Starting phenix.real_space_refine on Thu Jul 2 02:06:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k1z_61985/07_2026/9k1z_61985.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k1z_61985/07_2026/9k1z_61985.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k1z_61985/07_2026/9k1z_61985.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k1z_61985/07_2026/9k1z_61985.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k1z_61985/07_2026/9k1z_61985.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k1z_61985/07_2026/9k1z_61985.map" } resolution = 3.27 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= -0.002 sd= 0.073 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 3654 2.51 5 N 872 2.21 5 O 964 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 5530 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3955 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 27, 'TRANS': 501} Chain breaks: 1 Unresolved non-hydrogen bonds: 269 Unresolved non-hydrogen angles: 337 Unresolved non-hydrogen dihedrals: 238 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 9, 'ASN:plan1': 5, 'PHE:plan': 5, 'TRP:plan': 1, 'ARG:plan': 6, 'TYR:plan': 6, 'ASP:plan': 3, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 184 Chain: "H" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 839 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 4, 'ASP:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 57 Chain: "L" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 726 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'ID7': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Time building chain proxies: 1.33, per 1000 atoms: 0.24 Number of scatterers: 5530 At special positions: 0 Unit cell: (80.4, 80.4, 108.272, 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 964 8.00 N 872 7.00 C 3654 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 209.9 milliseconds 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1368 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 5 sheets defined 61.1% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 47 through 59 removed outlier: 3.560A pdb=" N VAL A 51 " --> pdb=" O LYS A 47 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N GLY A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N GLY A 57 " --> pdb=" O SER A 53 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE A 58 " --> pdb=" O VAL A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 65 removed outlier: 3.706A pdb=" N VAL A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 74 removed outlier: 3.615A pdb=" N TYR A 69 " --> pdb=" O TRP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 106 removed outlier: 4.024A pdb=" N LEU A 80 " --> pdb=" O GLY A 76 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE A 81 " --> pdb=" O GLY A 77 " (cutoff:3.500A) Proline residue: A 82 - end of helix removed outlier: 6.358A pdb=" N LEU A 92 " --> pdb=" O PHE A 88 " (cutoff:3.500A) Proline residue: A 93 - end of helix removed outlier: 3.704A pdb=" N THR A 105 " --> pdb=" O ILE A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 113 removed outlier: 4.373A pdb=" N TRP A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 116 No H-bonds generated for 'chain 'A' and resid 114 through 116' Processing helix chain 'A' and resid 117 through 120 Processing helix chain 'A' and resid 121 through 152 removed outlier: 4.140A pdb=" N TYR A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE A 139 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.936A pdb=" N HIS A 161 " --> pdb=" O PRO A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 178 removed outlier: 4.099A 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 237 Processing helix chain 'A' and resid 245 through 267 Proline residue: A 253 - end of helix removed outlier: 3.503A pdb=" N LEU A 267 " --> pdb=" O ARG A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 279 removed outlier: 3.796A pdb=" N GLY A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 286 removed outlier: 3.625A pdb=" N LEU A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU A 286 " --> pdb=" O ILE A 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 281 through 286' Processing helix chain 'A' and resid 287 through 302 removed outlier: 3.712A pdb=" N TRP A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 315 removed outlier: 3.845A pdb=" N LEU A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N GLY A 313 " --> pdb=" O MET A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 356 removed outlier: 3.584A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 Processing helix chain 'A' and resid 368 through 380 Proline residue: A 375 - end of helix Processing helix chain 'A' and resid 383 through 417 removed outlier: 3.562A pdb=" N TRP A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 3.751A 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 removed outlier: 3.874A pdb=" N ILE A 430 " --> pdb=" O TYR A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 448 removed outlier: 3.919A pdb=" N THR A 448 " --> pdb=" O THR A 445 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 445 through 448' Processing helix chain 'A' and resid 450 through 462 removed outlier: 3.773A pdb=" N VAL A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 482 removed outlier: 3.826A pdb=" N LEU A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 497 Processing helix chain 'A' and resid 501 through 510 removed outlier: 3.608A pdb=" N LYS A 505 " --> pdb=" O GLY A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 526 Processing helix chain 'A' and resid 539 through 555 removed outlier: 4.017A pdb=" N SER A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 567 Processing helix chain 'A' and resid 571 through 581 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.012A 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 removed outlier: 3.521A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 removed outlier: 7.074A pdb=" N MET H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N GLU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.843A 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: 5.490A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) 339 hydrogen bonds defined for protein. 960 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: 0.67 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: 1.23 - 1.35: 1676 1.35 - 1.46: 1590 1.46 - 1.58: 2367 1.58 - 1.70: 1 1.70 - 1.82: 57 Bond restraints: 5691 Sorted by residual: bond pdb=" CG PRO A 280 " pdb=" CD PRO A 280 " ideal model delta sigma weight residual 1.503 1.258 0.245 3.40e-02 8.65e+02 5.18e+01 bond pdb=" N PRO A 280 " pdb=" CD PRO A 280 " ideal model delta sigma weight residual 1.473 1.538 -0.065 1.40e-02 5.10e+03 2.16e+01 bond pdb=" CB PRO A 280 " pdb=" CG PRO A 280 " ideal model delta sigma weight residual 1.492 1.706 -0.214 5.00e-02 4.00e+02 1.82e+01 bond pdb=" C2 ID7 A 701 " pdb=" C3 ID7 A 701 " ideal model delta sigma weight residual 1.530 1.469 0.061 2.00e-02 2.50e+03 9.32e+00 bond pdb=" N PRO A 280 " pdb=" CA PRO A 280 " ideal model delta sigma weight residual 1.469 1.434 0.034 1.28e-02 6.10e+03 7.23e+00 ... (remaining 5686 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 7755 3.36 - 6.72: 35 6.72 - 10.08: 5 10.08 - 13.44: 2 13.44 - 16.80: 2 Bond angle restraints: 7799 Sorted by residual: angle pdb=" CA PRO A 280 " pdb=" N PRO A 280 " pdb=" CD PRO A 280 " ideal model delta sigma weight residual 112.00 95.20 16.80 1.40e+00 5.10e-01 1.44e+02 angle pdb=" N PRO A 280 " pdb=" CD PRO A 280 " pdb=" CG PRO A 280 " ideal model delta sigma weight residual 103.20 89.48 13.72 1.50e+00 4.44e-01 8.37e+01 angle pdb=" N PRO A 280 " pdb=" CA PRO A 280 " pdb=" CB PRO A 280 " ideal model delta sigma weight residual 103.25 97.65 5.60 1.05e+00 9.07e-01 2.84e+01 angle pdb=" CA PRO A 280 " pdb=" CB PRO A 280 " pdb=" CG PRO A 280 " ideal model delta sigma weight residual 104.50 94.93 9.57 1.90e+00 2.77e-01 2.54e+01 angle pdb=" CA PRO A 502 " pdb=" N PRO A 502 " pdb=" CD PRO A 502 " ideal model delta sigma weight residual 112.00 106.24 5.76 1.40e+00 5.10e-01 1.69e+01 ... (remaining 7794 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.86: 2899 16.86 - 33.73: 227 33.73 - 50.59: 69 50.59 - 67.45: 8 67.45 - 84.32: 5 Dihedral angle restraints: 3208 sinusoidal: 1052 harmonic: 2156 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 89 " pdb=" CB CYS L 89 " ideal model delta sinusoidal sigma weight residual 93.00 61.73 31.27 1 1.00e+01 1.00e-02 1.39e+01 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 -164.39 -15.61 0 5.00e+00 4.00e-02 9.75e+00 dihedral pdb=" CB GLU H 50 " pdb=" CG GLU H 50 " pdb=" CD GLU H 50 " pdb=" OE1 GLU H 50 " ideal model delta sinusoidal sigma weight residual 0.00 -84.32 84.32 1 3.00e+01 1.11e-03 9.61e+00 ... (remaining 3205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 750 0.052 - 0.104: 131 0.104 - 0.156: 14 0.156 - 0.209: 2 0.209 - 0.261: 1 Chirality restraints: 898 Sorted by residual: chirality pdb=" C2 ID7 A 701 " pdb=" C1 ID7 A 701 " pdb=" C3 ID7 A 701 " pdb=" C6 ID7 A 701 " both_signs ideal model delta sigma weight residual False 2.52 2.78 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA PRO A 502 " pdb=" N PRO A 502 " pdb=" C PRO A 502 " pdb=" CB PRO A 502 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 9.00e-01 chirality pdb=" CA PRO A 280 " pdb=" N PRO A 280 " pdb=" C PRO A 280 " pdb=" CB PRO A 280 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 6.95e-01 ... (remaining 895 not shown) Planarity restraints: 968 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 279 " -0.073 5.00e-02 4.00e+02 9.81e-02 1.54e+01 pdb=" N PRO A 280 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO A 280 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 280 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 501 " -0.057 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO A 502 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO A 502 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 502 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 528 " -0.045 5.00e-02 4.00e+02 6.88e-02 7.58e+00 pdb=" N PRO A 529 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 529 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 529 " -0.038 5.00e-02 4.00e+02 ... (remaining 965 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 135 2.71 - 3.26: 5629 3.26 - 3.81: 9294 3.81 - 4.35: 11168 4.35 - 4.90: 19734 Nonbonded interactions: 45960 Sorted by model distance: nonbonded pdb=" OG1 THR A 168 " pdb=" OE1 GLU A 197 " model vdw 2.165 3.040 nonbonded pdb=" O SER A 207 " pdb=" OH TYR A 453 " model vdw 2.293 3.040 nonbonded pdb=" O TYR A 247 " pdb=" OG1 THR A 251 " model vdw 2.303 3.040 nonbonded pdb=" ND2 ASN A 63 " pdb=" OD1 ASN A 333 " model vdw 2.305 3.120 nonbonded pdb=" O GLY A 89 " pdb=" OG SER A 507 " model vdw 2.319 3.040 ... (remaining 45955 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: 1.580 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.570 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 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 : 0.005 0.245 5694 Z= 0.186 Angle : 0.689 16.799 7805 Z= 0.380 Chirality : 0.040 0.261 898 Planarity : 0.006 0.098 968 Dihedral : 13.765 84.317 1831 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.19 % Allowed : 15.47 % Favored : 84.34 % 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: 1.21 (0.32), residues: 746 helix: 1.32 (0.28), residues: 370 sheet: 0.62 (0.55), residues: 97 loop : 0.33 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 67 TYR 0.012 0.001 TYR A 277 PHE 0.014 0.001 PHE A 338 TRP 0.018 0.001 TRP A 470 HIS 0.003 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.19 ( 5691) covalent geometry : angle 0.68916 / 0.38 ( 7799) SS BOND : bond 0.00278 / 0.14 ( 3) SS BOND : angle 0.93658 / 0.47 ( 6) hydrogen bonds : bond 0.15914 / 9.99 ( 339) hydrogen bonds : angle 6.37131 / 4.67 ( 960) *********************** 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 102 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.198 Fit side-chains REVERT: A 256 MET cc_start: 0.8248 (tpt) cc_final: 0.7965 (tpt) REVERT: A 282 ILE cc_start: 0.7052 (OUTLIER) cc_final: 0.6779 (mm) REVERT: A 406 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8240 (mm-30) outliers start: 1 outliers final: 0 residues processed: 102 average time/residue: 0.0734 time to fit residues: 9.9687 Evaluate side-chains 95 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.0770 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 410 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.147109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.126539 restraints weight = 7179.362| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.61 r_work: 0.3323 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5694 Z= 0.164 Angle : 0.575 6.916 7805 Z= 0.293 Chirality : 0.042 0.165 898 Planarity : 0.005 0.055 968 Dihedral : 6.027 59.932 819 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.96 % Allowed : 12.64 % Favored : 83.40 % 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: 1.23 (0.32), residues: 746 helix: 1.47 (0.28), residues: 367 sheet: 0.71 (0.57), residues: 88 loop : 0.13 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 67 TYR 0.019 0.001 TYR A 69 PHE 0.021 0.002 PHE A 342 TRP 0.017 0.002 TRP A 470 HIS 0.004 0.001 HIS L 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 ( 5691) covalent geometry : angle 0.57244 / 0.29 ( 7799) SS BOND : bond 0.00523 / 0.26 ( 3) SS BOND : angle 1.87487 / 0.94 ( 6) hydrogen bonds : bond 0.04075 / 2.72 ( 339) hydrogen bonds : angle 5.10638 / 3.72 ( 960) *********************** 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 119 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.150 Fit side-chains REVERT: A 69 TYR cc_start: 0.9240 (OUTLIER) cc_final: 0.8606 (p90) REVERT: A 256 MET cc_start: 0.8332 (tpt) cc_final: 0.8012 (tpt) REVERT: A 282 ILE cc_start: 0.7388 (OUTLIER) cc_final: 0.7019 (mm) REVERT: A 302 TYR cc_start: 0.8793 (m-80) cc_final: 0.8477 (m-80) REVERT: A 524 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7926 (mm) REVERT: H 65 THR cc_start: 0.8009 (OUTLIER) cc_final: 0.7768 (t) REVERT: H 69 THR cc_start: 0.8383 (t) cc_final: 0.7937 (p) outliers start: 21 outliers final: 12 residues processed: 109 average time/residue: 0.0712 time to fit residues: 10.3752 Evaluate side-chains 105 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 104 ARG Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 86 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 63 optimal weight: 0.0010 chunk 32 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.146922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.126459 restraints weight = 7103.361| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.61 r_work: 0.3295 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5694 Z= 0.136 Angle : 0.532 9.389 7805 Z= 0.270 Chirality : 0.040 0.163 898 Planarity : 0.004 0.049 968 Dihedral : 5.928 59.415 819 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 4.15 % Allowed : 12.64 % Favored : 83.21 % 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: 1.17 (0.32), residues: 746 helix: 1.50 (0.28), residues: 368 sheet: 0.66 (0.56), residues: 93 loop : -0.03 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 201 TYR 0.017 0.001 TYR A 69 PHE 0.016 0.001 PHE A 342 TRP 0.015 0.001 TRP A 470 HIS 0.002 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 5691) covalent geometry : angle 0.53028 / 0.27 ( 7799) SS BOND : bond 0.00368 / 0.18 ( 3) SS BOND : angle 1.59671 / 0.82 ( 6) hydrogen bonds : bond 0.03717 / 2.45 ( 339) hydrogen bonds : angle 4.87556 / 3.52 ( 960) *********************** 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 114 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.124 Fit side-chains REVERT: A 69 TYR cc_start: 0.9205 (OUTLIER) cc_final: 0.8465 (p90) REVERT: A 219 ASP cc_start: 0.7348 (t70) cc_final: 0.7135 (t70) REVERT: A 282 ILE cc_start: 0.7529 (OUTLIER) cc_final: 0.7125 (mm) REVERT: A 302 TYR cc_start: 0.8809 (m-80) cc_final: 0.8539 (m-80) REVERT: A 524 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7903 (mm) REVERT: A 554 MET cc_start: 0.7902 (mmm) cc_final: 0.7492 (mmm) REVERT: H 65 THR cc_start: 0.7999 (OUTLIER) cc_final: 0.7708 (t) REVERT: H 69 THR cc_start: 0.8303 (t) cc_final: 0.7933 (p) REVERT: L 92 PHE cc_start: 0.8370 (OUTLIER) cc_final: 0.6765 (m-80) outliers start: 22 outliers final: 13 residues processed: 108 average time/residue: 0.0707 time to fit residues: 10.2305 Evaluate side-chains 106 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 92 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 20 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.145856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.125362 restraints weight = 7111.765| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.60 r_work: 0.3289 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5694 Z= 0.134 Angle : 0.521 6.580 7805 Z= 0.264 Chirality : 0.041 0.174 898 Planarity : 0.004 0.043 968 Dihedral : 5.810 57.349 819 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.96 % Allowed : 13.40 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.32), residues: 746 helix: 1.52 (0.28), residues: 368 sheet: 0.69 (0.56), residues: 93 loop : -0.14 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 201 TYR 0.017 0.001 TYR A 69 PHE 0.014 0.001 PHE A 342 TRP 0.014 0.001 TRP A 470 HIS 0.002 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.13 ( 5691) covalent geometry : angle 0.52011 / 0.26 ( 7799) SS BOND : bond 0.00363 / 0.18 ( 3) SS BOND : angle 1.45257 / 0.74 ( 6) hydrogen bonds : bond 0.03569 / 2.37 ( 339) hydrogen bonds : angle 4.79369 / 3.45 ( 960) *********************** 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: 21 poor density : 90 time to evaluate : 0.222 Fit side-chains REVERT: A 69 TYR cc_start: 0.9253 (OUTLIER) cc_final: 0.8589 (p90) REVERT: A 282 ILE cc_start: 0.7634 (OUTLIER) cc_final: 0.7232 (mm) REVERT: A 302 TYR cc_start: 0.8745 (m-80) cc_final: 0.8534 (m-80) REVERT: A 394 MET cc_start: 0.9170 (tmm) cc_final: 0.8969 (tmm) REVERT: A 524 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7948 (mm) REVERT: H 65 THR cc_start: 0.8145 (OUTLIER) cc_final: 0.7870 (t) REVERT: L 92 PHE cc_start: 0.8398 (OUTLIER) cc_final: 0.6477 (m-80) outliers start: 21 outliers final: 15 residues processed: 104 average time/residue: 0.0734 time to fit residues: 10.2149 Evaluate side-chains 102 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 104 ARG Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 92 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 52 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 47 optimal weight: 0.1980 chunk 32 optimal weight: 0.7980 chunk 69 optimal weight: 0.0870 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.148003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.127380 restraints weight = 7288.066| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.64 r_work: 0.3330 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5694 Z= 0.108 Angle : 0.487 5.431 7805 Z= 0.248 Chirality : 0.039 0.139 898 Planarity : 0.004 0.040 968 Dihedral : 5.501 53.120 819 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.58 % Allowed : 14.53 % Favored : 81.89 % 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 (0.32), residues: 746 helix: 1.62 (0.28), residues: 368 sheet: 0.79 (0.56), residues: 92 loop : -0.06 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 201 TYR 0.015 0.001 TYR A 69 PHE 0.012 0.001 PHE A 342 TRP 0.015 0.001 TRP A 470 HIS 0.002 0.000 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 5691) covalent geometry : angle 0.48631 / 0.25 ( 7799) SS BOND : bond 0.00329 / 0.16 ( 3) SS BOND : angle 1.18125 / 0.60 ( 6) hydrogen bonds : bond 0.03322 / 2.21 ( 339) hydrogen bonds : angle 4.65647 / 3.34 ( 960) *********************** 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 108 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.194 Fit side-chains REVERT: A 69 TYR cc_start: 0.9202 (OUTLIER) cc_final: 0.8464 (p90) REVERT: A 282 ILE cc_start: 0.7662 (OUTLIER) cc_final: 0.7262 (mm) REVERT: A 302 TYR cc_start: 0.8696 (m-80) cc_final: 0.8426 (m-80) REVERT: A 524 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7836 (mm) REVERT: H 65 THR cc_start: 0.8041 (OUTLIER) cc_final: 0.7810 (t) REVERT: L 92 PHE cc_start: 0.8368 (OUTLIER) cc_final: 0.6407 (m-80) outliers start: 19 outliers final: 12 residues processed: 101 average time/residue: 0.0619 time to fit residues: 8.5205 Evaluate side-chains 102 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 92 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 3 optimal weight: 0.0770 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 47 optimal weight: 0.0980 chunk 28 optimal weight: 0.5980 chunk 25 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.148590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.128008 restraints weight = 7143.162| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.64 r_work: 0.3337 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5694 Z= 0.104 Angle : 0.486 7.273 7805 Z= 0.244 Chirality : 0.039 0.135 898 Planarity : 0.004 0.039 968 Dihedral : 5.062 44.936 819 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.77 % Allowed : 15.09 % Favored : 81.13 % 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: 1.41 (0.32), residues: 746 helix: 1.72 (0.28), residues: 369 sheet: 0.80 (0.56), residues: 92 loop : 0.03 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 201 TYR 0.015 0.001 TYR A 69 PHE 0.012 0.001 PHE A 342 TRP 0.014 0.001 TRP A 470 HIS 0.002 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 ( 5691) covalent geometry : angle 0.48502 / 0.24 ( 7799) SS BOND : bond 0.00332 / 0.16 ( 3) SS BOND : angle 1.11112 / 0.57 ( 6) hydrogen bonds : bond 0.03193 / 2.12 ( 339) hydrogen bonds : angle 4.55964 / 3.26 ( 960) *********************** 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 114 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.195 Fit side-chains REVERT: A 69 TYR cc_start: 0.9185 (OUTLIER) cc_final: 0.8446 (p90) REVERT: A 282 ILE cc_start: 0.7685 (OUTLIER) cc_final: 0.7293 (mm) REVERT: A 302 TYR cc_start: 0.8659 (m-80) cc_final: 0.8410 (m-80) REVERT: H 65 THR cc_start: 0.8111 (OUTLIER) cc_final: 0.7892 (t) REVERT: L 92 PHE cc_start: 0.8404 (OUTLIER) cc_final: 0.6395 (m-80) outliers start: 20 outliers final: 13 residues processed: 105 average time/residue: 0.0534 time to fit residues: 7.8837 Evaluate side-chains 103 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 104 ARG Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 92 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 42 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 33 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.147648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.127050 restraints weight = 7164.504| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.64 r_work: 0.3276 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 5694 Z= 0.142 Angle : 0.506 5.487 7805 Z= 0.259 Chirality : 0.040 0.152 898 Planarity : 0.004 0.040 968 Dihedral : 4.921 39.737 819 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.58 % Allowed : 14.91 % Favored : 81.51 % 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: 1.36 (0.32), residues: 746 helix: 1.72 (0.28), residues: 361 sheet: 0.80 (0.57), residues: 92 loop : -0.01 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 201 TYR 0.017 0.001 TYR A 69 PHE 0.011 0.001 PHE A 392 TRP 0.012 0.001 TRP A 470 HIS 0.002 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.14 ( 5691) covalent geometry : angle 0.50488 / 0.26 ( 7799) SS BOND : bond 0.00373 / 0.18 ( 3) SS BOND : angle 1.26901 / 0.65 ( 6) hydrogen bonds : bond 0.03504 / 2.36 ( 339) hydrogen bonds : angle 4.67068 / 3.35 ( 960) *********************** 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 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 Fit side-chains REVERT: A 69 TYR cc_start: 0.9266 (OUTLIER) cc_final: 0.8509 (p90) REVERT: A 204 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8634 (mp) REVERT: A 282 ILE cc_start: 0.7771 (OUTLIER) cc_final: 0.7361 (mm) REVERT: A 302 TYR cc_start: 0.8791 (m-80) cc_final: 0.8528 (m-80) REVERT: L 92 PHE cc_start: 0.8501 (OUTLIER) cc_final: 0.6550 (m-80) outliers start: 19 outliers final: 14 residues processed: 98 average time/residue: 0.0690 time to fit residues: 9.0623 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 : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 104 ARG Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 92 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 23 optimal weight: 0.9980 chunk 3 optimal weight: 0.4980 chunk 61 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.147759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.127160 restraints weight = 7110.041| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.63 r_work: 0.3304 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5694 Z= 0.132 Angle : 0.512 7.773 7805 Z= 0.258 Chirality : 0.040 0.139 898 Planarity : 0.004 0.041 968 Dihedral : 4.576 33.207 819 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.21 % Allowed : 15.28 % Favored : 81.51 % 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: 1.39 (0.32), residues: 746 helix: 1.76 (0.28), residues: 361 sheet: 0.81 (0.57), residues: 92 loop : -0.03 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 201 TYR 0.018 0.001 TYR A 69 PHE 0.010 0.001 PHE A 392 TRP 0.011 0.001 TRP A 470 HIS 0.002 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 ( 5691) covalent geometry : angle 0.51104 / 0.26 ( 7799) SS BOND : bond 0.00356 / 0.18 ( 3) SS BOND : angle 1.23394 / 0.64 ( 6) hydrogen bonds : bond 0.03439 / 2.31 ( 339) hydrogen bonds : angle 4.66780 / 3.34 ( 960) *********************** 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 101 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.195 Fit side-chains REVERT: A 69 TYR cc_start: 0.9264 (OUTLIER) cc_final: 0.8494 (p90) REVERT: A 282 ILE cc_start: 0.7808 (OUTLIER) cc_final: 0.7402 (mm) REVERT: A 302 TYR cc_start: 0.8789 (m-80) cc_final: 0.8543 (m-80) REVERT: A 554 MET cc_start: 0.7920 (mmm) cc_final: 0.7623 (mmm) REVERT: L 92 PHE cc_start: 0.8509 (OUTLIER) cc_final: 0.6492 (m-80) outliers start: 17 outliers final: 14 residues processed: 94 average time/residue: 0.0645 time to fit residues: 8.2046 Evaluate side-chains 100 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 104 ARG Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 92 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 23 optimal weight: 0.1980 chunk 56 optimal weight: 0.0070 chunk 47 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 35 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 58 optimal weight: 0.0970 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.150627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.130366 restraints weight = 7060.272| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.61 r_work: 0.3317 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5694 Z= 0.101 Angle : 0.484 5.442 7805 Z= 0.245 Chirality : 0.039 0.134 898 Planarity : 0.004 0.041 968 Dihedral : 4.143 31.921 819 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.02 % Allowed : 15.28 % Favored : 81.70 % 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: 1.54 (0.32), residues: 746 helix: 1.93 (0.28), residues: 361 sheet: 0.87 (0.57), residues: 92 loop : -0.01 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 201 TYR 0.014 0.001 TYR A 69 PHE 0.011 0.001 PHE A 338 TRP 0.014 0.001 TRP A 470 HIS 0.002 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 ( 5691) covalent geometry : angle 0.48356 / 0.24 ( 7799) SS BOND : bond 0.00318 / 0.16 ( 3) SS BOND : angle 1.05967 / 0.54 ( 6) hydrogen bonds : bond 0.03177 / 2.11 ( 339) hydrogen bonds : angle 4.54110 / 3.24 ( 960) *********************** 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 106 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.122 Fit side-chains REVERT: A 69 TYR cc_start: 0.9167 (OUTLIER) cc_final: 0.8418 (p90) REVERT: A 204 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8642 (mp) REVERT: A 282 ILE cc_start: 0.7803 (OUTLIER) cc_final: 0.7409 (mm) REVERT: A 302 TYR cc_start: 0.8699 (m-80) cc_final: 0.8445 (m-80) REVERT: A 554 MET cc_start: 0.7889 (mmm) cc_final: 0.7582 (mmm) REVERT: L 92 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.6526 (m-80) outliers start: 16 outliers final: 11 residues processed: 100 average time/residue: 0.0690 time to fit residues: 9.1290 Evaluate side-chains 103 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 92 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 32 optimal weight: 0.0270 chunk 43 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.147757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.127168 restraints weight = 7162.522| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.64 r_work: 0.3328 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5694 Z= 0.111 Angle : 0.499 7.099 7805 Z= 0.250 Chirality : 0.039 0.135 898 Planarity : 0.004 0.041 968 Dihedral : 4.084 31.784 819 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.83 % Allowed : 15.85 % Favored : 81.32 % 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: 1.57 (0.32), residues: 746 helix: 1.95 (0.28), residues: 361 sheet: 0.90 (0.57), residues: 92 loop : -0.01 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 201 TYR 0.016 0.001 TYR A 69 PHE 0.011 0.001 PHE A 338 TRP 0.012 0.001 TRP A 470 HIS 0.002 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 ( 5691) covalent geometry : angle 0.49807 / 0.25 ( 7799) SS BOND : bond 0.00321 / 0.16 ( 3) SS BOND : angle 1.07059 / 0.55 ( 6) hydrogen bonds : bond 0.03223 / 2.15 ( 339) hydrogen bonds : angle 4.54375 / 3.24 ( 960) ********************** 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 103 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.189 Fit side-chains REVERT: A 69 TYR cc_start: 0.9216 (OUTLIER) cc_final: 0.8435 (p90) REVERT: A 204 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8643 (mp) REVERT: A 282 ILE cc_start: 0.7803 (OUTLIER) cc_final: 0.7410 (mm) REVERT: A 302 TYR cc_start: 0.8720 (m-80) cc_final: 0.8477 (m-80) REVERT: A 554 MET cc_start: 0.7901 (mmm) cc_final: 0.7586 (mmm) REVERT: H 67 ARG cc_start: 0.8235 (ptp90) cc_final: 0.7992 (ptm-80) REVERT: L 92 PHE cc_start: 0.8512 (OUTLIER) cc_final: 0.6532 (m-80) outliers start: 15 outliers final: 11 residues processed: 97 average time/residue: 0.0606 time to fit residues: 8.0876 Evaluate side-chains 101 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 92 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 58 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 46 optimal weight: 0.2980 chunk 57 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.148103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.127479 restraints weight = 7138.713| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.64 r_work: 0.3306 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5694 Z= 0.131 Angle : 0.517 8.280 7805 Z= 0.260 Chirality : 0.040 0.139 898 Planarity : 0.004 0.041 968 Dihedral : 4.149 32.453 819 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.02 % Allowed : 15.85 % Favored : 81.13 % 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: 1.50 (0.32), residues: 746 helix: 1.84 (0.28), residues: 364 sheet: 0.90 (0.57), residues: 92 loop : 0.01 (0.38), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 201 TYR 0.017 0.001 TYR A 69 PHE 0.010 0.001 PHE A 345 TRP 0.012 0.001 TRP A 470 HIS 0.002 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 ( 5691) covalent geometry : angle 0.51651 / 0.26 ( 7799) SS BOND : bond 0.00345 / 0.17 ( 3) SS BOND : angle 1.19039 / 0.62 ( 6) hydrogen bonds : bond 0.03408 / 2.29 ( 339) hydrogen bonds : angle 4.62499 / 3.31 ( 960) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1349.85 seconds wall clock time: 23 minutes 50.06 seconds (1430.06 seconds total)