Starting phenix.real_space_refine on Thu Jun 4 05:31:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6g19_4338/06_2026/6g19_4338.cif Found real_map, /net/cci-nas-00/data/ceres_data/6g19_4338/06_2026/6g19_4338.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6g19_4338/06_2026/6g19_4338.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6g19_4338/06_2026/6g19_4338.map" model { file = "/net/cci-nas-00/data/ceres_data/6g19_4338/06_2026/6g19_4338.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6g19_4338/06_2026/6g19_4338.cif" } resolution = 3.68 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= 0.001 sd= 0.014 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 31 5.49 5 S 35 5.16 5 C 3744 2.51 5 N 1063 2.21 5 O 1227 1.98 5 H 4402 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10503 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 682, 9874 Classifications: {'peptide': 682} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 20, 'TRANS': 661} Chain breaks: 3 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'TYR:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "X" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 308 Classifications: {'RNA': 14} Modifications used: {'rna3p_pur': 11, 'rna3p_pyr': 3} Link IDs: {'rna3p': 13} Chain: "Y" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 289 Classifications: {'RNA': 14} Modifications used: {'rna3p_pur': 3, 'rna3p_pyr': 11} Link IDs: {'rna3p': 13} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8332 SG CYS A 907 76.675 29.214 39.358 1.00 65.66 S ATOM 8379 SG CYS A 910 80.223 28.202 39.486 1.00 67.22 S ATOM 9041 SG CYS A 962 79.043 29.305 42.876 1.00 65.66 S ATOM 9060 SG CYS A 964 79.343 31.478 40.866 1.00 66.49 S Time building chain proxies: 2.35, per 1000 atoms: 0.22 Number of scatterers: 10503 At special positions: 0 Unit cell: (101.65, 87.74, 69.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 35 16.00 P 31 15.00 O 1227 8.00 N 1063 7.00 C 3744 6.00 H 4402 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: 0.96 Conformation dependent library (CDL) restraints added in 316.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 964 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 910 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 962 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 907 " Number of angles added : 6 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1304 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 7 sheets defined 52.3% alpha, 9.4% beta 14 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'A' and resid 310 through 318 removed outlier: 3.809A pdb=" N GLU A 315 " --> pdb=" O PRO A 311 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A 316 " --> pdb=" O TYR A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 322 Processing helix chain 'A' and resid 335 through 354 Processing helix chain 'A' and resid 367 through 377 removed outlier: 3.951A pdb=" N GLU A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 383 removed outlier: 4.066A pdb=" N TYR A 381 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 405 removed outlier: 3.637A pdb=" N VAL A 405 " --> pdb=" O PHE A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 428 removed outlier: 3.603A pdb=" N GLU A 419 " --> pdb=" O ALA A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 438 Processing helix chain 'A' and resid 446 through 449 Processing helix chain 'A' and resid 456 through 474 Processing helix chain 'A' and resid 499 through 514 Processing helix chain 'A' and resid 525 through 533 removed outlier: 4.025A pdb=" N LEU A 529 " --> pdb=" O ASN A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 567 removed outlier: 3.530A pdb=" N LYS A 554 " --> pdb=" O PRO A 550 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE A 558 " --> pdb=" O LYS A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 594 Processing helix chain 'A' and resid 598 through 618 removed outlier: 3.750A pdb=" N LYS A 607 " --> pdb=" O GLU A 603 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR A 617 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 643 removed outlier: 3.704A pdb=" N ALA A 623 " --> pdb=" O ARG A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 692 removed outlier: 3.786A pdb=" N ASP A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ASN A 683 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LYS A 685 " --> pdb=" O PHE A 681 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N MET A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU A 692 " --> pdb=" O LYS A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 697 removed outlier: 4.122A pdb=" N GLU A 697 " --> pdb=" O PRO A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 716 removed outlier: 3.547A pdb=" N GLN A 711 " --> pdb=" O THR A 707 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU A 716 " --> pdb=" O PHE A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 741 removed outlier: 3.855A pdb=" N THR A 731 " --> pdb=" O THR A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 747 removed outlier: 3.906A pdb=" N ALA A 745 " --> pdb=" O ASN A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 781 Processing helix chain 'A' and resid 812 through 821 Processing helix chain 'A' and resid 840 through 863 removed outlier: 3.812A pdb=" N TYR A 855 " --> pdb=" O GLU A 851 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS A 856 " --> pdb=" O LYS A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 890 removed outlier: 4.193A pdb=" N LYS A 887 " --> pdb=" O GLU A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 939 removed outlier: 3.586A pdb=" N LEU A 938 " --> pdb=" O GLU A 934 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N TYR A 939 " --> pdb=" O PHE A 935 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 326 through 329 removed outlier: 6.389A pdb=" N ILE A 326 " --> pdb=" O GLY A 487 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N THR A 489 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE A 328 " --> pdb=" O THR A 489 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE A 441 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LEU A 488 " --> pdb=" O ILE A 441 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE A 443 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ILE A 361 " --> pdb=" O ILE A 442 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ASP A 444 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LEU A 363 " --> pdb=" O ASP A 444 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL A 360 " --> pdb=" O ILE A 411 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N SER A 413 " --> pdb=" O VAL A 360 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N VAL A 362 " --> pdb=" O SER A 413 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 537 through 542 removed outlier: 3.535A pdb=" N THR A 834 " --> pdb=" O VAL A 541 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 751 through 752 removed outlier: 6.785A pdb=" N HIS A 752 " --> pdb=" O ILE A 787 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE A 722 " --> pdb=" O ILE A 803 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 912 through 916 removed outlier: 6.461A pdb=" N LEU A 913 " --> pdb=" O CYS A 907 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N CYS A 907 " --> pdb=" O LEU A 913 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 920 through 923 Processing sheet with id=AA6, first strand: chain 'A' and resid 940 through 942 removed outlier: 3.723A pdb=" N GLU A 959 " --> pdb=" O ARG A 942 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 969 through 970 removed outlier: 3.669A pdb=" N THR A 970 " --> pdb=" O CYS A 981 " (cutoff:3.500A) 255 hydrogen bonds defined for protein. 741 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 37 hydrogen bonds 74 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 2.47 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 4391 1.01 - 1.21: 11 1.21 - 1.41: 2456 1.41 - 1.61: 3742 1.61 - 1.81: 58 Bond restraints: 10658 Sorted by residual: bond pdb=" O3A ANP A1102 " pdb=" PB ANP A1102 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.19e+01 bond pdb=" N3B ANP A1102 " pdb=" PG ANP A1102 " ideal model delta sigma weight residual 1.795 1.688 0.107 2.00e-02 2.50e+03 2.84e+01 bond pdb=" CG ASN A 897 " pdb=" ND2 ASN A 897 " ideal model delta sigma weight residual 1.328 1.248 0.080 2.10e-02 2.27e+03 1.46e+01 bond pdb=" CB TYR A 455 " pdb=" CG TYR A 455 " ideal model delta sigma weight residual 1.512 1.434 0.078 2.20e-02 2.07e+03 1.24e+01 bond pdb=" O5' ANP A1102 " pdb=" PA ANP A1102 " ideal model delta sigma weight residual 1.655 1.585 0.070 2.00e-02 2.50e+03 1.23e+01 ... (remaining 10653 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.95: 18600 10.95 - 21.91: 8 21.91 - 32.86: 0 32.86 - 43.82: 0 43.82 - 54.77: 14 Bond angle restraints: 18622 Sorted by residual: angle pdb=" C MET A 886 " pdb=" N LYS A 887 " pdb=" H LYS A 887 " ideal model delta sigma weight residual 125.01 70.24 54.77 3.00e+00 1.11e-01 3.33e+02 angle pdb=" CA LYS A 887 " pdb=" N LYS A 887 " pdb=" H LYS A 887 " ideal model delta sigma weight residual 114.71 60.05 54.66 3.00e+00 1.11e-01 3.32e+02 angle pdb=" C LYS A 884 " pdb=" N LYS A 885 " pdb=" H LYS A 885 " ideal model delta sigma weight residual 124.88 70.39 54.49 3.00e+00 1.11e-01 3.30e+02 angle pdb=" C LYS A 887 " pdb=" N VAL A 888 " pdb=" H VAL A 888 " ideal model delta sigma weight residual 125.00 71.06 53.94 3.00e+00 1.11e-01 3.23e+02 angle pdb=" CA VAL A 888 " pdb=" N VAL A 888 " pdb=" H VAL A 888 " ideal model delta sigma weight residual 114.70 61.07 53.63 3.00e+00 1.11e-01 3.20e+02 ... (remaining 18617 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.19: 5061 18.19 - 36.39: 217 36.39 - 54.58: 53 54.58 - 72.78: 43 72.78 - 90.97: 15 Dihedral angle restraints: 5389 sinusoidal: 3123 harmonic: 2266 Sorted by residual: dihedral pdb=" CA VAL A 454 " pdb=" C VAL A 454 " pdb=" N TYR A 455 " pdb=" CA TYR A 455 " ideal model delta harmonic sigma weight residual 180.00 93.60 86.40 0 5.00e+00 4.00e-02 2.99e+02 dihedral pdb=" CA GLU A 793 " pdb=" C GLU A 793 " pdb=" N GLU A 794 " pdb=" CA GLU A 794 " ideal model delta harmonic sigma weight residual 180.00 142.00 38.00 0 5.00e+00 4.00e-02 5.78e+01 dihedral pdb=" CA GLU A 548 " pdb=" C GLU A 548 " pdb=" N ASN A 549 " pdb=" CA ASN A 549 " ideal model delta harmonic sigma weight residual -180.00 -145.43 -34.57 0 5.00e+00 4.00e-02 4.78e+01 ... (remaining 5386 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 694 0.055 - 0.109: 229 0.109 - 0.164: 50 0.164 - 0.219: 12 0.219 - 0.273: 2 Chirality restraints: 987 Sorted by residual: chirality pdb=" CB VAL A 929 " pdb=" CA VAL A 929 " pdb=" CG1 VAL A 929 " pdb=" CG2 VAL A 929 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C3' ANP A1102 " pdb=" C2' ANP A1102 " pdb=" C4' ANP A1102 " pdb=" O3' ANP A1102 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CB VAL A 494 " pdb=" CA VAL A 494 " pdb=" CG1 VAL A 494 " pdb=" CG2 VAL A 494 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 984 not shown) Planarity restraints: 1564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 455 " 0.017 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C TYR A 455 " -0.060 2.00e-02 2.50e+03 pdb=" O TYR A 455 " 0.023 2.00e-02 2.50e+03 pdb=" N ASN A 456 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 599 " 0.160 9.50e-02 1.11e+02 5.67e-02 1.10e+01 pdb=" NE ARG A 599 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG A 599 " 0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG A 599 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 599 " 0.037 2.00e-02 2.50e+03 pdb="HH11 ARG A 599 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 599 " -0.022 2.00e-02 2.50e+03 pdb="HH21 ARG A 599 " -0.025 2.00e-02 2.50e+03 pdb="HH22 ARG A 599 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 944 " -0.010 2.00e-02 2.50e+03 2.05e-02 4.22e+00 pdb=" CG ASN A 944 " 0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN A 944 " -0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN A 944 " -0.012 2.00e-02 2.50e+03 ... (remaining 1561 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 360 2.18 - 2.78: 18953 2.78 - 3.39: 24797 3.39 - 3.99: 33662 3.99 - 4.60: 53504 Nonbonded interactions: 131276 Sorted by model distance: nonbonded pdb=" H LYS A 498 " pdb=" HA LYS A 498 " model vdw 1.573 1.816 nonbonded pdb=" H VAL A 888 " pdb=" HA VAL A 888 " model vdw 1.578 1.816 nonbonded pdb=" H LYS A 887 " pdb=" HA LYS A 887 " model vdw 1.612 1.816 nonbonded pdb=" H LYS A 885 " pdb=" HA LYS A 885 " model vdw 1.650 1.816 nonbonded pdb=" H GLY A 795 " pdb=" HA3 GLY A 795 " model vdw 1.652 1.816 ... (remaining 131271 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: 0.760 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: 0.070 Extract box with map and model: 0.140 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.450 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 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 : 0.013 0.144 6260 Z= 0.530 Angle : 1.214 27.742 8559 Z= 0.618 Chirality : 0.057 0.273 987 Planarity : 0.006 0.086 979 Dihedral : 14.452 90.973 2625 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.24 % Favored : 89.47 % Rotamer: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.76 % 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: -4.18 (0.27), residues: 674 helix: -1.69 (0.24), residues: 332 sheet: -3.14 (0.46), residues: 89 loop : -4.04 (0.31), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 619 TYR 0.025 0.003 TYR A 455 PHE 0.014 0.002 PHE A 517 TRP 0.011 0.002 TRP A 737 HIS 0.011 0.002 HIS A 506 Details of bonding type rmsd/Z covalent geometry : bond 0.01274 / 0.53 ( 6256) covalent geometry : angle 1.14869 / 0.61 ( 8553) hydrogen bonds : bond 0.12679 / 8.64 ( 292) hydrogen bonds : angle 6.10044 / 4.23 ( 815) metal coordination : bond 0.05547 / 2.75 ( 4) metal coordination : angle 14.91553 / 7.43 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue LEU 669 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue SER 838 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue SER 880 is missing expected H atoms. Skipping. Residue ILE 881 is missing expected H atoms. Skipping. Residue LEU 882 is missing expected H atoms. Skipping. Residue LYS 884 is missing expected H atoms. Skipping. Residue LYS 885 is missing expected H atoms. Skipping. Residue MET 886 is missing expected H atoms. Skipping. Residue LYS 887 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 179 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 SER cc_start: 0.7952 (m) cc_final: 0.7656 (p) REVERT: A 515 ASP cc_start: 0.7569 (t0) cc_final: 0.7348 (t0) REVERT: A 639 PHE cc_start: 0.7356 (m-10) cc_final: 0.6742 (t80) REVERT: A 959 GLU cc_start: 0.7590 (tt0) cc_final: 0.7198 (mt-10) REVERT: A 973 VAL cc_start: 0.9014 (t) cc_final: 0.8663 (m) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.1989 time to fit residues: 44.4637 Evaluate side-chains 96 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 GLN A 396 GLN A 457 ASN A 563 GLN A 678 ASN A 862 GLN ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.149504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.130548 restraints weight = 22400.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.135372 restraints weight = 10323.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.138374 restraints weight = 6220.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.140282 restraints weight = 4371.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.141685 restraints weight = 3378.137| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6260 Z= 0.130 Angle : 0.761 21.410 8559 Z= 0.408 Chirality : 0.040 0.172 987 Planarity : 0.005 0.104 979 Dihedral : 16.027 77.052 1200 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 1.97 % Allowed : 9.21 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.30), residues: 674 helix: 0.05 (0.27), residues: 336 sheet: -2.72 (0.47), residues: 94 loop : -3.83 (0.34), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 599 TYR 0.017 0.002 TYR A 342 PHE 0.016 0.001 PHE A 551 TRP 0.010 0.001 TRP A 968 HIS 0.004 0.001 HIS A 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 6256) covalent geometry : angle 0.75062 / 0.41 ( 8553) hydrogen bonds : bond 0.04229 / 2.75 ( 292) hydrogen bonds : angle 4.49798 / 3.10 ( 815) metal coordination : bond 0.00501 / 0.25 ( 4) metal coordination : angle 4.69757 / 2.34 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue LEU 669 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue SER 838 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue SER 880 is missing expected H atoms. Skipping. Residue ILE 881 is missing expected H atoms. Skipping. Residue LEU 882 is missing expected H atoms. Skipping. Residue LYS 884 is missing expected H atoms. Skipping. Residue LYS 885 is missing expected H atoms. Skipping. Residue MET 886 is missing expected H atoms. Skipping. Residue LYS 887 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 122 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 SER cc_start: 0.7903 (m) cc_final: 0.7336 (p) REVERT: A 515 ASP cc_start: 0.7774 (t0) cc_final: 0.7559 (t0) REVERT: A 614 ILE cc_start: 0.7771 (pt) cc_final: 0.7125 (mt) REVERT: A 639 PHE cc_start: 0.7243 (m-10) cc_final: 0.6752 (t80) REVERT: A 854 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7568 (ptt) REVERT: A 973 VAL cc_start: 0.9004 (t) cc_final: 0.8727 (m) outliers start: 12 outliers final: 7 residues processed: 115 average time/residue: 0.1478 time to fit residues: 22.8703 Evaluate side-chains 89 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 793 GLU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 854 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 50 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 919 ASN A 966 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.140677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.121148 restraints weight = 23075.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.125820 restraints weight = 10831.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.128736 restraints weight = 6613.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.130631 restraints weight = 4718.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.131870 restraints weight = 3699.657| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6260 Z= 0.203 Angle : 0.789 21.521 8559 Z= 0.419 Chirality : 0.041 0.150 987 Planarity : 0.004 0.051 979 Dihedral : 15.500 81.492 1200 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.50 % Favored : 90.36 % Rotamer: Outliers : 2.14 % Allowed : 11.84 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.31), residues: 674 helix: 0.72 (0.28), residues: 336 sheet: -2.81 (0.43), residues: 106 loop : -3.62 (0.34), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 985 TYR 0.015 0.002 TYR A 455 PHE 0.012 0.001 PHE A 401 TRP 0.004 0.001 TRP A 737 HIS 0.009 0.001 HIS A 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.20 ( 6256) covalent geometry : angle 0.76219 / 0.42 ( 8553) hydrogen bonds : bond 0.04284 / 2.75 ( 292) hydrogen bonds : angle 4.28309 / 2.98 ( 815) metal coordination : bond 0.01065 / 0.53 ( 4) metal coordination : angle 7.74688 / 3.30 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue LEU 669 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue SER 838 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue SER 880 is missing expected H atoms. Skipping. Residue ILE 881 is missing expected H atoms. Skipping. Residue LEU 882 is missing expected H atoms. Skipping. Residue LYS 884 is missing expected H atoms. Skipping. Residue LYS 885 is missing expected H atoms. Skipping. Residue MET 886 is missing expected H atoms. Skipping. Residue LYS 887 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 105 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 SER cc_start: 0.7915 (m) cc_final: 0.7390 (p) REVERT: A 515 ASP cc_start: 0.7949 (t0) cc_final: 0.7721 (t0) REVERT: A 973 VAL cc_start: 0.9283 (t) cc_final: 0.9080 (m) outliers start: 13 outliers final: 7 residues processed: 100 average time/residue: 0.1416 time to fit residues: 19.2642 Evaluate side-chains 81 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 966 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 53 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 GLN ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.141139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.121977 restraints weight = 23020.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.126610 restraints weight = 10685.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.129560 restraints weight = 6491.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.131259 restraints weight = 4602.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.132545 restraints weight = 3651.898| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6260 Z= 0.145 Angle : 0.716 21.191 8559 Z= 0.391 Chirality : 0.039 0.145 987 Planarity : 0.003 0.041 979 Dihedral : 15.350 79.381 1200 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 2.30 % Allowed : 12.34 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.32), residues: 674 helix: 1.18 (0.28), residues: 337 sheet: -2.56 (0.44), residues: 104 loop : -3.51 (0.35), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 375 TYR 0.012 0.001 TYR A 455 PHE 0.012 0.001 PHE A 401 TRP 0.003 0.001 TRP A 582 HIS 0.005 0.001 HIS A 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 ( 6256) covalent geometry : angle 0.70803 / 0.39 ( 8553) hydrogen bonds : bond 0.03738 / 2.42 ( 292) hydrogen bonds : angle 4.04914 / 2.82 ( 815) metal coordination : bond 0.00536 / 0.26 ( 4) metal coordination : angle 4.13555 / 1.72 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue LEU 669 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue SER 838 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue SER 880 is missing expected H atoms. Skipping. Residue ILE 881 is missing expected H atoms. Skipping. Residue LEU 882 is missing expected H atoms. Skipping. Residue LYS 884 is missing expected H atoms. Skipping. Residue LYS 885 is missing expected H atoms. Skipping. Residue MET 886 is missing expected H atoms. Skipping. Residue LYS 887 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 93 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 400 SER cc_start: 0.7793 (m) cc_final: 0.7312 (p) REVERT: A 515 ASP cc_start: 0.8036 (t0) cc_final: 0.7834 (t0) outliers start: 14 outliers final: 13 residues processed: 88 average time/residue: 0.1452 time to fit residues: 17.2342 Evaluate side-chains 86 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 793 GLU Chi-restraints excluded: chain A residue 801 CYS Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 979 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 19 optimal weight: 2.9990 chunk 61 optimal weight: 0.0070 chunk 66 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 41 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.144167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.125026 restraints weight = 22805.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.129731 restraints weight = 10633.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.132687 restraints weight = 6457.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.134558 restraints weight = 4572.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.135663 restraints weight = 3569.404| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6260 Z= 0.098 Angle : 0.678 21.081 8559 Z= 0.370 Chirality : 0.038 0.153 987 Planarity : 0.003 0.041 979 Dihedral : 15.236 79.566 1200 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.75 % Favored : 91.10 % Rotamer: Outliers : 1.97 % Allowed : 12.99 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.33), residues: 674 helix: 1.65 (0.29), residues: 332 sheet: -1.90 (0.47), residues: 97 loop : -3.36 (0.36), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 375 TYR 0.009 0.001 TYR A 455 PHE 0.009 0.001 PHE A 401 TRP 0.003 0.000 TRP A 582 HIS 0.003 0.001 HIS A 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 ( 6256) covalent geometry : angle 0.67158 / 0.37 ( 8553) hydrogen bonds : bond 0.03262 / 2.11 ( 292) hydrogen bonds : angle 3.76222 / 2.64 ( 815) metal coordination : bond 0.00387 / 0.19 ( 4) metal coordination : angle 3.55785 / 1.44 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue LEU 669 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue SER 838 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue SER 880 is missing expected H atoms. Skipping. Residue ILE 881 is missing expected H atoms. Skipping. Residue LEU 882 is missing expected H atoms. Skipping. Residue LYS 884 is missing expected H atoms. Skipping. Residue LYS 885 is missing expected H atoms. Skipping. Residue MET 886 is missing expected H atoms. Skipping. Residue LYS 887 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 98 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 400 SER cc_start: 0.7717 (m) cc_final: 0.7286 (p) REVERT: A 973 VAL cc_start: 0.9356 (t) cc_final: 0.9093 (m) outliers start: 12 outliers final: 10 residues processed: 91 average time/residue: 0.1253 time to fit residues: 16.1291 Evaluate side-chains 87 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 793 GLU Chi-restraints excluded: chain A residue 801 CYS Chi-restraints excluded: chain A residue 979 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 20 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.141163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.122042 restraints weight = 23102.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.126655 restraints weight = 10836.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.129330 restraints weight = 6614.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.131319 restraints weight = 4811.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.132584 restraints weight = 3740.811| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.4921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6260 Z= 0.145 Angle : 0.703 21.223 8559 Z= 0.383 Chirality : 0.038 0.135 987 Planarity : 0.003 0.036 979 Dihedral : 15.276 79.376 1200 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 2.30 % Allowed : 13.65 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.33), residues: 674 helix: 1.73 (0.29), residues: 333 sheet: -1.86 (0.47), residues: 97 loop : -3.31 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 375 TYR 0.009 0.001 TYR A 312 PHE 0.012 0.001 PHE A 401 TRP 0.004 0.001 TRP A 385 HIS 0.005 0.001 HIS A 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 6256) covalent geometry : angle 0.69657 / 0.38 ( 8553) hydrogen bonds : bond 0.03512 / 2.29 ( 292) hydrogen bonds : angle 3.80949 / 2.67 ( 815) metal coordination : bond 0.00587 / 0.29 ( 4) metal coordination : angle 3.58454 / 1.42 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue LEU 669 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue SER 838 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue SER 880 is missing expected H atoms. Skipping. Residue ILE 881 is missing expected H atoms. Skipping. Residue LEU 882 is missing expected H atoms. Skipping. Residue LYS 884 is missing expected H atoms. Skipping. Residue LYS 885 is missing expected H atoms. Skipping. Residue MET 886 is missing expected H atoms. Skipping. Residue LYS 887 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 99 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.304 Fit side-chains revert: symmetry clash REVERT: A 400 SER cc_start: 0.7839 (m) cc_final: 0.7419 (p) outliers start: 14 outliers final: 14 residues processed: 92 average time/residue: 0.1199 time to fit residues: 15.4274 Evaluate side-chains 91 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 793 GLU Chi-restraints excluded: chain A residue 801 CYS Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 961 ILE Chi-restraints excluded: chain A residue 979 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 19 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.141783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.122739 restraints weight = 23045.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.127375 restraints weight = 10723.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.130218 restraints weight = 6530.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.132071 restraints weight = 4680.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.133206 restraints weight = 3674.886| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.5061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6260 Z= 0.110 Angle : 0.674 21.130 8559 Z= 0.369 Chirality : 0.037 0.142 987 Planarity : 0.003 0.037 979 Dihedral : 15.128 79.019 1200 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % Rotamer: Outliers : 1.81 % Allowed : 14.47 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.34), residues: 674 helix: 1.90 (0.29), residues: 333 sheet: -1.90 (0.47), residues: 100 loop : -3.25 (0.36), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 714 TYR 0.009 0.001 TYR A 830 PHE 0.009 0.001 PHE A 401 TRP 0.002 0.001 TRP A 385 HIS 0.003 0.001 HIS A 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 ( 6256) covalent geometry : angle 0.66855 / 0.37 ( 8553) hydrogen bonds : bond 0.03251 / 2.10 ( 292) hydrogen bonds : angle 3.68768 / 2.60 ( 815) metal coordination : bond 0.00512 / 0.26 ( 4) metal coordination : angle 3.18546 / 1.27 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue LEU 669 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue SER 838 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue SER 880 is missing expected H atoms. Skipping. Residue ILE 881 is missing expected H atoms. Skipping. Residue LEU 882 is missing expected H atoms. Skipping. Residue LYS 884 is missing expected H atoms. Skipping. Residue LYS 885 is missing expected H atoms. Skipping. Residue MET 886 is missing expected H atoms. Skipping. Residue LYS 887 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 96 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 400 SER cc_start: 0.7797 (m) cc_final: 0.7387 (p) outliers start: 11 outliers final: 9 residues processed: 89 average time/residue: 0.1302 time to fit residues: 16.2037 Evaluate side-chains 89 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 801 CYS Chi-restraints excluded: chain A residue 979 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 45 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 61 optimal weight: 0.0000 chunk 7 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.140067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.121020 restraints weight = 22992.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.125519 restraints weight = 10775.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.128353 restraints weight = 6622.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.130003 restraints weight = 4752.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.131373 restraints weight = 3810.836| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.5230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6260 Z= 0.146 Angle : 0.695 21.168 8559 Z= 0.381 Chirality : 0.038 0.134 987 Planarity : 0.003 0.035 979 Dihedral : 15.089 77.860 1200 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.24 % Favored : 89.76 % Rotamer: Outliers : 1.97 % Allowed : 14.64 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.34), residues: 674 helix: 1.86 (0.29), residues: 334 sheet: -1.99 (0.47), residues: 100 loop : -3.28 (0.36), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 714 TYR 0.008 0.001 TYR A 312 PHE 0.011 0.001 PHE A 401 TRP 0.004 0.001 TRP A 385 HIS 0.004 0.001 HIS A 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 ( 6256) covalent geometry : angle 0.68992 / 0.38 ( 8553) hydrogen bonds : bond 0.03419 / 2.23 ( 292) hydrogen bonds : angle 3.79774 / 2.66 ( 815) metal coordination : bond 0.00600 / 0.30 ( 4) metal coordination : angle 3.37424 / 1.34 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue LEU 669 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue SER 838 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue SER 880 is missing expected H atoms. Skipping. Residue ILE 881 is missing expected H atoms. Skipping. Residue LEU 882 is missing expected H atoms. Skipping. Residue LYS 884 is missing expected H atoms. Skipping. Residue LYS 885 is missing expected H atoms. Skipping. Residue MET 886 is missing expected H atoms. Skipping. Residue LYS 887 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 93 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 SER cc_start: 0.7921 (m) cc_final: 0.7497 (p) outliers start: 12 outliers final: 11 residues processed: 89 average time/residue: 0.1245 time to fit residues: 15.6610 Evaluate side-chains 89 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 793 GLU Chi-restraints excluded: chain A residue 801 CYS Chi-restraints excluded: chain A residue 979 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.142485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.123456 restraints weight = 23004.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.128005 restraints weight = 10676.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.130839 restraints weight = 6537.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.132660 restraints weight = 4678.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.133729 restraints weight = 3701.802| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.5325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 6260 Z= 0.105 Angle : 0.674 21.079 8559 Z= 0.371 Chirality : 0.037 0.141 987 Planarity : 0.003 0.036 979 Dihedral : 15.013 76.570 1200 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 1.97 % Allowed : 15.30 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.34), residues: 674 helix: 1.97 (0.29), residues: 334 sheet: -1.85 (0.49), residues: 100 loop : -3.20 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 714 TYR 0.008 0.001 TYR A 631 PHE 0.009 0.001 PHE A 401 TRP 0.001 0.000 TRP A 968 HIS 0.002 0.001 HIS A 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 ( 6256) covalent geometry : angle 0.67085 / 0.37 ( 8553) hydrogen bonds : bond 0.03187 / 2.07 ( 292) hydrogen bonds : angle 3.69353 / 2.60 ( 815) metal coordination : bond 0.00456 / 0.23 ( 4) metal coordination : angle 2.71450 / 1.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue LEU 669 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue SER 838 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue SER 880 is missing expected H atoms. Skipping. Residue ILE 881 is missing expected H atoms. Skipping. Residue LEU 882 is missing expected H atoms. Skipping. Residue LYS 884 is missing expected H atoms. Skipping. Residue LYS 885 is missing expected H atoms. Skipping. Residue MET 886 is missing expected H atoms. Skipping. Residue LYS 887 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 97 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 SER cc_start: 0.8013 (m) cc_final: 0.7606 (p) outliers start: 12 outliers final: 11 residues processed: 92 average time/residue: 0.1248 time to fit residues: 16.1213 Evaluate side-chains 88 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 793 GLU Chi-restraints excluded: chain A residue 801 CYS Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 979 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 45 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 GLN ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.142389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.123476 restraints weight = 22985.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.127989 restraints weight = 10701.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.130818 restraints weight = 6572.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.132637 restraints weight = 4707.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.133743 restraints weight = 3713.194| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.5438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6260 Z= 0.108 Angle : 0.672 21.156 8559 Z= 0.369 Chirality : 0.037 0.139 987 Planarity : 0.003 0.035 979 Dihedral : 15.020 74.175 1200 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 1.81 % Allowed : 15.30 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.34), residues: 674 helix: 2.00 (0.29), residues: 334 sheet: -1.87 (0.49), residues: 102 loop : -3.15 (0.37), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 714 TYR 0.010 0.001 TYR A 830 PHE 0.009 0.001 PHE A 401 TRP 0.003 0.001 TRP A 968 HIS 0.002 0.001 HIS A 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 ( 6256) covalent geometry : angle 0.66852 / 0.37 ( 8553) hydrogen bonds : bond 0.03135 / 2.03 ( 292) hydrogen bonds : angle 3.65025 / 2.58 ( 815) metal coordination : bond 0.00450 / 0.23 ( 4) metal coordination : angle 2.69943 / 1.05 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue LEU 669 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue SER 838 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue SER 880 is missing expected H atoms. Skipping. Residue ILE 881 is missing expected H atoms. Skipping. Residue LEU 882 is missing expected H atoms. Skipping. Residue LYS 884 is missing expected H atoms. Skipping. Residue LYS 885 is missing expected H atoms. Skipping. Residue MET 886 is missing expected H atoms. Skipping. Residue LYS 887 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 95 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 SER cc_start: 0.7974 (m) cc_final: 0.7569 (p) REVERT: A 883 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8254 (tm-30) outliers start: 11 outliers final: 11 residues processed: 91 average time/residue: 0.1247 time to fit residues: 16.2071 Evaluate side-chains 93 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 793 GLU Chi-restraints excluded: chain A residue 801 CYS Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 979 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 25 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 50 optimal weight: 0.0370 chunk 69 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.7464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.142860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.124189 restraints weight = 23193.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.128756 restraints weight = 10492.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.131614 restraints weight = 6303.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.133377 restraints weight = 4461.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.134653 restraints weight = 3513.144| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.5550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 6260 Z= 0.100 Angle : 0.674 21.053 8559 Z= 0.370 Chirality : 0.037 0.141 987 Planarity : 0.003 0.035 979 Dihedral : 14.982 74.057 1200 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 1.48 % Allowed : 15.95 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.34), residues: 674 helix: 2.10 (0.29), residues: 334 sheet: -1.81 (0.49), residues: 102 loop : -3.07 (0.37), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 714 TYR 0.008 0.001 TYR A 631 PHE 0.007 0.001 PHE A 401 TRP 0.002 0.000 TRP A 968 HIS 0.002 0.000 HIS A 928 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 ( 6256) covalent geometry : angle 0.67157 / 0.37 ( 8553) hydrogen bonds : bond 0.03038 / 1.97 ( 292) hydrogen bonds : angle 3.60272 / 2.56 ( 815) metal coordination : bond 0.00385 / 0.19 ( 4) metal coordination : angle 2.43944 / 0.94 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1847.71 seconds wall clock time: 32 minutes 20.38 seconds (1940.38 seconds total)