Starting phenix.real_space_refine on Fri Jul 3 04:15:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9t0c_55395/07_2026/9t0c_55395.cif Found real_map, /net/cci-nas-00/data/ceres_data/9t0c_55395/07_2026/9t0c_55395.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9t0c_55395/07_2026/9t0c_55395.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9t0c_55395/07_2026/9t0c_55395.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9t0c_55395/07_2026/9t0c_55395.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9t0c_55395/07_2026/9t0c_55395.map" } resolution = 4.5 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= 0.011 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 26 5.16 5 C 3867 2.51 5 N 1026 2.21 5 O 1120 1.98 5 H 5565 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11604 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 7271 Classifications: {'peptide': 514} Link IDs: {'PTRANS': 17, 'TRANS': 496} Chain breaks: 19 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 404 Unresolved non-hydrogen angles: 514 Unresolved non-hydrogen dihedrals: 329 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'ASN:plan1': 8, 'GLN:plan1': 4, 'TYR:plan': 5, 'ASP:plan': 4, 'GLU:plan': 11, 'HIS:plan': 2, 'PHE:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 198 Chain: "B" Number of atoms: 4333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 4333 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 16, 'TRANS': 290} Chain breaks: 11 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 138 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'PHE:plan': 4, 'GLU:plan': 5, 'ASP:plan': 2, 'GLN:plan1': 1, 'TYR:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 73 Time building chain proxies: 1.90, per 1000 atoms: 0.16 Number of scatterers: 11604 At special positions: 0 Unit cell: (76.692, 93.324, 154.308, 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) S 26 16.00 O 1120 8.00 N 1026 7.00 C 3867 6.00 H 5565 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.00 Conformation dependent library (CDL) restraints added in 258.4 milliseconds 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1566 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 10 sheets defined 7.1% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 592 through 602 removed outlier: 3.837A pdb=" N PHE A 602 " --> pdb=" O ILE A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 751 No H-bonds generated for 'chain 'A' and resid 748 through 751' Processing helix chain 'A' and resid 894 through 904 removed outlier: 4.460A pdb=" N CYS A 904 " --> pdb=" O CYS A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1053 removed outlier: 3.639A pdb=" N ILE A1053 " --> pdb=" O ARG A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1234 through 1244 Processing helix chain 'A' and resid 1321 through 1333 Proline residue: A1332 - end of helix Processing helix chain 'B' and resid 443 through 446 No H-bonds generated for 'chain 'B' and resid 443 through 446' Processing sheet with id=A, first strand: chain 'A' and resid 742 through 745 removed outlier: 3.876A pdb=" N ILE A 742 " --> pdb=" O SER A 791 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE A 793 " --> pdb=" O ILE A 742 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR A 829 " --> pdb=" O VAL A 806 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY A 863 " --> pdb=" O LEU A 830 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU A 832 " --> pdb=" O ALA A 861 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ALA A 861 " --> pdb=" O LEU A 832 " (cutoff:3.500A) Processing sheet with id=B, first strand: chain 'A' and resid 868 through 870 removed outlier: 4.011A pdb=" N ASN A 869 " --> pdb=" O LYS A 884 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS A 884 " --> pdb=" O ASN A 869 " (cutoff:3.500A) No H-bonds generated for sheet with id=B Processing sheet with id=C, first strand: chain 'A' and resid 888 through 893 Processing sheet with id=D, first strand: chain 'A' and resid 1271 through 1273 removed outlier: 3.608A pdb=" N ILE A1306 " --> pdb=" O LEU A1273 " (cutoff:3.500A) Processing sheet with id=E, first strand: chain 'B' and resid 59 through 61 removed outlier: 3.782A pdb=" N LEU B 59 " --> pdb=" O ILE B 78 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE B 78 " --> pdb=" O LEU B 59 " (cutoff:3.500A) Processing sheet with id=F, first strand: chain 'B' and resid 98 through 100 Processing sheet with id=G, first strand: chain 'B' and resid 270 through 272 removed outlier: 3.667A pdb=" N ILE B 270 " --> pdb=" O PHE B 284 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE B 284 " --> pdb=" O ILE B 270 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL B 272 " --> pdb=" O TYR B 282 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TYR B 282 " --> pdb=" O VAL B 272 " (cutoff:3.500A) No H-bonds generated for sheet with id=G Processing sheet with id=H, first strand: chain 'B' and resid 429 through 431 removed outlier: 3.962A pdb=" N VAL B 465 " --> pdb=" O MET B 481 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N MET B 481 " --> pdb=" O VAL B 465 " (cutoff:3.500A) Processing sheet with id=I, first strand: chain 'B' and resid 434 through 436 Processing sheet with id=J, first strand: chain 'B' and resid 226 through 231 removed outlier: 3.897A pdb=" N MET B 239 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASN B 231 " --> pdb=" O PRO B 237 " (cutoff:3.500A) 71 hydrogen bonds defined for protein. 156 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: 2.08 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5553 1.03 - 1.23: 14 1.23 - 1.42: 2494 1.42 - 1.62: 3584 1.62 - 1.81: 40 Bond restraints: 11685 Sorted by residual: bond pdb=" N ILE A 933 " pdb=" CA ILE A 933 " ideal model delta sigma weight residual 1.460 1.491 -0.032 1.25e-02 6.40e+03 6.36e+00 bond pdb=" N ILE A 933 " pdb=" H ILE A 933 " ideal model delta sigma weight residual 0.860 0.902 -0.042 2.00e-02 2.50e+03 4.50e+00 bond pdb=" N ASP A 928 " pdb=" H ASP A 928 " ideal model delta sigma weight residual 0.860 0.902 -0.042 2.00e-02 2.50e+03 4.43e+00 bond pdb=" C ASP A 928 " pdb=" N VAL A 929 " ideal model delta sigma weight residual 1.332 1.310 0.022 1.36e-02 5.41e+03 2.57e+00 bond pdb=" C ASP A 928 " pdb=" O ASP A 928 " ideal model delta sigma weight residual 1.233 1.217 0.017 1.28e-02 6.10e+03 1.73e+00 ... (remaining 11680 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 19931 1.17 - 2.34: 983 2.34 - 3.51: 86 3.51 - 4.68: 15 4.68 - 5.85: 6 Bond angle restraints: 21021 Sorted by residual: angle pdb=" CA ASP A 928 " pdb=" C ASP A 928 " pdb=" O ASP A 928 " ideal model delta sigma weight residual 121.82 117.02 4.80 1.21e+00 6.83e-01 1.58e+01 angle pdb=" CA ASP A 928 " pdb=" CB ASP A 928 " pdb=" CG ASP A 928 " ideal model delta sigma weight residual 112.60 116.49 -3.89 1.00e+00 1.00e+00 1.51e+01 angle pdb=" N ASP A 928 " pdb=" CA ASP A 928 " pdb=" C ASP A 928 " ideal model delta sigma weight residual 110.36 105.01 5.35 1.55e+00 4.16e-01 1.19e+01 angle pdb=" N ILE B 64 " pdb=" CA ILE B 64 " pdb=" C ILE B 64 " ideal model delta sigma weight residual 113.71 110.44 3.27 9.50e-01 1.11e+00 1.19e+01 angle pdb=" N GLN B 110 " pdb=" CA GLN B 110 " pdb=" CB GLN B 110 " ideal model delta sigma weight residual 114.17 110.39 3.78 1.14e+00 7.69e-01 1.10e+01 ... (remaining 21016 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 5050 17.53 - 35.07: 398 35.07 - 52.60: 94 52.60 - 70.13: 22 70.13 - 87.66: 4 Dihedral angle restraints: 5568 sinusoidal: 2832 harmonic: 2736 Sorted by residual: dihedral pdb=" CA ILE B 118 " pdb=" C ILE B 118 " pdb=" N ASN B 119 " pdb=" CA ASN B 119 " ideal model delta harmonic sigma weight residual 180.00 150.21 29.79 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" CA GLU A1218 " pdb=" C GLU A1218 " pdb=" N LEU A1219 " pdb=" CA LEU A1219 " ideal model delta harmonic sigma weight residual 180.00 -161.69 -18.31 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA LEU B 148 " pdb=" C LEU B 148 " pdb=" N VAL B 149 " pdb=" CA VAL B 149 " ideal model delta harmonic sigma weight residual -180.00 -161.95 -18.05 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 5565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 590 0.030 - 0.060: 223 0.060 - 0.089: 80 0.089 - 0.119: 69 0.119 - 0.149: 27 Chirality restraints: 989 Sorted by residual: chirality pdb=" CA ILE A 805 " pdb=" N ILE A 805 " pdb=" C ILE A 805 " pdb=" CB ILE A 805 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.55e-01 chirality pdb=" CA ILE B 491 " pdb=" N ILE B 491 " pdb=" C ILE B 491 " pdb=" CB ILE B 491 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" CA ILE A 742 " pdb=" N ILE A 742 " pdb=" C ILE A 742 " pdb=" CB ILE A 742 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.19e-01 ... (remaining 986 not shown) Planarity restraints: 1808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 928 " 0.026 2.00e-02 2.50e+03 4.79e-02 2.29e+01 pdb=" N VAL A 929 " -0.082 2.00e-02 2.50e+03 pdb=" CA VAL A 929 " 0.022 2.00e-02 2.50e+03 pdb=" H VAL A 929 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 748 " 0.021 2.00e-02 2.50e+03 1.24e-02 6.10e+00 pdb=" CG TRP A 748 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP A 748 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP A 748 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 748 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 748 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 748 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 748 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 748 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 748 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 TRP A 748 " 0.007 2.00e-02 2.50e+03 pdb=" HE1 TRP A 748 " 0.001 2.00e-02 2.50e+03 pdb=" HE3 TRP A 748 " -0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 748 " 0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 748 " -0.000 2.00e-02 2.50e+03 pdb=" HH2 TRP A 748 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 933 " 0.010 2.00e-02 2.50e+03 1.89e-02 3.59e+00 pdb=" N ASP A 934 " -0.033 2.00e-02 2.50e+03 pdb=" CA ASP A 934 " 0.008 2.00e-02 2.50e+03 pdb=" H ASP A 934 " 0.014 2.00e-02 2.50e+03 ... (remaining 1805 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.40: 4838 2.40 - 2.95: 24582 2.95 - 3.50: 24051 3.50 - 4.05: 32201 4.05 - 4.60: 45972 Nonbonded interactions: 131644 Sorted by model distance: nonbonded pdb=" H ASN B 119 " pdb=" H THR B 120 " model vdw 1.849 2.100 nonbonded pdb=" H TYR A 745 " pdb=" HZ3 TRP A 748 " model vdw 1.875 2.100 nonbonded pdb=" HB3 ARG B 292 " pdb=" HE2 TYR B 294 " model vdw 1.889 2.270 nonbonded pdb=" HZ2 LYS A1047 " pdb="HH22 ARG A1050 " model vdw 1.894 2.100 nonbonded pdb="HH22 ARG A1209 " pdb=" H PHE A1213 " model vdw 1.898 2.100 ... (remaining 131639 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 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: 9.080 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: 0.050 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.050 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 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 : 0.002 0.032 6120 Z= 0.125 Angle : 0.581 5.350 8276 Z= 0.325 Chirality : 0.047 0.149 989 Planarity : 0.003 0.047 1050 Dihedral : 13.865 87.665 2103 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.49 % Favored : 88.38 % Rotamer: Outliers : 0.34 % Allowed : 0.17 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.73 (0.28), residues: 757 helix: -2.44 (0.59), residues: 60 sheet: -2.84 (0.31), residues: 262 loop : -3.56 (0.26), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1050 TYR 0.021 0.001 TYR A 745 PHE 0.009 0.001 PHE A1185 TRP 0.041 0.003 TRP A 748 HIS 0.003 0.001 HIS B 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 ( 6120) covalent geometry : angle 0.58112 / 0.33 ( 8276) hydrogen bonds : bond 0.09457 / 7.79 ( 71) hydrogen bonds : angle 6.00390 / 4.20 ( 156) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 542 is missing expected H atoms. Skipping. Residue ILE 543 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue THR 545 is missing expected H atoms. Skipping. Residue MET 546 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue SER 548 is missing expected H atoms. Skipping. Residue ILE 549 is missing expected H atoms. Skipping. Residue THR 550 is missing expected H atoms. Skipping. Residue ILE 551 is missing expected H atoms. Skipping. Residue SER 552 is missing expected H atoms. Skipping. Residue LEU 554 is missing expected H atoms. Skipping. Residue SER 556 is missing expected H atoms. Skipping. Residue SER 562 is missing expected H atoms. Skipping. Residue TYR 563 is missing expected H atoms. Skipping. Residue THR 566 is missing expected H atoms. Skipping. Residue LEU 567 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue LEU 571 is missing expected H atoms. Skipping. Residue ILE 572 is missing expected H atoms. Skipping. Residue TYR 573 is missing expected H atoms. Skipping. Residue SER 574 is missing expected H atoms. Skipping. Residue SER 575 is missing expected H atoms. Skipping. Residue VAL 576 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue ILE 580 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue VAL 583 is missing expected H atoms. Skipping. Residue ILE 584 is missing expected H atoms. Skipping. Residue TYR 589 is missing expected H atoms. Skipping. Residue SER 590 is missing expected H atoms. Skipping. Residue ILE 592 is missing expected H atoms. Skipping. Residue LEU 595 is missing expected H atoms. Skipping. Residue VAL 596 is missing expected H atoms. Skipping. Residue ILE 599 is missing expected H atoms. Skipping. Residue SER 600 is missing expected H atoms. Skipping. Residue LEU 644 is missing expected H atoms. Skipping. Residue SER 645 is missing expected H atoms. Skipping. Residue SER 649 is missing expected H atoms. Skipping. Residue LEU 650 is missing expected H atoms. Skipping. Residue LYS 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue SER 654 is missing expected H atoms. Skipping. Residue MET 655 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue LYS 658 is missing expected H atoms. Skipping. Residue VAL 659 is missing expected H atoms. Skipping. Residue ILE 662 is missing expected H atoms. Skipping. Residue ILE 663 is missing expected H atoms. Skipping. Residue SER 669 is missing expected H atoms. Skipping. Residue VAL 670 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LEU 674 is missing expected H atoms. Skipping. Residue SER 675 is missing expected H atoms. Skipping. Residue ILE 681 is missing expected H atoms. Skipping. Residue THR 682 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue ILE 687 is missing expected H atoms. Skipping. Residue VAL 688 is missing expected H atoms. Skipping. Residue TYR 689 is missing expected H atoms. Skipping. Residue THR 691 is missing expected H atoms. Skipping. Residue LYS 692 is missing expected H atoms. Skipping. Residue LEU 694 is missing expected H atoms. Skipping. Residue LYS 695 is missing expected H atoms. Skipping. Residue VAL 696 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue ILE 709 is missing expected H atoms. Skipping. Residue MET 710 is missing expected H atoms. Skipping. Residue SER 711 is missing expected H atoms. Skipping. Residue VAL 712 is missing expected H atoms. Skipping. Residue VAL 713 is missing expected H atoms. Skipping. Residue LEU 714 is missing expected H atoms. Skipping. Residue LYS 716 is missing expected H atoms. Skipping. Residue VAL 718 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue TYR 724 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue ILE 296 is missing expected H atoms. Skipping. Residue SER 297 is missing expected H atoms. Skipping. Residue SER 299 is missing expected H atoms. Skipping. Residue SER 302 is missing expected H atoms. Skipping. Residue TYR 304 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue VAL 307 is missing expected H atoms. Skipping. Residue THR 308 is missing expected H atoms. Skipping. Residue SER 310 is missing expected H atoms. Skipping. Residue SER 311 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 316 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue SER 414 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue LYS 416 is missing expected H atoms. Skipping. Residue LEU 417 is missing expected H atoms. Skipping. Residue VAL 419 is missing expected H atoms. Skipping. Residue VAL 425 is missing expected H atoms. Skipping. Residue MET 426 is missing expected H atoms. Skipping. Residue THR 427 is missing expected H atoms. Skipping. Residue ILE 428 is missing expected H atoms. Skipping. Residue SER 429 is missing expected H atoms. Skipping. Residue SER 430 is missing expected H atoms. Skipping. Residue ILE 431 is missing expected H atoms. Skipping. Residue SER 433 is missing expected H atoms. Skipping. Residue ILE 435 is missing expected H atoms. Skipping. Residue ILE 437 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue TYR 442 is missing expected H atoms. Skipping. Residue LEU 445 is missing expected H atoms. Skipping. Residue MET 462 is missing expected H atoms. Skipping. Residue LYS 463 is missing expected H atoms. Skipping. Evaluate side-chains 70 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 275 ILE cc_start: 0.8319 (mm) cc_final: 0.7959 (mm) outliers start: 2 outliers final: 0 residues processed: 70 average time/residue: 0.1314 time to fit residues: 13.1159 Evaluate side-chains 61 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.0980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.3980 chunk 45 optimal weight: 0.0050 chunk 74 optimal weight: 7.9990 overall best weight: 0.4194 ------------------------------------------------------------------------------- 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 = 0.3879 r_free = 0.3879 target = 0.141977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.135932 restraints weight = 35914.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.135548 restraints weight = 52895.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.136054 restraints weight = 42096.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.135935 restraints weight = 29843.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.136138 restraints weight = 28143.504| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.0319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6120 Z= 0.099 Angle : 0.506 4.554 8276 Z= 0.272 Chirality : 0.046 0.152 989 Planarity : 0.003 0.035 1050 Dihedral : 4.477 27.936 839 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.47 % Favored : 86.53 % Rotamer: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.67 (0.28), residues: 757 helix: -2.38 (0.60), residues: 60 sheet: -2.72 (0.32), residues: 259 loop : -3.57 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1050 TYR 0.012 0.001 TYR A 745 PHE 0.007 0.001 PHE B 230 TRP 0.018 0.002 TRP A 748 HIS 0.004 0.001 HIS A 795 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 ( 6120) covalent geometry : angle 0.50558 / 0.27 ( 8276) hydrogen bonds : bond 0.04112 / 3.16 ( 71) hydrogen bonds : angle 5.76140 / 3.97 ( 156) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 542 is missing expected H atoms. Skipping. Residue ILE 543 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue THR 545 is missing expected H atoms. Skipping. Residue MET 546 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue SER 548 is missing expected H atoms. Skipping. Residue ILE 549 is missing expected H atoms. Skipping. Residue THR 550 is missing expected H atoms. Skipping. Residue ILE 551 is missing expected H atoms. Skipping. Residue SER 552 is missing expected H atoms. Skipping. Residue LEU 554 is missing expected H atoms. Skipping. Residue SER 556 is missing expected H atoms. Skipping. Residue SER 562 is missing expected H atoms. Skipping. Residue TYR 563 is missing expected H atoms. Skipping. Residue THR 566 is missing expected H atoms. Skipping. Residue LEU 567 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue LEU 571 is missing expected H atoms. Skipping. Residue ILE 572 is missing expected H atoms. Skipping. Residue TYR 573 is missing expected H atoms. Skipping. Residue SER 574 is missing expected H atoms. Skipping. Residue SER 575 is missing expected H atoms. Skipping. Residue VAL 576 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue ILE 580 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue VAL 583 is missing expected H atoms. Skipping. Residue ILE 584 is missing expected H atoms. Skipping. Residue TYR 589 is missing expected H atoms. Skipping. Residue SER 590 is missing expected H atoms. Skipping. Residue ILE 592 is missing expected H atoms. Skipping. Residue LEU 595 is missing expected H atoms. Skipping. Residue VAL 596 is missing expected H atoms. Skipping. Residue ILE 599 is missing expected H atoms. Skipping. Residue SER 600 is missing expected H atoms. Skipping. Residue LEU 644 is missing expected H atoms. Skipping. Residue SER 645 is missing expected H atoms. Skipping. Residue SER 649 is missing expected H atoms. Skipping. Residue LEU 650 is missing expected H atoms. Skipping. Residue LYS 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue SER 654 is missing expected H atoms. Skipping. Residue MET 655 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue LYS 658 is missing expected H atoms. Skipping. Residue VAL 659 is missing expected H atoms. Skipping. Residue ILE 662 is missing expected H atoms. Skipping. Residue ILE 663 is missing expected H atoms. Skipping. Residue SER 669 is missing expected H atoms. Skipping. Residue VAL 670 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LEU 674 is missing expected H atoms. Skipping. Residue SER 675 is missing expected H atoms. Skipping. Residue ILE 681 is missing expected H atoms. Skipping. Residue THR 682 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue ILE 687 is missing expected H atoms. Skipping. Residue VAL 688 is missing expected H atoms. Skipping. Residue TYR 689 is missing expected H atoms. Skipping. Residue THR 691 is missing expected H atoms. Skipping. Residue LYS 692 is missing expected H atoms. Skipping. Residue LEU 694 is missing expected H atoms. Skipping. Residue LYS 695 is missing expected H atoms. Skipping. Residue VAL 696 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue ILE 709 is missing expected H atoms. Skipping. Residue MET 710 is missing expected H atoms. Skipping. Residue SER 711 is missing expected H atoms. Skipping. Residue VAL 712 is missing expected H atoms. Skipping. Residue VAL 713 is missing expected H atoms. Skipping. Residue LEU 714 is missing expected H atoms. Skipping. Residue LYS 716 is missing expected H atoms. Skipping. Residue VAL 718 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue TYR 724 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue ILE 296 is missing expected H atoms. Skipping. Residue SER 297 is missing expected H atoms. Skipping. Residue SER 299 is missing expected H atoms. Skipping. Residue SER 302 is missing expected H atoms. Skipping. Residue TYR 304 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue VAL 307 is missing expected H atoms. Skipping. Residue THR 308 is missing expected H atoms. Skipping. Residue SER 310 is missing expected H atoms. Skipping. Residue SER 311 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 316 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue SER 414 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue LYS 416 is missing expected H atoms. Skipping. Residue LEU 417 is missing expected H atoms. Skipping. Residue VAL 419 is missing expected H atoms. Skipping. Residue VAL 425 is missing expected H atoms. Skipping. Residue MET 426 is missing expected H atoms. Skipping. Residue THR 427 is missing expected H atoms. Skipping. Residue ILE 428 is missing expected H atoms. Skipping. Residue SER 429 is missing expected H atoms. Skipping. Residue SER 430 is missing expected H atoms. Skipping. Residue ILE 431 is missing expected H atoms. Skipping. Residue SER 433 is missing expected H atoms. Skipping. Residue ILE 435 is missing expected H atoms. Skipping. Residue ILE 437 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue TYR 442 is missing expected H atoms. Skipping. Residue LEU 445 is missing expected H atoms. Skipping. Residue MET 462 is missing expected H atoms. Skipping. Residue LYS 463 is missing expected H atoms. Skipping. Evaluate side-chains 66 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1140 time to fit residues: 10.8758 Evaluate side-chains 58 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 73 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 7 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 77 optimal weight: 0.3980 chunk 32 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3852 r_free = 0.3852 target = 0.139233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.131043 restraints weight = 37001.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.130416 restraints weight = 60636.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.131016 restraints weight = 58787.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.131128 restraints weight = 38100.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.131156 restraints weight = 35045.707| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.0833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6120 Z= 0.154 Angle : 0.562 5.235 8276 Z= 0.307 Chirality : 0.047 0.156 989 Planarity : 0.004 0.036 1050 Dihedral : 4.797 27.887 839 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 17.97 % Favored : 81.90 % Rotamer: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.88 (0.27), residues: 757 helix: -2.30 (0.61), residues: 59 sheet: -3.16 (0.32), residues: 253 loop : -3.55 (0.25), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 286 TYR 0.016 0.001 TYR A 745 PHE 0.015 0.002 PHE B 230 TRP 0.012 0.002 TRP A 748 HIS 0.007 0.001 HIS A 795 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 6120) covalent geometry : angle 0.56183 / 0.31 ( 8276) hydrogen bonds : bond 0.04353 / 3.35 ( 71) hydrogen bonds : angle 5.60346 / 3.87 ( 156) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 542 is missing expected H atoms. Skipping. Residue ILE 543 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue THR 545 is missing expected H atoms. Skipping. Residue MET 546 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue SER 548 is missing expected H atoms. Skipping. Residue ILE 549 is missing expected H atoms. Skipping. Residue THR 550 is missing expected H atoms. Skipping. Residue ILE 551 is missing expected H atoms. Skipping. Residue SER 552 is missing expected H atoms. Skipping. Residue LEU 554 is missing expected H atoms. Skipping. Residue SER 556 is missing expected H atoms. Skipping. Residue SER 562 is missing expected H atoms. Skipping. Residue TYR 563 is missing expected H atoms. Skipping. Residue THR 566 is missing expected H atoms. Skipping. Residue LEU 567 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue LEU 571 is missing expected H atoms. Skipping. Residue ILE 572 is missing expected H atoms. Skipping. Residue TYR 573 is missing expected H atoms. Skipping. Residue SER 574 is missing expected H atoms. Skipping. Residue SER 575 is missing expected H atoms. Skipping. Residue VAL 576 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue ILE 580 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue VAL 583 is missing expected H atoms. Skipping. Residue ILE 584 is missing expected H atoms. Skipping. Residue TYR 589 is missing expected H atoms. Skipping. Residue SER 590 is missing expected H atoms. Skipping. Residue ILE 592 is missing expected H atoms. Skipping. Residue LEU 595 is missing expected H atoms. Skipping. Residue VAL 596 is missing expected H atoms. Skipping. Residue ILE 599 is missing expected H atoms. Skipping. Residue SER 600 is missing expected H atoms. Skipping. Residue LEU 644 is missing expected H atoms. Skipping. Residue SER 645 is missing expected H atoms. Skipping. Residue SER 649 is missing expected H atoms. Skipping. Residue LEU 650 is missing expected H atoms. Skipping. Residue LYS 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue SER 654 is missing expected H atoms. Skipping. Residue MET 655 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue LYS 658 is missing expected H atoms. Skipping. Residue VAL 659 is missing expected H atoms. Skipping. Residue ILE 662 is missing expected H atoms. Skipping. Residue ILE 663 is missing expected H atoms. Skipping. Residue SER 669 is missing expected H atoms. Skipping. Residue VAL 670 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LEU 674 is missing expected H atoms. Skipping. Residue SER 675 is missing expected H atoms. Skipping. Residue ILE 681 is missing expected H atoms. Skipping. Residue THR 682 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue ILE 687 is missing expected H atoms. Skipping. Residue VAL 688 is missing expected H atoms. Skipping. Residue TYR 689 is missing expected H atoms. Skipping. Residue THR 691 is missing expected H atoms. Skipping. Residue LYS 692 is missing expected H atoms. Skipping. Residue LEU 694 is missing expected H atoms. Skipping. Residue LYS 695 is missing expected H atoms. Skipping. Residue VAL 696 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue ILE 709 is missing expected H atoms. Skipping. Residue MET 710 is missing expected H atoms. Skipping. Residue SER 711 is missing expected H atoms. Skipping. Residue VAL 712 is missing expected H atoms. Skipping. Residue VAL 713 is missing expected H atoms. Skipping. Residue LEU 714 is missing expected H atoms. Skipping. Residue LYS 716 is missing expected H atoms. Skipping. Residue VAL 718 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue TYR 724 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue ILE 296 is missing expected H atoms. Skipping. Residue SER 297 is missing expected H atoms. Skipping. Residue SER 299 is missing expected H atoms. Skipping. Residue SER 302 is missing expected H atoms. Skipping. Residue TYR 304 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue VAL 307 is missing expected H atoms. Skipping. Residue THR 308 is missing expected H atoms. Skipping. Residue SER 310 is missing expected H atoms. Skipping. Residue SER 311 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 316 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue SER 414 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue LYS 416 is missing expected H atoms. Skipping. Residue LEU 417 is missing expected H atoms. Skipping. Residue VAL 419 is missing expected H atoms. Skipping. Residue VAL 425 is missing expected H atoms. Skipping. Residue MET 426 is missing expected H atoms. Skipping. Residue THR 427 is missing expected H atoms. Skipping. Residue ILE 428 is missing expected H atoms. Skipping. Residue SER 429 is missing expected H atoms. Skipping. Residue SER 430 is missing expected H atoms. Skipping. Residue ILE 431 is missing expected H atoms. Skipping. Residue SER 433 is missing expected H atoms. Skipping. Residue ILE 435 is missing expected H atoms. Skipping. Residue ILE 437 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue TYR 442 is missing expected H atoms. Skipping. Residue LEU 445 is missing expected H atoms. Skipping. Residue MET 462 is missing expected H atoms. Skipping. Residue LYS 463 is missing expected H atoms. Skipping. Evaluate side-chains 67 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 783 TRP cc_start: 0.6360 (m-10) cc_final: 0.5836 (m100) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.1260 time to fit residues: 11.8818 Evaluate side-chains 59 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 34 optimal weight: 0.1980 chunk 3 optimal weight: 6.9990 chunk 61 optimal weight: 0.0040 chunk 58 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 77 optimal weight: 0.0980 chunk 49 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 7 optimal weight: 9.9990 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 739 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.143382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.131404 restraints weight = 364222.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.132284 restraints weight = 220586.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.130905 restraints weight = 217799.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.130337 restraints weight = 220570.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.130289 restraints weight = 207300.375| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.0974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6120 Z= 0.105 Angle : 0.518 5.218 8276 Z= 0.279 Chirality : 0.046 0.154 989 Planarity : 0.004 0.048 1050 Dihedral : 4.636 29.443 839 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.47 % Favored : 86.39 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.67 (0.28), residues: 757 helix: -2.25 (0.62), residues: 59 sheet: -2.82 (0.34), residues: 232 loop : -3.53 (0.25), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1050 TYR 0.012 0.001 TYR A 745 PHE 0.008 0.001 PHE B 230 TRP 0.008 0.001 TRP A 748 HIS 0.004 0.001 HIS A 795 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 6120) covalent geometry : angle 0.51759 / 0.28 ( 8276) hydrogen bonds : bond 0.03745 / 2.86 ( 71) hydrogen bonds : angle 5.44901 / 3.78 ( 156) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 542 is missing expected H atoms. Skipping. Residue ILE 543 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue THR 545 is missing expected H atoms. Skipping. Residue MET 546 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue SER 548 is missing expected H atoms. Skipping. Residue ILE 549 is missing expected H atoms. Skipping. Residue THR 550 is missing expected H atoms. Skipping. Residue ILE 551 is missing expected H atoms. Skipping. Residue SER 552 is missing expected H atoms. Skipping. Residue LEU 554 is missing expected H atoms. Skipping. Residue SER 556 is missing expected H atoms. Skipping. Residue SER 562 is missing expected H atoms. Skipping. Residue TYR 563 is missing expected H atoms. Skipping. Residue THR 566 is missing expected H atoms. Skipping. Residue LEU 567 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue LEU 571 is missing expected H atoms. Skipping. Residue ILE 572 is missing expected H atoms. Skipping. Residue TYR 573 is missing expected H atoms. Skipping. Residue SER 574 is missing expected H atoms. Skipping. Residue SER 575 is missing expected H atoms. Skipping. Residue VAL 576 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue ILE 580 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue VAL 583 is missing expected H atoms. Skipping. Residue ILE 584 is missing expected H atoms. Skipping. Residue TYR 589 is missing expected H atoms. Skipping. Residue SER 590 is missing expected H atoms. Skipping. Residue ILE 592 is missing expected H atoms. Skipping. Residue LEU 595 is missing expected H atoms. Skipping. Residue VAL 596 is missing expected H atoms. Skipping. Residue ILE 599 is missing expected H atoms. Skipping. Residue SER 600 is missing expected H atoms. Skipping. Residue LEU 644 is missing expected H atoms. Skipping. Residue SER 645 is missing expected H atoms. Skipping. Residue SER 649 is missing expected H atoms. Skipping. Residue LEU 650 is missing expected H atoms. Skipping. Residue LYS 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue SER 654 is missing expected H atoms. Skipping. Residue MET 655 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue LYS 658 is missing expected H atoms. Skipping. Residue VAL 659 is missing expected H atoms. Skipping. Residue ILE 662 is missing expected H atoms. Skipping. Residue ILE 663 is missing expected H atoms. Skipping. Residue SER 669 is missing expected H atoms. Skipping. Residue VAL 670 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LEU 674 is missing expected H atoms. Skipping. Residue SER 675 is missing expected H atoms. Skipping. Residue ILE 681 is missing expected H atoms. Skipping. Residue THR 682 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue ILE 687 is missing expected H atoms. Skipping. Residue VAL 688 is missing expected H atoms. Skipping. Residue TYR 689 is missing expected H atoms. Skipping. Residue THR 691 is missing expected H atoms. Skipping. Residue LYS 692 is missing expected H atoms. Skipping. Residue LEU 694 is missing expected H atoms. Skipping. Residue LYS 695 is missing expected H atoms. Skipping. Residue VAL 696 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue ILE 709 is missing expected H atoms. Skipping. Residue MET 710 is missing expected H atoms. Skipping. Residue SER 711 is missing expected H atoms. Skipping. Residue VAL 712 is missing expected H atoms. Skipping. Residue VAL 713 is missing expected H atoms. Skipping. Residue LEU 714 is missing expected H atoms. Skipping. Residue LYS 716 is missing expected H atoms. Skipping. Residue VAL 718 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue TYR 724 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue ILE 296 is missing expected H atoms. Skipping. Residue SER 297 is missing expected H atoms. Skipping. Residue SER 299 is missing expected H atoms. Skipping. Residue SER 302 is missing expected H atoms. Skipping. Residue TYR 304 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue VAL 307 is missing expected H atoms. Skipping. Residue THR 308 is missing expected H atoms. Skipping. Residue SER 310 is missing expected H atoms. Skipping. Residue SER 311 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 316 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue SER 414 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue LYS 416 is missing expected H atoms. Skipping. Residue LEU 417 is missing expected H atoms. Skipping. Residue VAL 419 is missing expected H atoms. Skipping. Residue VAL 425 is missing expected H atoms. Skipping. Residue MET 426 is missing expected H atoms. Skipping. Residue THR 427 is missing expected H atoms. Skipping. Residue ILE 428 is missing expected H atoms. Skipping. Residue SER 429 is missing expected H atoms. Skipping. Residue SER 430 is missing expected H atoms. Skipping. Residue ILE 431 is missing expected H atoms. Skipping. Residue SER 433 is missing expected H atoms. Skipping. Residue ILE 435 is missing expected H atoms. Skipping. Residue ILE 437 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue TYR 442 is missing expected H atoms. Skipping. Residue LEU 445 is missing expected H atoms. Skipping. Residue MET 462 is missing expected H atoms. Skipping. Residue LYS 463 is missing expected H atoms. Skipping. Evaluate side-chains 74 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 783 TRP cc_start: 0.6258 (m-10) cc_final: 0.5835 (m100) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1689 time to fit residues: 16.6157 Evaluate side-chains 59 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 29 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- 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 = 0.3815 r_free = 0.3815 target = 0.136204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.130275 restraints weight = 37544.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.126723 restraints weight = 50673.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.124529 restraints weight = 35520.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.124661 restraints weight = 34680.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.124743 restraints weight = 31182.990| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6120 Z= 0.216 Angle : 0.642 5.971 8276 Z= 0.354 Chirality : 0.049 0.163 989 Planarity : 0.005 0.039 1050 Dihedral : 5.191 28.029 839 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 21.53 % Favored : 78.34 % Rotamer: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.23 (0.27), residues: 757 helix: -2.34 (0.61), residues: 59 sheet: -3.53 (0.31), residues: 257 loop : -3.71 (0.25), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 741 TYR 0.015 0.002 TYR A1314 PHE 0.021 0.002 PHE B 230 TRP 0.009 0.002 TRP A1046 HIS 0.009 0.001 HIS A 795 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.22 ( 6120) covalent geometry : angle 0.64176 / 0.35 ( 8276) hydrogen bonds : bond 0.04717 / 3.61 ( 71) hydrogen bonds : angle 5.68578 / 3.91 ( 156) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 542 is missing expected H atoms. Skipping. Residue ILE 543 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue THR 545 is missing expected H atoms. Skipping. Residue MET 546 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue SER 548 is missing expected H atoms. Skipping. Residue ILE 549 is missing expected H atoms. Skipping. Residue THR 550 is missing expected H atoms. Skipping. Residue ILE 551 is missing expected H atoms. Skipping. Residue SER 552 is missing expected H atoms. Skipping. Residue LEU 554 is missing expected H atoms. Skipping. Residue SER 556 is missing expected H atoms. Skipping. Residue SER 562 is missing expected H atoms. Skipping. Residue TYR 563 is missing expected H atoms. Skipping. Residue THR 566 is missing expected H atoms. Skipping. Residue LEU 567 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue LEU 571 is missing expected H atoms. Skipping. Residue ILE 572 is missing expected H atoms. Skipping. Residue TYR 573 is missing expected H atoms. Skipping. Residue SER 574 is missing expected H atoms. Skipping. Residue SER 575 is missing expected H atoms. Skipping. Residue VAL 576 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue ILE 580 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue VAL 583 is missing expected H atoms. Skipping. Residue ILE 584 is missing expected H atoms. Skipping. Residue TYR 589 is missing expected H atoms. Skipping. Residue SER 590 is missing expected H atoms. Skipping. Residue ILE 592 is missing expected H atoms. Skipping. Residue LEU 595 is missing expected H atoms. Skipping. Residue VAL 596 is missing expected H atoms. Skipping. Residue ILE 599 is missing expected H atoms. Skipping. Residue SER 600 is missing expected H atoms. Skipping. Residue LEU 644 is missing expected H atoms. Skipping. Residue SER 645 is missing expected H atoms. Skipping. Residue SER 649 is missing expected H atoms. Skipping. Residue LEU 650 is missing expected H atoms. Skipping. Residue LYS 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue SER 654 is missing expected H atoms. Skipping. Residue MET 655 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue LYS 658 is missing expected H atoms. Skipping. Residue VAL 659 is missing expected H atoms. Skipping. Residue ILE 662 is missing expected H atoms. Skipping. Residue ILE 663 is missing expected H atoms. Skipping. Residue SER 669 is missing expected H atoms. Skipping. Residue VAL 670 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LEU 674 is missing expected H atoms. Skipping. Residue SER 675 is missing expected H atoms. Skipping. Residue ILE 681 is missing expected H atoms. Skipping. Residue THR 682 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue ILE 687 is missing expected H atoms. Skipping. Residue VAL 688 is missing expected H atoms. Skipping. Residue TYR 689 is missing expected H atoms. Skipping. Residue THR 691 is missing expected H atoms. Skipping. Residue LYS 692 is missing expected H atoms. Skipping. Residue LEU 694 is missing expected H atoms. Skipping. Residue LYS 695 is missing expected H atoms. Skipping. Residue VAL 696 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue ILE 709 is missing expected H atoms. Skipping. Residue MET 710 is missing expected H atoms. Skipping. Residue SER 711 is missing expected H atoms. Skipping. Residue VAL 712 is missing expected H atoms. Skipping. Residue VAL 713 is missing expected H atoms. Skipping. Residue LEU 714 is missing expected H atoms. Skipping. Residue LYS 716 is missing expected H atoms. Skipping. Residue VAL 718 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue TYR 724 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue ILE 296 is missing expected H atoms. Skipping. Residue SER 297 is missing expected H atoms. Skipping. Residue SER 299 is missing expected H atoms. Skipping. Residue SER 302 is missing expected H atoms. Skipping. Residue TYR 304 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue VAL 307 is missing expected H atoms. Skipping. Residue THR 308 is missing expected H atoms. Skipping. Residue SER 310 is missing expected H atoms. Skipping. Residue SER 311 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 316 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue SER 414 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue LYS 416 is missing expected H atoms. Skipping. Residue LEU 417 is missing expected H atoms. Skipping. Residue VAL 419 is missing expected H atoms. Skipping. Residue VAL 425 is missing expected H atoms. Skipping. Residue MET 426 is missing expected H atoms. Skipping. Residue THR 427 is missing expected H atoms. Skipping. Residue ILE 428 is missing expected H atoms. Skipping. Residue SER 429 is missing expected H atoms. Skipping. Residue SER 430 is missing expected H atoms. Skipping. Residue ILE 431 is missing expected H atoms. Skipping. Residue SER 433 is missing expected H atoms. Skipping. Residue ILE 435 is missing expected H atoms. Skipping. Residue ILE 437 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue TYR 442 is missing expected H atoms. Skipping. Residue LEU 445 is missing expected H atoms. Skipping. Residue MET 462 is missing expected H atoms. Skipping. Residue LYS 463 is missing expected H atoms. Skipping. Evaluate side-chains 65 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 783 TRP cc_start: 0.6435 (m-10) cc_final: 0.5705 (m100) REVERT: A 1052 PHE cc_start: 0.7434 (m-10) cc_final: 0.6941 (t80) REVERT: B 14 ASN cc_start: 0.6264 (p0) cc_final: 0.6045 (p0) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1383 time to fit residues: 12.6705 Evaluate side-chains 55 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 59 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 4 optimal weight: 9.9990 chunk 57 optimal weight: 0.5980 chunk 78 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 55 optimal weight: 0.2980 chunk 44 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3846 r_free = 0.3846 target = 0.138805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.132048 restraints weight = 36690.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.128589 restraints weight = 58957.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.127335 restraints weight = 36610.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.127546 restraints weight = 33606.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.129208 restraints weight = 28356.817| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6120 Z= 0.118 Angle : 0.548 5.360 8276 Z= 0.298 Chirality : 0.047 0.158 989 Planarity : 0.004 0.041 1050 Dihedral : 4.980 30.933 839 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.66 % Favored : 85.20 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -5.03 (0.27), residues: 757 helix: -2.31 (0.62), residues: 59 sheet: -3.34 (0.31), residues: 255 loop : -3.60 (0.25), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 286 TYR 0.031 0.001 TYR A 745 PHE 0.011 0.001 PHE A 900 TRP 0.025 0.002 TRP A 748 HIS 0.002 0.001 HIS B 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 6120) covalent geometry : angle 0.54793 / 0.30 ( 8276) hydrogen bonds : bond 0.03732 / 2.85 ( 71) hydrogen bonds : angle 5.48534 / 3.79 ( 156) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 542 is missing expected H atoms. Skipping. Residue ILE 543 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue THR 545 is missing expected H atoms. Skipping. Residue MET 546 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue SER 548 is missing expected H atoms. Skipping. Residue ILE 549 is missing expected H atoms. Skipping. Residue THR 550 is missing expected H atoms. Skipping. Residue ILE 551 is missing expected H atoms. Skipping. Residue SER 552 is missing expected H atoms. Skipping. Residue LEU 554 is missing expected H atoms. Skipping. Residue SER 556 is missing expected H atoms. Skipping. Residue SER 562 is missing expected H atoms. Skipping. Residue TYR 563 is missing expected H atoms. Skipping. Residue THR 566 is missing expected H atoms. Skipping. Residue LEU 567 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue LEU 571 is missing expected H atoms. Skipping. Residue ILE 572 is missing expected H atoms. Skipping. Residue TYR 573 is missing expected H atoms. Skipping. Residue SER 574 is missing expected H atoms. Skipping. Residue SER 575 is missing expected H atoms. Skipping. Residue VAL 576 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue ILE 580 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue VAL 583 is missing expected H atoms. Skipping. Residue ILE 584 is missing expected H atoms. Skipping. Residue TYR 589 is missing expected H atoms. Skipping. Residue SER 590 is missing expected H atoms. Skipping. Residue ILE 592 is missing expected H atoms. Skipping. Residue LEU 595 is missing expected H atoms. Skipping. Residue VAL 596 is missing expected H atoms. Skipping. Residue ILE 599 is missing expected H atoms. Skipping. Residue SER 600 is missing expected H atoms. Skipping. Residue LEU 644 is missing expected H atoms. Skipping. Residue SER 645 is missing expected H atoms. Skipping. Residue SER 649 is missing expected H atoms. Skipping. Residue LEU 650 is missing expected H atoms. Skipping. Residue LYS 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue SER 654 is missing expected H atoms. Skipping. Residue MET 655 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue LYS 658 is missing expected H atoms. Skipping. Residue VAL 659 is missing expected H atoms. Skipping. Residue ILE 662 is missing expected H atoms. Skipping. Residue ILE 663 is missing expected H atoms. Skipping. Residue SER 669 is missing expected H atoms. Skipping. Residue VAL 670 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LEU 674 is missing expected H atoms. Skipping. Residue SER 675 is missing expected H atoms. Skipping. Residue ILE 681 is missing expected H atoms. Skipping. Residue THR 682 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue ILE 687 is missing expected H atoms. Skipping. Residue VAL 688 is missing expected H atoms. Skipping. Residue TYR 689 is missing expected H atoms. Skipping. Residue THR 691 is missing expected H atoms. Skipping. Residue LYS 692 is missing expected H atoms. Skipping. Residue LEU 694 is missing expected H atoms. Skipping. Residue LYS 695 is missing expected H atoms. Skipping. Residue VAL 696 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue ILE 709 is missing expected H atoms. Skipping. Residue MET 710 is missing expected H atoms. Skipping. Residue SER 711 is missing expected H atoms. Skipping. Residue VAL 712 is missing expected H atoms. Skipping. Residue VAL 713 is missing expected H atoms. Skipping. Residue LEU 714 is missing expected H atoms. Skipping. Residue LYS 716 is missing expected H atoms. Skipping. Residue VAL 718 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue TYR 724 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue ILE 296 is missing expected H atoms. Skipping. Residue SER 297 is missing expected H atoms. Skipping. Residue SER 299 is missing expected H atoms. Skipping. Residue SER 302 is missing expected H atoms. Skipping. Residue TYR 304 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue VAL 307 is missing expected H atoms. Skipping. Residue THR 308 is missing expected H atoms. Skipping. Residue SER 310 is missing expected H atoms. Skipping. Residue SER 311 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 316 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue SER 414 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue LYS 416 is missing expected H atoms. Skipping. Residue LEU 417 is missing expected H atoms. Skipping. Residue VAL 419 is missing expected H atoms. Skipping. Residue VAL 425 is missing expected H atoms. Skipping. Residue MET 426 is missing expected H atoms. Skipping. Residue THR 427 is missing expected H atoms. Skipping. Residue ILE 428 is missing expected H atoms. Skipping. Residue SER 429 is missing expected H atoms. Skipping. Residue SER 430 is missing expected H atoms. Skipping. Residue ILE 431 is missing expected H atoms. Skipping. Residue SER 433 is missing expected H atoms. Skipping. Residue ILE 435 is missing expected H atoms. Skipping. Residue ILE 437 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue TYR 442 is missing expected H atoms. Skipping. Residue LEU 445 is missing expected H atoms. Skipping. Residue MET 462 is missing expected H atoms. Skipping. Residue LYS 463 is missing expected H atoms. Skipping. Evaluate side-chains 67 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 783 TRP cc_start: 0.6319 (m-10) cc_final: 0.5599 (m100) REVERT: B 275 ILE cc_start: 0.8502 (mm) cc_final: 0.8223 (mm) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.1407 time to fit residues: 13.3062 Evaluate side-chains 60 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 44 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 34 optimal weight: 0.3980 chunk 42 optimal weight: 0.5980 chunk 5 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 283 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.138086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.131413 restraints weight = 36835.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.129479 restraints weight = 54780.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.127863 restraints weight = 38069.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.128014 restraints weight = 34700.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.128106 restraints weight = 28416.984| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6120 Z= 0.143 Angle : 0.564 5.365 8276 Z= 0.307 Chirality : 0.047 0.157 989 Planarity : 0.004 0.037 1050 Dihedral : 4.980 29.617 839 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 19.02 % Favored : 80.85 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.12 (0.27), residues: 757 helix: -2.49 (0.58), residues: 64 sheet: -3.27 (0.32), residues: 245 loop : -3.75 (0.24), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1050 TYR 0.013 0.001 TYR A 745 PHE 0.013 0.001 PHE B 230 TRP 0.021 0.002 TRP A 748 HIS 0.005 0.001 HIS A 795 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 6120) covalent geometry : angle 0.56393 / 0.31 ( 8276) hydrogen bonds : bond 0.03900 / 2.98 ( 71) hydrogen bonds : angle 5.51529 / 3.80 ( 156) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 542 is missing expected H atoms. Skipping. Residue ILE 543 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue THR 545 is missing expected H atoms. Skipping. Residue MET 546 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue SER 548 is missing expected H atoms. Skipping. Residue ILE 549 is missing expected H atoms. Skipping. Residue THR 550 is missing expected H atoms. Skipping. Residue ILE 551 is missing expected H atoms. Skipping. Residue SER 552 is missing expected H atoms. Skipping. Residue LEU 554 is missing expected H atoms. Skipping. Residue SER 556 is missing expected H atoms. Skipping. Residue SER 562 is missing expected H atoms. Skipping. Residue TYR 563 is missing expected H atoms. Skipping. Residue THR 566 is missing expected H atoms. Skipping. Residue LEU 567 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue LEU 571 is missing expected H atoms. Skipping. Residue ILE 572 is missing expected H atoms. Skipping. Residue TYR 573 is missing expected H atoms. Skipping. Residue SER 574 is missing expected H atoms. Skipping. Residue SER 575 is missing expected H atoms. Skipping. Residue VAL 576 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue ILE 580 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue VAL 583 is missing expected H atoms. Skipping. Residue ILE 584 is missing expected H atoms. Skipping. Residue TYR 589 is missing expected H atoms. Skipping. Residue SER 590 is missing expected H atoms. Skipping. Residue ILE 592 is missing expected H atoms. Skipping. Residue LEU 595 is missing expected H atoms. Skipping. Residue VAL 596 is missing expected H atoms. Skipping. Residue ILE 599 is missing expected H atoms. Skipping. Residue SER 600 is missing expected H atoms. Skipping. Residue LEU 644 is missing expected H atoms. Skipping. Residue SER 645 is missing expected H atoms. Skipping. Residue SER 649 is missing expected H atoms. Skipping. Residue LEU 650 is missing expected H atoms. Skipping. Residue LYS 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue SER 654 is missing expected H atoms. Skipping. Residue MET 655 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue LYS 658 is missing expected H atoms. Skipping. Residue VAL 659 is missing expected H atoms. Skipping. Residue ILE 662 is missing expected H atoms. Skipping. Residue ILE 663 is missing expected H atoms. Skipping. Residue SER 669 is missing expected H atoms. Skipping. Residue VAL 670 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LEU 674 is missing expected H atoms. Skipping. Residue SER 675 is missing expected H atoms. Skipping. Residue ILE 681 is missing expected H atoms. Skipping. Residue THR 682 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue ILE 687 is missing expected H atoms. Skipping. Residue VAL 688 is missing expected H atoms. Skipping. Residue TYR 689 is missing expected H atoms. Skipping. Residue THR 691 is missing expected H atoms. Skipping. Residue LYS 692 is missing expected H atoms. Skipping. Residue LEU 694 is missing expected H atoms. Skipping. Residue LYS 695 is missing expected H atoms. Skipping. Residue VAL 696 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue ILE 709 is missing expected H atoms. Skipping. Residue MET 710 is missing expected H atoms. Skipping. Residue SER 711 is missing expected H atoms. Skipping. Residue VAL 712 is missing expected H atoms. Skipping. Residue VAL 713 is missing expected H atoms. Skipping. Residue LEU 714 is missing expected H atoms. Skipping. Residue LYS 716 is missing expected H atoms. Skipping. Residue VAL 718 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue TYR 724 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue ILE 296 is missing expected H atoms. Skipping. Residue SER 297 is missing expected H atoms. Skipping. Residue SER 299 is missing expected H atoms. Skipping. Residue SER 302 is missing expected H atoms. Skipping. Residue TYR 304 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue VAL 307 is missing expected H atoms. Skipping. Residue THR 308 is missing expected H atoms. Skipping. Residue SER 310 is missing expected H atoms. Skipping. Residue SER 311 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 316 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue SER 414 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue LYS 416 is missing expected H atoms. Skipping. Residue LEU 417 is missing expected H atoms. Skipping. Residue VAL 419 is missing expected H atoms. Skipping. Residue VAL 425 is missing expected H atoms. Skipping. Residue MET 426 is missing expected H atoms. Skipping. Residue THR 427 is missing expected H atoms. Skipping. Residue ILE 428 is missing expected H atoms. Skipping. Residue SER 429 is missing expected H atoms. Skipping. Residue SER 430 is missing expected H atoms. Skipping. Residue ILE 431 is missing expected H atoms. Skipping. Residue SER 433 is missing expected H atoms. Skipping. Residue ILE 435 is missing expected H atoms. Skipping. Residue ILE 437 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue TYR 442 is missing expected H atoms. Skipping. Residue LEU 445 is missing expected H atoms. Skipping. Residue MET 462 is missing expected H atoms. Skipping. Residue LYS 463 is missing expected H atoms. Skipping. Evaluate side-chains 69 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 783 TRP cc_start: 0.6384 (m-10) cc_final: 0.5621 (m100) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.1391 time to fit residues: 13.5515 Evaluate side-chains 60 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 77 optimal weight: 0.0270 chunk 64 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 60 optimal weight: 0.2980 chunk 41 optimal weight: 0.9990 chunk 61 optimal weight: 0.0980 chunk 48 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.3638 ------------------------------------------------------------------------------- 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 = 0.3861 r_free = 0.3861 target = 0.140039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.133667 restraints weight = 36377.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.130981 restraints weight = 54635.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.129720 restraints weight = 36098.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.129839 restraints weight = 31115.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.129914 restraints weight = 26735.667| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6120 Z= 0.096 Angle : 0.521 4.846 8276 Z= 0.279 Chirality : 0.047 0.153 989 Planarity : 0.004 0.041 1050 Dihedral : 4.748 30.925 839 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.47 % Favored : 86.39 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -4.90 (0.27), residues: 757 helix: -2.41 (0.59), residues: 64 sheet: -3.08 (0.33), residues: 246 loop : -3.62 (0.25), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 286 TYR 0.014 0.001 TYR A 745 PHE 0.009 0.001 PHE B 31 TRP 0.021 0.001 TRP A 748 HIS 0.002 0.001 HIS A 795 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 ( 6120) covalent geometry : angle 0.52077 / 0.28 ( 8276) hydrogen bonds : bond 0.03365 / 2.56 ( 71) hydrogen bonds : angle 5.40637 / 3.74 ( 156) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 542 is missing expected H atoms. Skipping. Residue ILE 543 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue THR 545 is missing expected H atoms. Skipping. Residue MET 546 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue SER 548 is missing expected H atoms. Skipping. Residue ILE 549 is missing expected H atoms. Skipping. Residue THR 550 is missing expected H atoms. Skipping. Residue ILE 551 is missing expected H atoms. Skipping. Residue SER 552 is missing expected H atoms. Skipping. Residue LEU 554 is missing expected H atoms. Skipping. Residue SER 556 is missing expected H atoms. Skipping. Residue SER 562 is missing expected H atoms. Skipping. Residue TYR 563 is missing expected H atoms. Skipping. Residue THR 566 is missing expected H atoms. Skipping. Residue LEU 567 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue LEU 571 is missing expected H atoms. Skipping. Residue ILE 572 is missing expected H atoms. Skipping. Residue TYR 573 is missing expected H atoms. Skipping. Residue SER 574 is missing expected H atoms. Skipping. Residue SER 575 is missing expected H atoms. Skipping. Residue VAL 576 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue ILE 580 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue VAL 583 is missing expected H atoms. Skipping. Residue ILE 584 is missing expected H atoms. Skipping. Residue TYR 589 is missing expected H atoms. Skipping. Residue SER 590 is missing expected H atoms. Skipping. Residue ILE 592 is missing expected H atoms. Skipping. Residue LEU 595 is missing expected H atoms. Skipping. Residue VAL 596 is missing expected H atoms. Skipping. Residue ILE 599 is missing expected H atoms. Skipping. Residue SER 600 is missing expected H atoms. Skipping. Residue LEU 644 is missing expected H atoms. Skipping. Residue SER 645 is missing expected H atoms. Skipping. Residue SER 649 is missing expected H atoms. Skipping. Residue LEU 650 is missing expected H atoms. Skipping. Residue LYS 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue SER 654 is missing expected H atoms. Skipping. Residue MET 655 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue LYS 658 is missing expected H atoms. Skipping. Residue VAL 659 is missing expected H atoms. Skipping. Residue ILE 662 is missing expected H atoms. Skipping. Residue ILE 663 is missing expected H atoms. Skipping. Residue SER 669 is missing expected H atoms. Skipping. Residue VAL 670 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LEU 674 is missing expected H atoms. Skipping. Residue SER 675 is missing expected H atoms. Skipping. Residue ILE 681 is missing expected H atoms. Skipping. Residue THR 682 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue ILE 687 is missing expected H atoms. Skipping. Residue VAL 688 is missing expected H atoms. Skipping. Residue TYR 689 is missing expected H atoms. Skipping. Residue THR 691 is missing expected H atoms. Skipping. Residue LYS 692 is missing expected H atoms. Skipping. Residue LEU 694 is missing expected H atoms. Skipping. Residue LYS 695 is missing expected H atoms. Skipping. Residue VAL 696 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue ILE 709 is missing expected H atoms. Skipping. Residue MET 710 is missing expected H atoms. Skipping. Residue SER 711 is missing expected H atoms. Skipping. Residue VAL 712 is missing expected H atoms. Skipping. Residue VAL 713 is missing expected H atoms. Skipping. Residue LEU 714 is missing expected H atoms. Skipping. Residue LYS 716 is missing expected H atoms. Skipping. Residue VAL 718 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue TYR 724 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue ILE 296 is missing expected H atoms. Skipping. Residue SER 297 is missing expected H atoms. Skipping. Residue SER 299 is missing expected H atoms. Skipping. Residue SER 302 is missing expected H atoms. Skipping. Residue TYR 304 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue VAL 307 is missing expected H atoms. Skipping. Residue THR 308 is missing expected H atoms. Skipping. Residue SER 310 is missing expected H atoms. Skipping. Residue SER 311 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 316 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue SER 414 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue LYS 416 is missing expected H atoms. Skipping. Residue LEU 417 is missing expected H atoms. Skipping. Residue VAL 419 is missing expected H atoms. Skipping. Residue VAL 425 is missing expected H atoms. Skipping. Residue MET 426 is missing expected H atoms. Skipping. Residue THR 427 is missing expected H atoms. Skipping. Residue ILE 428 is missing expected H atoms. Skipping. Residue SER 429 is missing expected H atoms. Skipping. Residue SER 430 is missing expected H atoms. Skipping. Residue ILE 431 is missing expected H atoms. Skipping. Residue SER 433 is missing expected H atoms. Skipping. Residue ILE 435 is missing expected H atoms. Skipping. Residue ILE 437 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue TYR 442 is missing expected H atoms. Skipping. Residue LEU 445 is missing expected H atoms. Skipping. Residue MET 462 is missing expected H atoms. Skipping. Residue LYS 463 is missing expected H atoms. Skipping. Evaluate side-chains 69 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.1409 time to fit residues: 13.6579 Evaluate side-chains 59 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 76 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 5 optimal weight: 10.0000 chunk 57 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3828 r_free = 0.3828 target = 0.137328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.130273 restraints weight = 37311.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.129701 restraints weight = 65341.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.130100 restraints weight = 59387.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.130226 restraints weight = 40117.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.130341 restraints weight = 37211.160| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6120 Z= 0.152 Angle : 0.576 5.372 8276 Z= 0.312 Chirality : 0.047 0.151 989 Planarity : 0.004 0.038 1050 Dihedral : 4.918 29.192 839 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 20.21 % Favored : 79.66 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.10 (0.27), residues: 757 helix: -2.50 (0.59), residues: 63 sheet: -3.25 (0.32), residues: 250 loop : -3.74 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1050 TYR 0.014 0.002 TYR A 745 PHE 0.014 0.002 PHE B 230 TRP 0.019 0.002 TRP A 748 HIS 0.006 0.001 HIS A 795 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 6120) covalent geometry : angle 0.57633 / 0.31 ( 8276) hydrogen bonds : bond 0.03872 / 2.94 ( 71) hydrogen bonds : angle 5.44055 / 3.74 ( 156) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 542 is missing expected H atoms. Skipping. Residue ILE 543 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue THR 545 is missing expected H atoms. Skipping. Residue MET 546 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue SER 548 is missing expected H atoms. Skipping. Residue ILE 549 is missing expected H atoms. Skipping. Residue THR 550 is missing expected H atoms. Skipping. Residue ILE 551 is missing expected H atoms. Skipping. Residue SER 552 is missing expected H atoms. Skipping. Residue LEU 554 is missing expected H atoms. Skipping. Residue SER 556 is missing expected H atoms. Skipping. Residue SER 562 is missing expected H atoms. Skipping. Residue TYR 563 is missing expected H atoms. Skipping. Residue THR 566 is missing expected H atoms. Skipping. Residue LEU 567 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue LEU 571 is missing expected H atoms. Skipping. Residue ILE 572 is missing expected H atoms. Skipping. Residue TYR 573 is missing expected H atoms. Skipping. Residue SER 574 is missing expected H atoms. Skipping. Residue SER 575 is missing expected H atoms. Skipping. Residue VAL 576 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue ILE 580 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue VAL 583 is missing expected H atoms. Skipping. Residue ILE 584 is missing expected H atoms. Skipping. Residue TYR 589 is missing expected H atoms. Skipping. Residue SER 590 is missing expected H atoms. Skipping. Residue ILE 592 is missing expected H atoms. Skipping. Residue LEU 595 is missing expected H atoms. Skipping. Residue VAL 596 is missing expected H atoms. Skipping. Residue ILE 599 is missing expected H atoms. Skipping. Residue SER 600 is missing expected H atoms. Skipping. Residue LEU 644 is missing expected H atoms. Skipping. Residue SER 645 is missing expected H atoms. Skipping. Residue SER 649 is missing expected H atoms. Skipping. Residue LEU 650 is missing expected H atoms. Skipping. Residue LYS 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue SER 654 is missing expected H atoms. Skipping. Residue MET 655 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue LYS 658 is missing expected H atoms. Skipping. Residue VAL 659 is missing expected H atoms. Skipping. Residue ILE 662 is missing expected H atoms. Skipping. Residue ILE 663 is missing expected H atoms. Skipping. Residue SER 669 is missing expected H atoms. Skipping. Residue VAL 670 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LEU 674 is missing expected H atoms. Skipping. Residue SER 675 is missing expected H atoms. Skipping. Residue ILE 681 is missing expected H atoms. Skipping. Residue THR 682 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue ILE 687 is missing expected H atoms. Skipping. Residue VAL 688 is missing expected H atoms. Skipping. Residue TYR 689 is missing expected H atoms. Skipping. Residue THR 691 is missing expected H atoms. Skipping. Residue LYS 692 is missing expected H atoms. Skipping. Residue LEU 694 is missing expected H atoms. Skipping. Residue LYS 695 is missing expected H atoms. Skipping. Residue VAL 696 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue ILE 709 is missing expected H atoms. Skipping. Residue MET 710 is missing expected H atoms. Skipping. Residue SER 711 is missing expected H atoms. Skipping. Residue VAL 712 is missing expected H atoms. Skipping. Residue VAL 713 is missing expected H atoms. Skipping. Residue LEU 714 is missing expected H atoms. Skipping. Residue LYS 716 is missing expected H atoms. Skipping. Residue VAL 718 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue TYR 724 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue ILE 296 is missing expected H atoms. Skipping. Residue SER 297 is missing expected H atoms. Skipping. Residue SER 299 is missing expected H atoms. Skipping. Residue SER 302 is missing expected H atoms. Skipping. Residue TYR 304 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue VAL 307 is missing expected H atoms. Skipping. Residue THR 308 is missing expected H atoms. Skipping. Residue SER 310 is missing expected H atoms. Skipping. Residue SER 311 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 316 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue SER 414 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue LYS 416 is missing expected H atoms. Skipping. Residue LEU 417 is missing expected H atoms. Skipping. Residue VAL 419 is missing expected H atoms. Skipping. Residue VAL 425 is missing expected H atoms. Skipping. Residue MET 426 is missing expected H atoms. Skipping. Residue THR 427 is missing expected H atoms. Skipping. Residue ILE 428 is missing expected H atoms. Skipping. Residue SER 429 is missing expected H atoms. Skipping. Residue SER 430 is missing expected H atoms. Skipping. Residue ILE 431 is missing expected H atoms. Skipping. Residue SER 433 is missing expected H atoms. Skipping. Residue ILE 435 is missing expected H atoms. Skipping. Residue ILE 437 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue TYR 442 is missing expected H atoms. Skipping. Residue LEU 445 is missing expected H atoms. Skipping. Residue MET 462 is missing expected H atoms. Skipping. Residue LYS 463 is missing expected H atoms. Skipping. Evaluate side-chains 67 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 783 TRP cc_start: 0.6393 (m-10) cc_final: 0.5603 (m100) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.1431 time to fit residues: 13.4683 Evaluate side-chains 59 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 53 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 13 optimal weight: 0.0570 chunk 10 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 51 optimal weight: 0.0870 overall best weight: 0.5876 ------------------------------------------------------------------------------- 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 = 0.3843 r_free = 0.3843 target = 0.138533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.131767 restraints weight = 36461.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.131202 restraints weight = 57224.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.131412 restraints weight = 44385.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.131395 restraints weight = 30239.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.131626 restraints weight = 27667.648| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6120 Z= 0.115 Angle : 0.542 5.322 8276 Z= 0.292 Chirality : 0.047 0.150 989 Planarity : 0.004 0.040 1050 Dihedral : 4.876 30.383 839 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.40 % Favored : 85.47 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -4.97 (0.27), residues: 757 helix: -2.48 (0.59), residues: 63 sheet: -3.13 (0.32), residues: 247 loop : -3.66 (0.25), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1050 TYR 0.013 0.001 TYR A 745 PHE 0.010 0.001 PHE B 36 TRP 0.019 0.001 TRP A 748 HIS 0.003 0.001 HIS A 795 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 6120) covalent geometry : angle 0.54212 / 0.29 ( 8276) hydrogen bonds : bond 0.03527 / 2.67 ( 71) hydrogen bonds : angle 5.37204 / 3.71 ( 156) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 542 is missing expected H atoms. Skipping. Residue ILE 543 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue THR 545 is missing expected H atoms. Skipping. Residue MET 546 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue SER 548 is missing expected H atoms. Skipping. Residue ILE 549 is missing expected H atoms. Skipping. Residue THR 550 is missing expected H atoms. Skipping. Residue ILE 551 is missing expected H atoms. Skipping. Residue SER 552 is missing expected H atoms. Skipping. Residue LEU 554 is missing expected H atoms. Skipping. Residue SER 556 is missing expected H atoms. Skipping. Residue SER 562 is missing expected H atoms. Skipping. Residue TYR 563 is missing expected H atoms. Skipping. Residue THR 566 is missing expected H atoms. Skipping. Residue LEU 567 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue LEU 571 is missing expected H atoms. Skipping. Residue ILE 572 is missing expected H atoms. Skipping. Residue TYR 573 is missing expected H atoms. Skipping. Residue SER 574 is missing expected H atoms. Skipping. Residue SER 575 is missing expected H atoms. Skipping. Residue VAL 576 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue ILE 580 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue VAL 583 is missing expected H atoms. Skipping. Residue ILE 584 is missing expected H atoms. Skipping. Residue TYR 589 is missing expected H atoms. Skipping. Residue SER 590 is missing expected H atoms. Skipping. Residue ILE 592 is missing expected H atoms. Skipping. Residue LEU 595 is missing expected H atoms. Skipping. Residue VAL 596 is missing expected H atoms. Skipping. Residue ILE 599 is missing expected H atoms. Skipping. Residue SER 600 is missing expected H atoms. Skipping. Residue LEU 644 is missing expected H atoms. Skipping. Residue SER 645 is missing expected H atoms. Skipping. Residue SER 649 is missing expected H atoms. Skipping. Residue LEU 650 is missing expected H atoms. Skipping. Residue LYS 651 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue SER 654 is missing expected H atoms. Skipping. Residue MET 655 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue LYS 658 is missing expected H atoms. Skipping. Residue VAL 659 is missing expected H atoms. Skipping. Residue ILE 662 is missing expected H atoms. Skipping. Residue ILE 663 is missing expected H atoms. Skipping. Residue SER 669 is missing expected H atoms. Skipping. Residue VAL 670 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LEU 674 is missing expected H atoms. Skipping. Residue SER 675 is missing expected H atoms. Skipping. Residue ILE 681 is missing expected H atoms. Skipping. Residue THR 682 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue ILE 687 is missing expected H atoms. Skipping. Residue VAL 688 is missing expected H atoms. Skipping. Residue TYR 689 is missing expected H atoms. Skipping. Residue THR 691 is missing expected H atoms. Skipping. Residue LYS 692 is missing expected H atoms. Skipping. Residue LEU 694 is missing expected H atoms. Skipping. Residue LYS 695 is missing expected H atoms. Skipping. Residue VAL 696 is missing expected H atoms. Skipping. Residue LYS 699 is missing expected H atoms. Skipping. Residue ILE 709 is missing expected H atoms. Skipping. Residue MET 710 is missing expected H atoms. Skipping. Residue SER 711 is missing expected H atoms. Skipping. Residue VAL 712 is missing expected H atoms. Skipping. Residue VAL 713 is missing expected H atoms. Skipping. Residue LEU 714 is missing expected H atoms. Skipping. Residue LYS 716 is missing expected H atoms. Skipping. Residue VAL 718 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue TYR 724 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue ILE 296 is missing expected H atoms. Skipping. Residue SER 297 is missing expected H atoms. Skipping. Residue SER 299 is missing expected H atoms. Skipping. Residue SER 302 is missing expected H atoms. Skipping. Residue TYR 304 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue VAL 307 is missing expected H atoms. Skipping. Residue THR 308 is missing expected H atoms. Skipping. Residue SER 310 is missing expected H atoms. Skipping. Residue SER 311 is missing expected H atoms. Skipping. Residue THR 313 is missing expected H atoms. Skipping. Residue VAL 314 is missing expected H atoms. Skipping. Residue ILE 316 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue LEU 319 is missing expected H atoms. Skipping. Residue SER 414 is missing expected H atoms. Skipping. Residue LEU 415 is missing expected H atoms. Skipping. Residue LYS 416 is missing expected H atoms. Skipping. Residue LEU 417 is missing expected H atoms. Skipping. Residue VAL 419 is missing expected H atoms. Skipping. Residue VAL 425 is missing expected H atoms. Skipping. Residue MET 426 is missing expected H atoms. Skipping. Residue THR 427 is missing expected H atoms. Skipping. Residue ILE 428 is missing expected H atoms. Skipping. Residue SER 429 is missing expected H atoms. Skipping. Residue SER 430 is missing expected H atoms. Skipping. Residue ILE 431 is missing expected H atoms. Skipping. Residue SER 433 is missing expected H atoms. Skipping. Residue ILE 435 is missing expected H atoms. Skipping. Residue ILE 437 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue TYR 442 is missing expected H atoms. Skipping. Residue LEU 445 is missing expected H atoms. Skipping. Residue MET 462 is missing expected H atoms. Skipping. Residue LYS 463 is missing expected H atoms. Skipping. Evaluate side-chains 68 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 783 TRP cc_start: 0.6494 (m-10) cc_final: 0.5654 (m100) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1446 time to fit residues: 13.8101 Evaluate side-chains 61 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 28 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 17 optimal weight: 0.1980 chunk 6 optimal weight: 7.9990 chunk 43 optimal weight: 0.3980 chunk 68 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.137530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.130708 restraints weight = 37224.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.130321 restraints weight = 54208.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.130733 restraints weight = 47691.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.130891 restraints weight = 33610.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.131012 restraints weight = 28615.101| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6120 Z= 0.130 Angle : 0.559 5.236 8276 Z= 0.302 Chirality : 0.047 0.150 989 Planarity : 0.004 0.035 1050 Dihedral : 4.869 29.419 839 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 18.63 % Favored : 81.24 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.05 (0.27), residues: 757 helix: -2.47 (0.59), residues: 63 sheet: -3.22 (0.32), residues: 250 loop : -3.70 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1050 TYR 0.014 0.001 TYR A 745 PHE 0.011 0.001 PHE B 36 TRP 0.020 0.002 TRP A 748 HIS 0.005 0.001 HIS A 795 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 6120) covalent geometry : angle 0.55921 / 0.30 ( 8276) hydrogen bonds : bond 0.03695 / 2.80 ( 71) hydrogen bonds : angle 5.38862 / 3.72 ( 156) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2056.06 seconds wall clock time: 35 minutes 51.05 seconds (2151.05 seconds total)