cc_start: 0.9128 (mmm) cc_final: 0.8723 (mmm) REVERT: L 44 SER cc_start: 0.8960 (p) cc_final: 0.8721 (m) outliers start: 21 outliers final: 18 residues processed: 99 average time/residue: 0.3210 time to fit residues: 33.8019 Evaluate side-chains 101 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.137 ------------------------------------------------------------------------------- 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 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 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: 0.6980 chunk 21 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN A 333 ASN A 567 GLN H 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.152612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.130632 restraints weight = 6696.507| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.63 r_work: 0.3410 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5778 Z= 0.138 Angle : 0.545 5.739 7914 Z= 0.278 Chirality : 0.040 0.136 897 Planarity : 0.004 0.046 980 Dihedral : 4.759 52.137 818 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.04 % Allowed : 14.89 % 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: 1.27 (0.31), residues: 746 helix: 1.87 (0.26), residues: 376 sheet: 0.15 (0.57), residues: 93 loop : -0.29 (0.39), residues: 277 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 0.001 PHE A 404 TRP 0.014 0.001 TRP A 470 HIS 0.004 0.001 HIS H 80 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 5775) covalent geometry : angle 0.54437 ( 7908) SS BOND : bond 0.00296 ( 3) SS BOND : angle 1.34609 ( 6) hydrogen bonds : bond 0.03666 ( 344) hydrogen bonds : angle 4.65321 ( 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 105 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.137 Fit side-chains REVERT: A 219 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.7903 (p0) REVERT: A 258 LEU cc_start: 0.8302 (tp) cc_final: 0.8058 (tp) REVERT: H 34 MET cc_start: 0.9159 (mmm) cc_final: 0.8888 (mmm) REVERT: L 44 SER cc_start: 0.8934 (p) cc_final: 0.8690 (m) outliers start: 22 outliers final: 17 residues processed: 97 average time/residue: 0.3072 time to fit residues: 31.7356 Evaluate side-chains 102 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.190 ------------------------------------------------------------------------------- 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 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 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 36 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 6 optimal weight: 0.0370 chunk 56 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 58 optimal weight: 0.1980 chunk 28 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN A 333 ASN H 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.154963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.133183 restraints weight = 6561.925| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.61 r_work: 0.3448 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2575 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= 0.109 Angle : 0.520 6.598 7914 Z= 0.264 Chirality : 0.039 0.136 897 Planarity : 0.004 0.043 980 Dihedral : 4.577 51.886 818 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.31 % Allowed : 16.18 % Favored : 80.51 % 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: 1.37 (0.31), residues: 746 helix: 2.00 (0.26), residues: 377 sheet: 0.09 (0.56), residues: 93 loop : -0.28 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 67 TYR 0.017 0.001 TYR A 69 PHE 0.015 0.001 PHE A 404 TRP 0.014 0.001 TRP A 470 HIS 0.003 0.001 HIS H 80 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 5775) covalent geometry : angle 0.51971 ( 7908) SS BOND : bond 0.00288 ( 3) SS BOND : angle 1.02270 ( 6) hydrogen bonds : bond 0.03337 ( 344) hydrogen bonds : angle 4.52695 ( 978) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1694.01 seconds wall clock time: 29 minutes 36.89 seconds (1776.89 seconds total)