Starting phenix.real_space_refine on Tue Feb 3 17:29:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k1z_61985/02_2026/9k1z_61985.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k1z_61985/02_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_61985/02_2026/9k1z_61985.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k1z_61985/02_2026/9k1z_61985.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k1z_61985/02_2026/9k1z_61985.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k1z_61985/02_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): 0.00s 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: 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, 10 Unusual residues: {' CL': 1, 'ID7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 0.99, per 1000 atoms: 0.18 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: 0.51 Conformation dependent library (CDL) restraints added in 389.8 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: 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: 0.20 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: 1.04 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: 1.23 - 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: 1.780 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.960 Find NCS groups from input model: 0.030 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:1.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 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 covalent geometry : bond 0.00522 ( 5691) covalent geometry : angle 0.68916 ( 7799) SS BOND : bond 0.00278 ( 3) SS BOND : angle 0.93658 ( 6) hydrogen bonds : bond 0.15914 ( 339) hydrogen bonds : angle 6.37131 ( 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 : 0.185 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: 0.0486 time to fit residues: 6.6537 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 : 0.122 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 410 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.147415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.126765 restraints weight = 7167.888| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.63 r_work: 0.3280 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5694 Z= 0.163 Angle : 0.573 6.902 7805 Z= 0.293 Chirality : 0.041 0.168 898 Planarity : 0.005 0.056 968 Dihedral : 6.018 59.835 819 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.77 % Allowed : 12.64 % Favored : 83.58 % 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 (0.32), residues: 746 helix: 1.50 (0.28), residues: 367 sheet: 0.69 (0.57), residues: 93 loop : 0.15 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 67 TYR 0.018 0.001 TYR A 69 PHE 0.019 0.002 PHE A 342 TRP 0.017 0.001 TRP A 470 HIS 0.004 0.001 HIS L 35 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 5691) covalent geometry : angle 0.57030 ( 7799) SS BOND : bond 0.00492 ( 3) SS BOND : angle 1.97212 ( 6) hydrogen bonds : bond 0.04080 ( 339) hydrogen bonds : angle 5.11596 ( 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 117 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.196 Fit side-chains REVERT: A 69 TYR cc_start: 0.9217 (OUTLIER) cc_final: 0.8681 (p90) REVERT: A 256 MET cc_start: 0.8325 (tpt) cc_final: 0.8006 (tpt) REVERT: A 282 ILE cc_start: 0.7379 (OUTLIER) cc_final: 0.7007 (mm) REVERT: A 302 TYR cc_start: 0.8803 (m-80) cc_final: 0.8492 (m-80) REVERT: A 524 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7918 (mm) REVERT: H 65 THR cc_start: 0.7993 (OUTLIER) cc_final: 0.7754 (t) REVERT: H 69 THR cc_start: 0.8392 (t) cc_final: 0.7942 (p) outliers start: 20 outliers final: 12 residues processed: 107 average time/residue: 0.0736 time to fit residues: 10.4438 Evaluate side-chains 103 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.205 ------------------------------------------------------------------------------- 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: 6.9990 chunk 11 optimal weight: 0.2980 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 63 optimal weight: 0.0050 chunk 32 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.147779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.127357 restraints weight = 7084.116| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.61 r_work: 0.3308 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5694 Z= 0.126 Angle : 0.528 9.243 7805 Z= 0.266 Chirality : 0.040 0.157 898 Planarity : 0.005 0.049 968 Dihedral : 5.893 59.180 819 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.15 % Allowed : 13.02 % Favored : 82.83 % 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: 1.25 (0.32), residues: 746 helix: 1.56 (0.28), residues: 368 sheet: 0.69 (0.56), residues: 93 loop : 0.02 (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 0.017 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 covalent geometry : bond 0.00295 ( 5691) covalent geometry : angle 0.52639 ( 7799) SS BOND : bond 0.00364 ( 3) SS BOND : angle 1.44124 ( 6) hydrogen bonds : bond 0.03678 ( 339) hydrogen bonds : angle 4.86503 ( 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 115 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.199 Fit side-chains REVERT: A 69 TYR cc_start: 0.9198 (OUTLIER) cc_final: 0.8564 (p90) REVERT: A 282 ILE cc_start: 0.7494 (OUTLIER) cc_final: 0.7110 (mm) REVERT: A 302 TYR cc_start: 0.8794 (m-80) cc_final: 0.8529 (m-80) REVERT: A 524 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7881 (mm) REVERT: A 554 MET cc_start: 0.7929 (mmm) cc_final: 0.7535 (mmm) REVERT: H 65 THR cc_start: 0.7982 (OUTLIER) cc_final: 0.7690 (t) REVERT: H 69 THR cc_start: 0.8277 (t) cc_final: 0.7905 (p) REVERT: L 92 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.6739 (m-80) outliers start: 22 outliers final: 13 residues processed: 109 average time/residue: 0.0695 time to fit residues: 10.1088 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 : 0.195 ------------------------------------------------------------------------------- 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: 2.9990 chunk 55 optimal weight: 0.6980 chunk 53 optimal weight: 0.0970 chunk 5 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 63 optimal weight: 0.1980 chunk 22 optimal weight: 0.3980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.149044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.128565 restraints weight = 7064.739| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.62 r_work: 0.3321 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5694 Z= 0.105 Angle : 0.498 6.331 7805 Z= 0.250 Chirality : 0.039 0.166 898 Planarity : 0.004 0.043 968 Dihedral : 5.714 57.205 819 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.40 % Allowed : 14.34 % Favored : 82.26 % 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 (0.32), residues: 746 helix: 1.67 (0.28), residues: 368 sheet: 0.70 (0.55), residues: 93 loop : -0.04 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 201 TYR 0.015 0.001 TYR A 69 PHE 0.015 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 covalent geometry : bond 0.00238 ( 5691) covalent geometry : angle 0.49677 ( 7799) SS BOND : bond 0.00329 ( 3) SS BOND : angle 1.38815 ( 6) hydrogen bonds : bond 0.03324 ( 339) hydrogen bonds : angle 4.69245 ( 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 112 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.210 Fit side-chains REVERT: A 69 TYR cc_start: 0.9165 (OUTLIER) cc_final: 0.8394 (p90) REVERT: A 282 ILE cc_start: 0.7514 (OUTLIER) cc_final: 0.7111 (mm) REVERT: A 302 TYR cc_start: 0.8657 (m-80) cc_final: 0.8404 (m-80) REVERT: A 524 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7875 (mm) REVERT: A 554 MET cc_start: 0.7855 (mmm) cc_final: 0.7408 (mmm) REVERT: H 65 THR cc_start: 0.8001 (OUTLIER) cc_final: 0.7722 (t) REVERT: L 92 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.6463 (m-80) outliers start: 18 outliers final: 9 residues processed: 106 average time/residue: 0.0647 time to fit residues: 9.1506 Evaluate side-chains 98 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 282 ILE 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 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 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: 1.9990 chunk 41 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 65 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.145616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.124879 restraints weight = 7309.452| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.64 r_work: 0.3235 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5694 Z= 0.148 Angle : 0.518 5.510 7805 Z= 0.265 Chirality : 0.041 0.149 898 Planarity : 0.004 0.041 968 Dihedral : 5.626 54.241 819 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.77 % Allowed : 13.40 % Favored : 82.83 % 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: 1.20 (0.32), residues: 746 helix: 1.58 (0.28), residues: 368 sheet: 0.68 (0.56), residues: 93 loop : -0.11 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 201 TYR 0.017 0.001 TYR A 69 PHE 0.012 0.001 PHE A 342 TRP 0.012 0.001 TRP A 470 HIS 0.002 0.001 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 5691) covalent geometry : angle 0.51640 ( 7799) SS BOND : bond 0.00361 ( 3) SS BOND : angle 1.33181 ( 6) hydrogen bonds : bond 0.03626 ( 339) hydrogen bonds : angle 4.76070 ( 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: 20 poor density : 88 time to evaluate : 0.193 Fit side-chains REVERT: A 69 TYR cc_start: 0.9256 (OUTLIER) cc_final: 0.8610 (p90) REVERT: A 282 ILE cc_start: 0.7662 (OUTLIER) cc_final: 0.7263 (mm) REVERT: A 302 TYR cc_start: 0.8815 (m-80) cc_final: 0.8594 (m-80) REVERT: A 524 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7987 (mm) REVERT: H 65 THR cc_start: 0.8111 (OUTLIER) cc_final: 0.7878 (t) REVERT: L 92 PHE cc_start: 0.8434 (OUTLIER) cc_final: 0.6404 (m-80) outliers start: 20 outliers final: 13 residues processed: 102 average time/residue: 0.0596 time to fit residues: 8.2505 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 : 0.190 ------------------------------------------------------------------------------- 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 383 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 3 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 13 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 18 optimal weight: 0.0670 chunk 32 optimal weight: 0.5980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.149614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.128934 restraints weight = 7097.647| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.65 r_work: 0.3305 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2077 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= 0.109 Angle : 0.492 7.210 7805 Z= 0.248 Chirality : 0.039 0.136 898 Planarity : 0.004 0.040 968 Dihedral : 5.222 47.564 819 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % 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: 1.34 (0.32), residues: 746 helix: 1.72 (0.28), residues: 366 sheet: 0.81 (0.56), residues: 92 loop : -0.07 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 201 TYR 0.015 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 covalent geometry : bond 0.00253 ( 5691) covalent geometry : angle 0.49154 ( 7799) SS BOND : bond 0.00344 ( 3) SS BOND : angle 1.20640 ( 6) hydrogen bonds : bond 0.03251 ( 339) hydrogen bonds : angle 4.63365 ( 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 105 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.201 Fit side-chains REVERT: A 69 TYR cc_start: 0.9209 (OUTLIER) cc_final: 0.8476 (p90) REVERT: A 282 ILE cc_start: 0.7691 (OUTLIER) cc_final: 0.7302 (mm) REVERT: A 302 TYR cc_start: 0.8687 (m-80) cc_final: 0.8437 (m-80) REVERT: A 554 MET cc_start: 0.7911 (mmm) cc_final: 0.7589 (mmm) REVERT: H 65 THR cc_start: 0.8114 (OUTLIER) cc_final: 0.7897 (t) REVERT: L 92 PHE cc_start: 0.8440 (OUTLIER) cc_final: 0.6398 (m-80) outliers start: 16 outliers final: 9 residues processed: 101 average time/residue: 0.0677 time to fit residues: 9.3242 Evaluate side-chains 97 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.198 ------------------------------------------------------------------------------- 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 383 LEU Chi-restraints excluded: chain A residue 435 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 42 optimal weight: 0.4980 chunk 56 optimal weight: 0.1980 chunk 6 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 0.0270 chunk 18 optimal weight: 5.9990 chunk 25 optimal weight: 0.0370 chunk 31 optimal weight: 0.3980 chunk 23 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.2316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.150051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.129176 restraints weight = 7185.433| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.69 r_work: 0.3352 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5694 Z= 0.092 Angle : 0.471 5.425 7805 Z= 0.239 Chirality : 0.039 0.138 898 Planarity : 0.004 0.039 968 Dihedral : 4.557 33.572 819 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.08 % Allowed : 16.04 % 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: 1.48 (0.32), residues: 746 helix: 1.80 (0.28), residues: 369 sheet: 0.87 (0.57), residues: 92 loop : -0.00 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 201 TYR 0.013 0.001 TYR A 69 PHE 0.012 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 covalent geometry : bond 0.00200 ( 5691) covalent geometry : angle 0.47056 ( 7799) SS BOND : bond 0.00298 ( 3) SS BOND : angle 0.98771 ( 6) hydrogen bonds : bond 0.03066 ( 339) hydrogen bonds : angle 4.52065 ( 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 109 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.120 Fit side-chains REVERT: A 69 TYR cc_start: 0.9103 (OUTLIER) cc_final: 0.8321 (p90) REVERT: A 282 ILE cc_start: 0.7636 (OUTLIER) cc_final: 0.7260 (mm) REVERT: A 302 TYR cc_start: 0.8597 (m-80) cc_final: 0.8367 (m-80) REVERT: A 554 MET cc_start: 0.7829 (mmm) cc_final: 0.7457 (mmm) REVERT: H 65 THR cc_start: 0.8077 (OUTLIER) cc_final: 0.7851 (t) REVERT: L 92 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.6355 (m-80) outliers start: 11 outliers final: 7 residues processed: 105 average time/residue: 0.0631 time to fit residues: 8.8092 Evaluate side-chains 102 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 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 282 ILE 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 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: 0.8980 chunk 3 optimal weight: 0.4980 chunk 61 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.146519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.125894 restraints weight = 7176.208| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.63 r_work: 0.3315 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5694 Z= 0.134 Angle : 0.513 7.194 7805 Z= 0.259 Chirality : 0.040 0.140 898 Planarity : 0.004 0.040 968 Dihedral : 4.408 32.837 819 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % 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: 1.51 (0.32), residues: 746 helix: 1.87 (0.28), residues: 361 sheet: 0.90 (0.58), residues: 92 loop : 0.00 (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 0.012 0.001 TRP A 470 HIS 0.002 0.001 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 5691) covalent geometry : angle 0.51129 ( 7799) SS BOND : bond 0.00419 ( 3) SS BOND : angle 1.51560 ( 6) hydrogen bonds : bond 0.03358 ( 339) hydrogen bonds : angle 4.59711 ( 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 103 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.126 Fit side-chains REVERT: A 69 TYR cc_start: 0.9258 (OUTLIER) cc_final: 0.8500 (p90) REVERT: A 204 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8638 (mp) REVERT: A 282 ILE cc_start: 0.7772 (OUTLIER) cc_final: 0.7400 (mm) REVERT: A 302 TYR cc_start: 0.8739 (m-80) cc_final: 0.8503 (m-80) REVERT: A 554 MET cc_start: 0.7916 (mmm) cc_final: 0.7515 (mmm) REVERT: H 69 THR cc_start: 0.8117 (t) cc_final: 0.7907 (t) REVERT: L 92 PHE cc_start: 0.8496 (OUTLIER) cc_final: 0.6546 (m-80) outliers start: 16 outliers final: 11 residues processed: 97 average time/residue: 0.0655 time to fit residues: 8.4720 Evaluate side-chains 100 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.192 ------------------------------------------------------------------------------- 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 383 LEU Chi-restraints excluded: chain A residue 435 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 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: 0.9980 chunk 56 optimal weight: 0.0870 chunk 47 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.0980 chunk 25 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.149443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.128987 restraints weight = 7103.609| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.63 r_work: 0.3283 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2323 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= 0.117 Angle : 0.494 5.458 7805 Z= 0.252 Chirality : 0.040 0.135 898 Planarity : 0.004 0.040 968 Dihedral : 4.215 32.542 819 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.64 % Allowed : 16.04 % 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: 1.56 (0.32), residues: 746 helix: 1.93 (0.28), residues: 361 sheet: 0.91 (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 0.010 0.001 PHE A 342 TRP 0.014 0.001 TRP A 470 HIS 0.001 0.001 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 5691) covalent geometry : angle 0.49258 ( 7799) SS BOND : bond 0.00320 ( 3) SS BOND : angle 1.57795 ( 6) hydrogen bonds : bond 0.03237 ( 339) hydrogen bonds : angle 4.56750 ( 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 101 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.194 Fit side-chains REVERT: A 69 TYR cc_start: 0.9228 (OUTLIER) cc_final: 0.8447 (p90) REVERT: A 282 ILE cc_start: 0.7787 (OUTLIER) cc_final: 0.7419 (mm) REVERT: A 302 TYR cc_start: 0.8705 (m-80) cc_final: 0.8466 (m-80) REVERT: A 554 MET cc_start: 0.7931 (mmm) cc_final: 0.7544 (mmm) REVERT: H 69 THR cc_start: 0.8173 (t) cc_final: 0.7837 (m) REVERT: L 92 PHE cc_start: 0.8494 (OUTLIER) cc_final: 0.6466 (m-80) outliers start: 14 outliers final: 11 residues processed: 95 average time/residue: 0.0707 time to fit residues: 9.0111 Evaluate side-chains 99 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 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 258 LEU Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 435 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 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: 0.2980 chunk 43 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.146943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.126003 restraints weight = 7203.233| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.69 r_work: 0.3312 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5694 Z= 0.121 Angle : 0.512 7.801 7805 Z= 0.257 Chirality : 0.040 0.136 898 Planarity : 0.004 0.040 968 Dihedral : 4.210 32.581 819 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.45 % Allowed : 16.23 % 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: 1.93 (0.28), residues: 361 sheet: 0.94 (0.57), residues: 92 loop : 0.02 (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 0.010 0.001 PHE A 338 TRP 0.013 0.001 TRP A 470 HIS 0.002 0.001 HIS L 35 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 5691) covalent geometry : angle 0.50995 ( 7799) SS BOND : bond 0.00325 ( 3) SS BOND : angle 1.62752 ( 6) hydrogen bonds : bond 0.03254 ( 339) hydrogen bonds : angle 4.57590 ( 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: 13 poor density : 90 time to evaluate : 0.201 Fit side-chains REVERT: A 69 TYR cc_start: 0.9220 (OUTLIER) cc_final: 0.8442 (p90) REVERT: A 282 ILE cc_start: 0.7793 (OUTLIER) cc_final: 0.7384 (mm) REVERT: A 302 TYR cc_start: 0.8743 (m-80) cc_final: 0.8459 (m-80) REVERT: A 554 MET cc_start: 0.7905 (mmm) cc_final: 0.7495 (mmm) REVERT: L 92 PHE cc_start: 0.8513 (OUTLIER) cc_final: 0.6454 (m-80) outliers start: 13 outliers final: 10 residues processed: 98 average time/residue: 0.0529 time to fit residues: 7.1798 Evaluate side-chains 102 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.176 ------------------------------------------------------------------------------- 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 383 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain H residue 20 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: 0.3980 chunk 3 optimal weight: 0.3980 chunk 8 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.146981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.126680 restraints weight = 7193.518| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.61 r_work: 0.3300 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5694 Z= 0.126 Angle : 0.512 6.667 7805 Z= 0.260 Chirality : 0.040 0.138 898 Planarity : 0.004 0.040 968 Dihedral : 4.195 32.397 819 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.87 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: 1.55 (0.32), residues: 746 helix: 1.91 (0.28), residues: 361 sheet: 0.97 (0.57), residues: 92 loop : -0.00 (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 0.010 0.001 PHE A 392 TRP 0.013 0.001 TRP A 470 HIS 0.001 0.001 HIS H 80 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 5691) covalent geometry : angle 0.51057 ( 7799) SS BOND : bond 0.00340 ( 3) SS BOND : angle 1.62930 ( 6) hydrogen bonds : bond 0.03309 ( 339) hydrogen bonds : angle 4.61593 ( 960) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1285.82 seconds wall clock time: 22 minutes 44.20 seconds (1364.20 seconds total)