Starting phenix.real_space_refine on Thu Jul 2 00:33:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wlb_66052/07_2026/9wlb_66052.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wlb_66052/07_2026/9wlb_66052.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wlb_66052/07_2026/9wlb_66052.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wlb_66052/07_2026/9wlb_66052.map" model { file = "/net/cci-nas-00/data/ceres_data/9wlb_66052/07_2026/9wlb_66052.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wlb_66052/07_2026/9wlb_66052.cif" } resolution = 3.74 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= -0.000 sd= 0.009 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 21 5.16 5 Cl 1 4.86 5 C 2919 2.51 5 N 768 2.21 5 O 860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4569 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 726 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 4, 'GLN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "D" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 911 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 3, 'TRANS': 122} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "H" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 797 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 3, 'TRANS': 115} Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 55 Chain: "R" Number of atoms: 1492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1492 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 11, 'TRANS': 182} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "L" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 642 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 91} Chain breaks: 3 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 3, 'ASP:plan': 2, 'GLU:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CL': 1} Chain breaks: 1 Time building chain proxies: 1.04, per 1000 atoms: 0.23 Number of scatterers: 4569 At special positions: 0 Unit cell: (70.85, 101.4, 105.3, 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 21 16.00 O 860 8.00 N 768 7.00 C 2919 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 89 " distance=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 101 " - pdb=" SG CYS H 106 " distance=2.03 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.03 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.03 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 488 " 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: 0.23 Conformation dependent library (CDL) restraints added in 138.0 milliseconds 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1156 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 15 sheets defined 7.5% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.553A pdb=" N SER D 31 " --> pdb=" O PRO D 28 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 32' Processing helix chain 'D' and resid 61 through 65 Processing helix chain 'D' and resid 87 through 91 removed outlier: 4.256A pdb=" N THR D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.703A pdb=" N ASP H 90 " --> pdb=" O ARG H 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 338 through 343 Processing helix chain 'R' and resid 349 through 353 removed outlier: 3.520A pdb=" N TRP R 353 " --> pdb=" O VAL R 350 " (cutoff:3.500A) Processing helix chain 'R' and resid 365 through 370 Processing helix chain 'R' and resid 405 through 410 removed outlier: 4.417A pdb=" N ARG R 408 " --> pdb=" O ASP R 405 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 34 removed outlier: 3.801A pdb=" N TYR L 33 " --> pdb=" O SER L 30 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU L 34 " --> pdb=" O SER L 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 30 through 34' Processing sheet with id=AA1, first strand: chain 'B' and resid 4 through 5 Processing sheet with id=AA2, first strand: chain 'B' and resid 10 through 11 Processing sheet with id=AA3, first strand: chain 'B' and resid 19 through 22 Processing sheet with id=AA4, first strand: chain 'B' and resid 46 through 47 removed outlier: 3.512A pdb=" N GLN B 91 " --> pdb=" O THR B 97 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'D' and resid 10 through 11 removed outlier: 6.881A pdb=" N GLU D 10 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TRP D 36 " --> pdb=" O GLY D 49 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 10 through 11 removed outlier: 6.881A pdb=" N GLU D 10 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N CYS D 96 " --> pdb=" O TRP D 117 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N TRP D 117 " --> pdb=" O CYS D 96 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG D 98 " --> pdb=" O ASP D 115 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA9, first strand: chain 'H' and resid 38 through 39 Processing sheet with id=AB1, first strand: chain 'H' and resid 97 through 98 Processing sheet with id=AB2, first strand: chain 'R' and resid 354 through 358 removed outlier: 3.736A pdb=" N SER R 399 " --> pdb=" O ASN R 354 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA R 397 " --> pdb=" O LYS R 356 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR R 396 " --> pdb=" O SER R 514 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AB4, first strand: chain 'R' and resid 473 through 474 removed outlier: 3.515A pdb=" N TYR R 489 " --> pdb=" O TYR R 473 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.747A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 45 through 47 117 hydrogen bonds defined for protein. 243 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: 0.42 Time building geometry restraints manager: 0.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 773 1.32 - 1.45: 1377 1.45 - 1.57: 2510 1.57 - 1.69: 1 1.69 - 1.81: 25 Bond restraints: 4686 Sorted by residual: bond pdb=" N PRO R 426 " pdb=" CD PRO R 426 " ideal model delta sigma weight residual 1.473 1.542 -0.069 1.40e-02 5.10e+03 2.46e+01 bond pdb=" N PRO H 99 " pdb=" CD PRO H 99 " ideal model delta sigma weight residual 1.473 1.535 -0.062 1.40e-02 5.10e+03 1.98e+01 bond pdb=" CG ASP D 99 " pdb=" OD2 ASP D 99 " ideal model delta sigma weight residual 1.249 1.199 0.050 1.90e-02 2.77e+03 6.95e+00 bond pdb=" CA TYR B 50 " pdb=" C TYR B 50 " ideal model delta sigma weight residual 1.523 1.491 0.032 1.30e-02 5.92e+03 6.08e+00 bond pdb=" N ARG B 46 " pdb=" CA ARG B 46 " ideal model delta sigma weight residual 1.455 1.484 -0.030 1.26e-02 6.30e+03 5.51e+00 ... (remaining 4681 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 6181 1.59 - 3.18: 197 3.18 - 4.78: 29 4.78 - 6.37: 5 6.37 - 7.96: 5 Bond angle restraints: 6417 Sorted by residual: angle pdb=" CA PRO B 81 " pdb=" N PRO B 81 " pdb=" CD PRO B 81 " ideal model delta sigma weight residual 112.00 105.64 6.36 1.40e+00 5.10e-01 2.06e+01 angle pdb=" CA ALA B 52 " pdb=" C ALA B 52 " pdb=" O ALA B 52 " ideal model delta sigma weight residual 120.42 115.74 4.68 1.06e+00 8.90e-01 1.95e+01 angle pdb=" CB ARG H 72 " pdb=" CG ARG H 72 " pdb=" CD ARG H 72 " ideal model delta sigma weight residual 111.30 119.26 -7.96 2.30e+00 1.89e-01 1.20e+01 angle pdb=" CG ARG H 72 " pdb=" CD ARG H 72 " pdb=" NE ARG H 72 " ideal model delta sigma weight residual 112.00 119.27 -7.27 2.20e+00 2.07e-01 1.09e+01 angle pdb=" CA ARG D 98 " pdb=" C ARG D 98 " pdb=" N ASP D 99 " ideal model delta sigma weight residual 115.85 119.89 -4.04 1.29e+00 6.01e-01 9.82e+00 ... (remaining 6412 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.11: 2321 16.11 - 32.23: 255 32.23 - 48.34: 72 48.34 - 64.46: 17 64.46 - 80.57: 4 Dihedral angle restraints: 2669 sinusoidal: 840 harmonic: 1829 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 93.00 145.83 -52.83 1 1.00e+01 1.00e-02 3.80e+01 dihedral pdb=" CB CYS R 379 " pdb=" SG CYS R 379 " pdb=" SG CYS R 432 " pdb=" CB CYS R 432 " ideal model delta sinusoidal sigma weight residual -86.00 -45.72 -40.28 1 1.00e+01 1.00e-02 2.28e+01 dihedral pdb=" CA LEU H 83 " pdb=" C LEU H 83 " pdb=" N SER H 84 " pdb=" CA SER H 84 " ideal model delta harmonic sigma weight residual 180.00 160.60 19.40 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 2666 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 454 0.035 - 0.070: 169 0.070 - 0.105: 67 0.105 - 0.141: 24 0.141 - 0.176: 1 Chirality restraints: 715 Sorted by residual: chirality pdb=" CA ILE D 111 " pdb=" N ILE D 111 " pdb=" C ILE D 111 " pdb=" CB ILE D 111 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.71e-01 chirality pdb=" CA VAL H 93 " pdb=" N VAL H 93 " pdb=" C VAL H 93 " pdb=" CB VAL H 93 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA ILE L 49 " pdb=" N ILE L 49 " pdb=" C ILE L 49 " pdb=" CB ILE L 49 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 ... (remaining 712 not shown) Planarity restraints: 832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 105 " -0.024 2.00e-02 2.50e+03 2.36e-02 1.39e+01 pdb=" CG TRP D 105 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP D 105 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP D 105 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 105 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 105 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 105 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 105 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 105 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP D 105 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 454 " 0.284 9.50e-02 1.11e+02 1.27e-01 9.93e+00 pdb=" NE ARG R 454 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG R 454 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG R 454 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG R 454 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 80 " -0.040 5.00e-02 4.00e+02 5.86e-02 5.49e+00 pdb=" N PRO B 81 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO B 81 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 81 " -0.033 5.00e-02 4.00e+02 ... (remaining 829 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 771 2.76 - 3.30: 4179 3.30 - 3.83: 7088 3.83 - 4.37: 8088 4.37 - 4.90: 14550 Nonbonded interactions: 34676 Sorted by model distance: nonbonded pdb=" OD1 ASP R 442 " pdb=" OH TYR R 451 " model vdw 2.227 3.040 nonbonded pdb=" O THR R 470 " pdb=" OG1 THR R 470 " model vdw 2.311 3.040 nonbonded pdb=" OG1 THR D 91 " pdb=" O VAL D 123 " model vdw 2.314 3.040 nonbonded pdb=" O THR H 117 " pdb=" OG1 THR H 117 " model vdw 2.357 3.040 nonbonded pdb=" NE1 TRP D 47 " pdb=" O GLY D 49 " model vdw 2.370 3.120 ... (remaining 34671 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 29.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.710 Find NCS groups from input model: 0.010 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:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 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 0.088 4694 Z= 0.282 Angle : 0.689 7.962 6433 Z= 0.398 Chirality : 0.046 0.176 715 Planarity : 0.007 0.127 832 Dihedral : 15.096 80.569 1489 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 0.24 % Allowed : 26.76 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -2.49 (0.35), residues: 627 helix: -3.55 (1.33), residues: 12 sheet: -1.67 (0.39), residues: 204 loop : -1.63 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG H 72 TYR 0.027 0.002 TYR D 100 PHE 0.012 0.001 PHE R 392 TRP 0.063 0.002 TRP D 105 HIS 0.004 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.28 ( 4686) covalent geometry : angle 0.68672 / 0.40 ( 6417) SS BOND : bond 0.00534 / 0.26 ( 8) SS BOND : angle 1.31216 / 0.70 ( 16) hydrogen bonds : bond 0.29900 / 19.90 ( 113) hydrogen bonds : angle 11.82763 / 8.10 ( 243) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 0.141 Fit side-chains REVERT: R 449 TYR cc_start: 0.9087 (m-10) cc_final: 0.8792 (m-80) outliers start: 1 outliers final: 1 residues processed: 99 average time/residue: 0.0499 time to fit residues: 6.7400 Evaluate side-chains 85 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 82 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.0980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 31 optimal weight: 0.0980 chunk 25 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3491 r_free = 0.3491 target = 0.118665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.101137 restraints weight = 8867.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.103947 restraints weight = 5226.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.105956 restraints weight = 3669.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.107337 restraints weight = 2839.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.108301 restraints weight = 2348.921| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3349 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3349 r_free = 0.3349 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3349 r_free = 0.3349 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3349 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 4694 Z= 0.123 Angle : 0.595 15.053 6433 Z= 0.309 Chirality : 0.046 0.319 715 Planarity : 0.005 0.050 832 Dihedral : 4.530 28.321 693 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 4.38 % Allowed : 29.68 % Favored : 65.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -2.26 (0.35), residues: 627 helix: -3.15 (1.59), residues: 12 sheet: -1.43 (0.39), residues: 203 loop : -1.52 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 72 TYR 0.014 0.001 TYR R 369 PHE 0.012 0.001 PHE L 72 TRP 0.017 0.001 TRP D 105 HIS 0.001 0.000 HIS R 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 ( 4686) covalent geometry : angle 0.58693 / 0.31 ( 6417) SS BOND : bond 0.00673 / 0.33 ( 8) SS BOND : angle 2.02666 / 1.25 ( 16) hydrogen bonds : bond 0.03925 / 2.68 ( 113) hydrogen bonds : angle 7.96546 / 5.57 ( 243) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: R 449 TYR cc_start: 0.9057 (m-10) cc_final: 0.8754 (m-80) outliers start: 18 outliers final: 12 residues processed: 102 average time/residue: 0.0583 time to fit residues: 7.8167 Evaluate side-chains 88 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 478 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 102 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 40 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 26 optimal weight: 0.0050 chunk 54 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 56 optimal weight: 0.5980 overall best weight: 1.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 65 GLN R 450 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.112727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.094766 restraints weight = 8895.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.097447 restraints weight = 5407.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.099345 restraints weight = 3880.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.100676 restraints weight = 3063.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.101487 restraints weight = 2574.923| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3243 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3243 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 4694 Z= 0.271 Angle : 0.647 9.872 6433 Z= 0.346 Chirality : 0.048 0.281 715 Planarity : 0.005 0.051 832 Dihedral : 4.970 19.846 690 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.80 % Favored : 88.20 % Rotamer: Outliers : 7.06 % Allowed : 26.52 % Favored : 66.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -2.45 (0.35), residues: 627 helix: -3.35 (1.12), residues: 20 sheet: -1.59 (0.38), residues: 207 loop : -1.57 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 72 TYR 0.014 0.002 TYR R 453 PHE 0.016 0.002 PHE R 486 TRP 0.016 0.002 TRP D 105 HIS 0.002 0.001 HIS H 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00626 / 0.27 ( 4686) covalent geometry : angle 0.64252 / 0.34 ( 6417) SS BOND : bond 0.01250 / 0.61 ( 8) SS BOND : angle 1.58010 / 0.94 ( 16) hydrogen bonds : bond 0.04330 / 2.87 ( 113) hydrogen bonds : angle 7.50626 / 5.24 ( 243) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 80 time to evaluate : 0.107 Fit side-chains REVERT: R 449 TYR cc_start: 0.9161 (m-10) cc_final: 0.8830 (m-80) REVERT: R 493 GLN cc_start: 0.8441 (tm-30) cc_final: 0.7689 (tm-30) outliers start: 29 outliers final: 19 residues processed: 99 average time/residue: 0.0392 time to fit residues: 5.4037 Evaluate side-chains 94 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain R residue 382 VAL Chi-restraints excluded: chain R residue 401 VAL Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 478 THR Chi-restraints excluded: chain R residue 492 LEU Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 102 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 44 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 33 optimal weight: 0.3980 chunk 2 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 92 HIS H 65 GLN R 450 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.115963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.098657 restraints weight = 8849.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.101318 restraints weight = 5370.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.103153 restraints weight = 3844.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.104495 restraints weight = 3040.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.105238 restraints weight = 2546.403| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3298 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3298 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4694 Z= 0.148 Angle : 0.567 10.342 6433 Z= 0.295 Chirality : 0.045 0.217 715 Planarity : 0.004 0.051 832 Dihedral : 4.593 19.135 690 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 4.87 % Allowed : 28.47 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -2.41 (0.34), residues: 627 helix: -3.29 (1.09), residues: 20 sheet: -1.51 (0.38), residues: 206 loop : -1.58 (0.32), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 72 TYR 0.018 0.001 TYR D 54 PHE 0.013 0.001 PHE R 486 TRP 0.014 0.001 TRP D 105 HIS 0.001 0.000 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 4686) covalent geometry : angle 0.56528 / 0.29 ( 6417) SS BOND : bond 0.00790 / 0.39 ( 8) SS BOND : angle 1.02024 / 0.60 ( 16) hydrogen bonds : bond 0.03388 / 2.30 ( 113) hydrogen bonds : angle 7.07622 / 4.94 ( 243) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: R 449 TYR cc_start: 0.9107 (m-10) cc_final: 0.8772 (m-80) outliers start: 20 outliers final: 15 residues processed: 94 average time/residue: 0.0415 time to fit residues: 5.5636 Evaluate side-chains 89 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain R residue 401 VAL Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 478 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 102 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 9 optimal weight: 0.8980 chunk 53 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 54 optimal weight: 0.8980 chunk 40 optimal weight: 0.2980 chunk 3 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 33 optimal weight: 0.0970 chunk 14 optimal weight: 0.0030 chunk 32 optimal weight: 0.0470 overall best weight: 0.2686 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 65 GLN R 450 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.119622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.102260 restraints weight = 8697.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.105135 restraints weight = 5096.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.107134 restraints weight = 3559.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.108577 restraints weight = 2754.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.109538 restraints weight = 2272.010| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3365 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3365 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4694 Z= 0.094 Angle : 0.534 10.207 6433 Z= 0.271 Chirality : 0.044 0.150 715 Planarity : 0.004 0.051 832 Dihedral : 4.163 17.905 690 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 4.38 % Allowed : 30.41 % Favored : 65.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -2.09 (0.35), residues: 627 helix: -3.21 (1.53), residues: 12 sheet: -1.30 (0.38), residues: 206 loop : -1.40 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 72 TYR 0.014 0.001 TYR D 54 PHE 0.009 0.001 PHE L 72 TRP 0.012 0.001 TRP D 47 HIS 0.002 0.000 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.09 ( 4686) covalent geometry : angle 0.53250 / 0.27 ( 6417) SS BOND : bond 0.00596 / 0.29 ( 8) SS BOND : angle 0.89185 / 0.56 ( 16) hydrogen bonds : bond 0.02952 / 2.05 ( 113) hydrogen bonds : angle 6.75986 / 4.71 ( 243) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.117 Fit side-chains revert: symmetry clash REVERT: D 17 SER cc_start: 0.8133 (m) cc_final: 0.7856 (m) REVERT: R 449 TYR cc_start: 0.9086 (m-10) cc_final: 0.8846 (m-80) outliers start: 18 outliers final: 10 residues processed: 101 average time/residue: 0.0476 time to fit residues: 6.7397 Evaluate side-chains 90 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain R residue 382 VAL Chi-restraints excluded: chain R residue 401 VAL Chi-restraints excluded: chain R residue 478 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 102 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 47 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 27 optimal weight: 0.2980 chunk 53 optimal weight: 8.9990 chunk 32 optimal weight: 0.0970 chunk 38 optimal weight: 8.9990 chunk 8 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 65 GLN R 450 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.118106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.100479 restraints weight = 8878.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.103333 restraints weight = 5246.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.105293 restraints weight = 3686.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.106633 restraints weight = 2868.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.107536 restraints weight = 2400.887| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3331 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4694 Z= 0.127 Angle : 0.543 9.163 6433 Z= 0.279 Chirality : 0.043 0.151 715 Planarity : 0.004 0.051 832 Dihedral : 4.213 18.829 690 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 4.38 % Allowed : 30.66 % Favored : 64.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -2.06 (0.34), residues: 627 helix: -3.14 (1.58), residues: 12 sheet: -1.27 (0.38), residues: 206 loop : -1.38 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 72 TYR 0.013 0.001 TYR R 508 PHE 0.020 0.001 PHE R 486 TRP 0.010 0.001 TRP D 105 HIS 0.003 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 4686) covalent geometry : angle 0.54156 / 0.28 ( 6417) SS BOND : bond 0.00636 / 0.31 ( 8) SS BOND : angle 1.03976 / 0.66 ( 16) hydrogen bonds : bond 0.02998 / 2.02 ( 113) hydrogen bonds : angle 6.60716 / 4.62 ( 243) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.173 Fit side-chains revert: symmetry clash REVERT: R 449 TYR cc_start: 0.9098 (m-10) cc_final: 0.8753 (m-80) REVERT: R 493 GLN cc_start: 0.8399 (tm-30) cc_final: 0.7690 (tm-30) outliers start: 18 outliers final: 16 residues processed: 92 average time/residue: 0.0392 time to fit residues: 5.1368 Evaluate side-chains 96 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain R residue 382 VAL Chi-restraints excluded: chain R residue 401 VAL Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 478 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 102 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 43 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 65 GLN R 450 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.115307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.097539 restraints weight = 8929.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.100293 restraints weight = 5353.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.102249 restraints weight = 3809.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.103615 restraints weight = 2983.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.104570 restraints weight = 2489.037| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3291 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.3291 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4694 Z= 0.190 Angle : 0.574 8.983 6433 Z= 0.298 Chirality : 0.044 0.169 715 Planarity : 0.004 0.050 832 Dihedral : 4.510 19.856 690 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 5.35 % Allowed : 30.41 % Favored : 64.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -2.09 (0.35), residues: 627 helix: -2.99 (1.72), residues: 12 sheet: -1.30 (0.38), residues: 203 loop : -1.41 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 72 TYR 0.023 0.002 TYR D 54 PHE 0.015 0.001 PHE R 486 TRP 0.015 0.001 TRP D 105 HIS 0.004 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 ( 4686) covalent geometry : angle 0.57161 / 0.30 ( 6417) SS BOND : bond 0.00706 / 0.34 ( 8) SS BOND : angle 1.27759 / 0.81 ( 16) hydrogen bonds : bond 0.03378 / 2.25 ( 113) hydrogen bonds : angle 6.66188 / 4.64 ( 243) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.107 Fit side-chains REVERT: R 449 TYR cc_start: 0.9141 (m-10) cc_final: 0.8805 (m-80) REVERT: R 493 GLN cc_start: 0.8459 (tm-30) cc_final: 0.7723 (tm-30) outliers start: 22 outliers final: 19 residues processed: 95 average time/residue: 0.0383 time to fit residues: 5.0451 Evaluate side-chains 97 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain R residue 382 VAL Chi-restraints excluded: chain R residue 401 VAL Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 478 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 102 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 35 optimal weight: 0.0980 chunk 47 optimal weight: 0.3980 chunk 21 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 5 optimal weight: 0.2980 chunk 13 optimal weight: 0.8980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 450 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.119177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.101674 restraints weight = 8915.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.104579 restraints weight = 5238.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.106594 restraints weight = 3651.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.107998 restraints weight = 2817.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.108912 restraints weight = 2334.231| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3355 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3355 r_free = 0.3355 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3355 r_free = 0.3355 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3355 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 4694 Z= 0.106 Angle : 0.546 10.905 6433 Z= 0.274 Chirality : 0.043 0.135 715 Planarity : 0.004 0.050 832 Dihedral : 4.120 18.028 690 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 4.38 % Allowed : 31.39 % Favored : 64.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -1.98 (0.35), residues: 627 helix: -3.19 (1.54), residues: 12 sheet: -1.16 (0.38), residues: 205 loop : -1.36 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 72 TYR 0.023 0.001 TYR D 54 PHE 0.009 0.001 PHE L 72 TRP 0.013 0.001 TRP D 105 HIS 0.002 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 4686) covalent geometry : angle 0.54409 / 0.27 ( 6417) SS BOND : bond 0.00596 / 0.29 ( 8) SS BOND : angle 1.07631 / 0.69 ( 16) hydrogen bonds : bond 0.02897 / 1.99 ( 113) hydrogen bonds : angle 6.40660 / 4.46 ( 243) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: R 449 TYR cc_start: 0.9113 (m-10) cc_final: 0.8770 (m-80) REVERT: R 493 GLN cc_start: 0.8358 (tm-30) cc_final: 0.7601 (tm-30) outliers start: 18 outliers final: 16 residues processed: 92 average time/residue: 0.0368 time to fit residues: 4.9324 Evaluate side-chains 90 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain R residue 382 VAL Chi-restraints excluded: chain R residue 401 VAL Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 478 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 102 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 25 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 34 optimal weight: 0.1980 chunk 13 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 90 GLN H 65 GLN R 450 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.117165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.099708 restraints weight = 8729.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.102480 restraints weight = 5191.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.104420 restraints weight = 3665.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.105813 restraints weight = 2858.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.106609 restraints weight = 2373.501| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3320 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3320 r_free = 0.3320 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3320 r_free = 0.3320 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3320 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4694 Z= 0.143 Angle : 0.562 11.041 6433 Z= 0.284 Chirality : 0.044 0.149 715 Planarity : 0.004 0.051 832 Dihedral : 4.291 19.292 690 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 5.11 % Allowed : 30.90 % Favored : 63.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -1.99 (0.34), residues: 627 helix: -3.18 (1.56), residues: 12 sheet: -1.19 (0.38), residues: 205 loop : -1.35 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 72 TYR 0.022 0.001 TYR D 54 PHE 0.010 0.001 PHE R 486 TRP 0.015 0.001 TRP D 105 HIS 0.004 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 4686) covalent geometry : angle 0.55998 / 0.28 ( 6417) SS BOND : bond 0.00646 / 0.31 ( 8) SS BOND : angle 1.16546 / 0.74 ( 16) hydrogen bonds : bond 0.03118 / 2.10 ( 113) hydrogen bonds : angle 6.40613 / 4.46 ( 243) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.177 Fit side-chains REVERT: R 449 TYR cc_start: 0.9118 (m-10) cc_final: 0.8760 (m-80) REVERT: R 493 GLN cc_start: 0.8420 (tm-30) cc_final: 0.7627 (tm-30) outliers start: 21 outliers final: 18 residues processed: 91 average time/residue: 0.0380 time to fit residues: 4.9776 Evaluate side-chains 92 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain R residue 382 VAL Chi-restraints excluded: chain R residue 401 VAL Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 478 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 102 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 0.0060 chunk 44 optimal weight: 0.1980 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 32 optimal weight: 0.4980 chunk 17 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 450 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.119114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.101525 restraints weight = 8799.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.104392 restraints weight = 5219.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.106396 restraints weight = 3664.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.107840 restraints weight = 2849.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.108852 restraints weight = 2350.809| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3357 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3357 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4694 Z= 0.114 Angle : 0.549 10.787 6433 Z= 0.278 Chirality : 0.043 0.135 715 Planarity : 0.004 0.050 832 Dihedral : 4.147 18.894 690 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 4.38 % Allowed : 31.39 % Favored : 64.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -2.00 (0.34), residues: 627 helix: -3.26 (1.05), residues: 20 sheet: -1.12 (0.38), residues: 205 loop : -1.35 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 72 TYR 0.010 0.001 TYR R 369 PHE 0.009 0.001 PHE L 72 TRP 0.023 0.001 TRP D 105 HIS 0.003 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 ( 4686) covalent geometry : angle 0.54727 / 0.28 ( 6417) SS BOND : bond 0.00600 / 0.29 ( 8) SS BOND : angle 1.10143 / 0.71 ( 16) hydrogen bonds : bond 0.02950 / 1.99 ( 113) hydrogen bonds : angle 6.31207 / 4.39 ( 243) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.136 Fit side-chains revert: symmetry clash REVERT: R 449 TYR cc_start: 0.9096 (m-10) cc_final: 0.8734 (m-80) REVERT: R 493 GLN cc_start: 0.8401 (tm-30) cc_final: 0.7586 (tm-30) outliers start: 18 outliers final: 18 residues processed: 89 average time/residue: 0.0348 time to fit residues: 4.4473 Evaluate side-chains 93 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain R residue 382 VAL Chi-restraints excluded: chain R residue 401 VAL Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 478 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 102 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 17 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 38 optimal weight: 0.0070 chunk 22 optimal weight: 3.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 450 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.118559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.100999 restraints weight = 8794.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.103790 restraints weight = 5242.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.105727 restraints weight = 3706.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.106826 restraints weight = 2898.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.108024 restraints weight = 2466.702| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3341 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3341 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4694 Z= 0.125 Angle : 0.550 10.483 6433 Z= 0.278 Chirality : 0.043 0.140 715 Planarity : 0.004 0.051 832 Dihedral : 4.165 19.356 690 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 4.38 % Allowed : 31.39 % Favored : 64.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -1.97 (0.34), residues: 627 helix: -3.28 (1.05), residues: 20 sheet: -1.11 (0.38), residues: 205 loop : -1.32 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 72 TYR 0.015 0.001 TYR R 508 PHE 0.009 0.001 PHE R 486 TRP 0.025 0.001 TRP D 105 HIS 0.003 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 ( 4686) covalent geometry : angle 0.54769 / 0.28 ( 6417) SS BOND : bond 0.00611 / 0.30 ( 8) SS BOND : angle 1.12874 / 0.72 ( 16) hydrogen bonds : bond 0.02980 / 1.99 ( 113) hydrogen bonds : angle 6.26710 / 4.36 ( 243) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1339.41 seconds wall clock time: 23 minutes 47.99 seconds (1427.99 seconds total)