Starting phenix.real_space_refine on Thu Aug 6 07:23:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8b9g_15931/08_2026/8b9g_15931.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b9g_15931/08_2026/8b9g_15931.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8b9g_15931/08_2026/8b9g_15931.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b9g_15931/08_2026/8b9g_15931.map" model { file = "/net/cci-nas-00/data/ceres_data/8b9g_15931/08_2026/8b9g_15931.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b9g_15931/08_2026/8b9g_15931.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8b9g_15931/08_2026/8b9g_15931.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8b9g_15931/08_2026/8b9g_15931.cif" } resolution = 2.86 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= 0.005 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7745 atoms to isotropic. 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 Al 1 5.89 5 P 12 5.49 5 S 48 5.16 5 C 4890 2.51 5 N 1333 2.21 5 O 1494 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.17s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7782 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7545 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 953, 7534 Classifications: {'peptide': 953} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 906} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 953, 7534 Classifications: {'peptide': 953} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 906} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 7666 Chain: "C" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 200 Classifications: {'RNAv2': 10} Modifications used: {'rna2p_pyr': 3, 'rna3p_pyr': 7} Link IDs: {'rna2p': 2, 'rna3p': 7} Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 37 Unusual residues: {'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 2, 'water': 5} Link IDs: {None: 6} Time building chain proxies: 3.23, per 1000 atoms: 0.42 Number of scatterers: 7782 At special positions: 0 Unit cell: (91.242, 92.886, 103.572, 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) S 48 16.00 P 12 15.00 Al 1 13.00 F 4 9.00 O 1494 8.00 N 1333 7.00 C 4890 6.00 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: 0.52 Conformation dependent library (CDL) restraints added in 498.7 milliseconds 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1822 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 7 sheets defined 51.7% alpha, 14.2% beta 0 base pairs and 2 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 166 through 182 removed outlier: 4.207A pdb=" N LYS A 171 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N GLU A 172 " --> pdb=" O GLU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 242 Processing helix chain 'A' and resid 268 through 283 Processing helix chain 'A' and resid 352 through 371 Processing helix chain 'A' and resid 371 through 383 removed outlier: 3.736A pdb=" N LYS A 383 " --> pdb=" O GLU A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.669A pdb=" N ALA A 388 " --> pdb=" O PRO A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 400 Processing helix chain 'A' and resid 412 through 428 removed outlier: 4.583A pdb=" N ALA A 418 " --> pdb=" O THR A 414 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N GLN A 419 " --> pdb=" O THR A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 433 Processing helix chain 'A' and resid 442 through 457 Processing helix chain 'A' and resid 487 through 494 Processing helix chain 'A' and resid 495 through 497 No H-bonds generated for 'chain 'A' and resid 495 through 497' Processing helix chain 'A' and resid 509 through 512 removed outlier: 3.772A pdb=" N ARG A 512 " --> pdb=" O ILE A 509 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 509 through 512' Processing helix chain 'A' and resid 513 through 530 Processing helix chain 'A' and resid 543 through 551 Processing helix chain 'A' and resid 570 through 579 Processing helix chain 'A' and resid 610 through 614 Processing helix chain 'A' and resid 620 through 630 Processing helix chain 'A' and resid 636 through 650 Processing helix chain 'A' and resid 662 through 675 Processing helix chain 'A' and resid 695 through 702 removed outlier: 3.780A pdb=" N VAL A 702 " --> pdb=" O GLU A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 721 Processing helix chain 'A' and resid 758 through 767 Processing helix chain 'A' and resid 782 through 789 Processing helix chain 'A' and resid 795 through 799 Processing helix chain 'A' and resid 802 through 812 Processing helix chain 'A' and resid 816 through 823 Processing helix chain 'A' and resid 829 through 843 Processing helix chain 'A' and resid 853 through 861 Processing helix chain 'A' and resid 865 through 878 Processing helix chain 'A' and resid 880 through 892 Processing helix chain 'A' and resid 908 through 913 Processing helix chain 'A' and resid 914 through 916 No H-bonds generated for 'chain 'A' and resid 914 through 916' Processing helix chain 'A' and resid 920 through 937 Processing helix chain 'A' and resid 939 through 951 Processing helix chain 'A' and resid 953 through 975 Processing helix chain 'A' and resid 977 through 982 removed outlier: 3.755A pdb=" N ILE A 982 " --> pdb=" O GLU A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1008 removed outlier: 3.725A pdb=" N LEU A1006 " --> pdb=" O ALA A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1077 Processing helix chain 'A' and resid 1086 through 1088 No H-bonds generated for 'chain 'A' and resid 1086 through 1088' Processing helix chain 'A' and resid 1101 through 1110 Processing helix chain 'A' and resid 1110 through 1125 removed outlier: 3.951A pdb=" N ALA A1114 " --> pdb=" O ALA A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1129 removed outlier: 3.605A pdb=" N ILE A1129 " --> pdb=" O PRO A1126 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1126 through 1129' Processing helix chain 'A' and resid 1133 through 1148 Processing sheet with id=AA1, first strand: chain 'A' and resid 188 through 192 Processing sheet with id=AA2, first strand: chain 'A' and resid 263 through 264 removed outlier: 6.148A pdb=" N TYR A 263 " --> pdb=" O ASP A1099 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 328 through 329 removed outlier: 4.380A pdb=" N ALA A 329 " --> pdb=" O LEU A 498 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 472 through 474 removed outlier: 6.819A pdb=" N GLY A 466 " --> pdb=" O PHE A 484 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N THR A 486 " --> pdb=" O GLY A 466 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N SER A 468 " --> pdb=" O THR A 486 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE A 436 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N CYS A 485 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N VAL A 438 " --> pdb=" O CYS A 485 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ASN A 435 " --> pdb=" O HIS A 503 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ILE A 505 " --> pdb=" O ASN A 435 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N TYR A 437 " --> pdb=" O ILE A 505 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ASP A 507 " --> pdb=" O TYR A 437 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR A 439 " --> pdb=" O ASP A 507 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 566 through 569 removed outlier: 6.103A pdb=" N GLN A 567 " --> pdb=" O CYS A 777 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N THR A 779 " --> pdb=" O GLN A 567 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N PHE A 569 " --> pdb=" O THR A 779 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL A 730 " --> pdb=" O PHE A 776 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N PHE A 778 " --> pdb=" O VAL A 730 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL A 732 " --> pdb=" O PHE A 778 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ALA A 655 " --> pdb=" O PHE A 731 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ILE A 733 " --> pdb=" O ALA A 655 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU A 657 " --> pdb=" O ILE A 733 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 737 through 744 Processing sheet with id=AA7, first strand: chain 'A' and resid 1012 through 1017 removed outlier: 6.948A pdb=" N LYS A1020 " --> pdb=" O LYS A1016 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ALA A1028 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N CYS A1063 " --> pdb=" O ALA A1028 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU A1030 " --> pdb=" O CYS A1063 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N GLN A1065 " --> pdb=" O LEU A1030 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL A1061 " --> pdb=" O ARG A1057 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ARG A1057 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N CYS A1063 " --> pdb=" O LYS A1055 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LYS A1055 " --> pdb=" O CYS A1063 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N GLN A1065 " --> pdb=" O GLY A1053 " (cutoff:3.500A) 377 hydrogen bonds defined for protein. 1080 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 2 stacking parallelities Total time for adding SS restraints: 1.59 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2546 1.34 - 1.48: 1851 1.48 - 1.61: 3470 1.61 - 1.74: 0 1.74 - 1.88: 77 Bond restraints: 7944 Sorted by residual: bond pdb=" F2 ALF A1202 " pdb="AL ALF A1202 " ideal model delta sigma weight residual 1.685 1.877 -0.192 2.00e-02 2.50e+03 9.20e+01 bond pdb=" F1 ALF A1202 " pdb="AL ALF A1202 " ideal model delta sigma weight residual 1.684 1.865 -0.181 2.00e-02 2.50e+03 8.20e+01 bond pdb=" F4 ALF A1202 " pdb="AL ALF A1202 " ideal model delta sigma weight residual 1.686 1.808 -0.122 2.00e-02 2.50e+03 3.70e+01 bond pdb=" F3 ALF A1202 " pdb="AL ALF A1202 " ideal model delta sigma weight residual 1.685 1.805 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" N GLU A 585 " pdb=" CA GLU A 585 " ideal model delta sigma weight residual 1.456 1.484 -0.028 1.40e-02 5.10e+03 3.98e+00 ... (remaining 7939 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.00: 10805 14.00 - 28.00: 4 28.00 - 42.01: 0 42.01 - 56.01: 0 56.01 - 70.01: 2 Bond angle restraints: 10811 Sorted by residual: angle pdb=" F1 ALF A1202 " pdb="AL ALF A1202 " pdb=" F2 ALF A1202 " ideal model delta sigma weight residual 108.68 178.69 -70.01 3.00e+00 1.11e-01 5.45e+02 angle pdb=" F3 ALF A1202 " pdb="AL ALF A1202 " pdb=" F4 ALF A1202 " ideal model delta sigma weight residual 109.63 178.75 -69.12 3.00e+00 1.11e-01 5.31e+02 angle pdb=" F2 ALF A1202 " pdb="AL ALF A1202 " pdb=" F3 ALF A1202 " ideal model delta sigma weight residual 109.59 89.09 20.50 3.00e+00 1.11e-01 4.67e+01 angle pdb=" F1 ALF A1202 " pdb="AL ALF A1202 " pdb=" F4 ALF A1202 " ideal model delta sigma weight residual 109.02 88.71 20.31 3.00e+00 1.11e-01 4.58e+01 angle pdb=" F1 ALF A1202 " pdb="AL ALF A1202 " pdb=" F3 ALF A1202 " ideal model delta sigma weight residual 109.69 90.05 19.64 3.00e+00 1.11e-01 4.29e+01 ... (remaining 10806 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.87: 4349 20.87 - 41.73: 386 41.73 - 62.60: 88 62.60 - 83.46: 15 83.46 - 104.33: 7 Dihedral angle restraints: 4845 sinusoidal: 2047 harmonic: 2798 Sorted by residual: dihedral pdb=" C4' U C 10 " pdb=" C3' U C 10 " pdb=" C2' U C 10 " pdb=" C1' U C 10 " ideal model delta sinusoidal sigma weight residual 36.34 -34.77 71.11 1 3.10e+00 1.04e-01 6.76e+02 dihedral pdb=" C4' U C 1 " pdb=" C3' U C 1 " pdb=" C2' U C 1 " pdb=" C1' U C 1 " ideal model delta sinusoidal sigma weight residual 36.34 -34.57 70.91 1 3.10e+00 1.04e-01 6.72e+02 dihedral pdb=" C4' U C 9 " pdb=" C3' U C 9 " pdb=" C2' U C 9 " pdb=" C1' U C 9 " ideal model delta sinusoidal sigma weight residual 36.34 -34.53 70.88 1 3.10e+00 1.04e-01 6.72e+02 ... (remaining 4842 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1032 0.060 - 0.120: 180 0.120 - 0.180: 22 0.180 - 0.239: 12 0.239 - 0.299: 3 Chirality restraints: 1249 Sorted by residual: chirality pdb=" C2' U C 9 " pdb=" C3' U C 9 " pdb=" O2' U C 9 " pdb=" C1' U C 9 " both_signs ideal model delta sigma weight residual False -2.79 -2.49 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" C2' U C 1 " pdb=" C3' U C 1 " pdb=" O2' U C 1 " pdb=" C1' U C 1 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" C2' U C 10 " pdb=" C3' U C 10 " pdb=" O2' U C 10 " pdb=" C1' U C 10 " both_signs ideal model delta sigma weight residual False -2.79 -2.52 -0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 1246 not shown) Planarity restraints: 1358 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 261 " 0.033 5.00e-02 4.00e+02 4.94e-02 3.91e+00 pdb=" N PRO A 262 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 262 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 262 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 865 " 0.031 5.00e-02 4.00e+02 4.75e-02 3.62e+00 pdb=" N PRO A 866 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 866 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 866 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 146 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.59e+00 pdb=" C GLN A 146 " -0.033 2.00e-02 2.50e+03 pdb=" O GLN A 146 " 0.012 2.00e-02 2.50e+03 pdb=" N ARG A 147 " 0.011 2.00e-02 2.50e+03 ... (remaining 1355 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.29: 12 2.29 - 2.94: 3313 2.94 - 3.59: 11713 3.59 - 4.25: 19485 4.25 - 4.90: 31715 Nonbonded interactions: 66238 Sorted by model distance: nonbonded pdb=" OG1 THR A 414 " pdb=" F4 ALF A1202 " model vdw 1.632 2.990 nonbonded pdb=" OD2 ASP A 507 " pdb=" F4 ALF A1202 " model vdw 1.858 2.990 nonbonded pdb=" O2A ADP A1201 " pdb=" O HOH A1301 " model vdw 2.056 3.040 nonbonded pdb=" O ILE A 574 " pdb=" OG1 THR A 578 " model vdw 2.139 3.040 nonbonded pdb=" OG1 THR A 414 " pdb="AL ALF A1202 " model vdw 2.167 2.760 ... (remaining 66233 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.230 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.040 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:7.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.192 7944 Z= 0.242 Angle : 1.212 70.010 10811 Z= 0.474 Chirality : 0.052 0.299 1249 Planarity : 0.005 0.049 1358 Dihedral : 16.900 104.328 3023 Min Nonbonded Distance : 1.632 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.43 % Favored : 97.35 % Rotamer: Outliers : 1.43 % Allowed : 17.52 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.28), residues: 947 helix: 1.76 (0.24), residues: 449 sheet: 0.08 (0.41), residues: 165 loop : 0.17 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 739 TYR 0.018 0.002 TYR A 890 PHE 0.018 0.002 PHE A 667 TRP 0.010 0.002 TRP A 932 HIS 0.004 0.001 HIS A 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.24 ( 7944) covalent geometry : angle 1.21217 / 0.47 (10811) hydrogen bonds : bond 0.11087 / 7.68 ( 377) hydrogen bonds : angle 4.78750 / 3.48 ( 1080) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.311 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 48 average time/residue: 0.7482 time to fit residues: 37.8775 Evaluate side-chains 32 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 1121 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 175 ASN A 196 HIS A 339 HIS A 342 ASN A 435 ASN ** A 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN A1011 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.064779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.049682 restraints weight = 46846.411| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 4.76 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2996 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7944 Z= 0.132 Angle : 0.687 15.859 10811 Z= 0.318 Chirality : 0.051 0.584 1249 Planarity : 0.004 0.049 1358 Dihedral : 7.808 83.213 1167 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.80 % Favored : 98.10 % Rotamer: Outliers : 2.03 % Allowed : 16.81 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.28), residues: 947 helix: 2.05 (0.25), residues: 452 sheet: 0.32 (0.42), residues: 159 loop : 0.17 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 934 TYR 0.006 0.001 TYR A 530 PHE 0.015 0.001 PHE A 667 TRP 0.010 0.001 TRP A 663 HIS 0.003 0.001 HIS A 746 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 7944) covalent geometry : angle 0.68733 / 0.32 (10811) hydrogen bonds : bond 0.03440 / 2.47 ( 377) hydrogen bonds : angle 4.10211 / 2.98 ( 1080) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 30 time to evaluate : 0.301 Fit side-chains REVERT: A 865 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7286 (mp0) REVERT: A 942 MET cc_start: 0.8314 (mmm) cc_final: 0.7839 (mtp) REVERT: A 950 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7850 (tppp) REVERT: A 954 MET cc_start: 0.7966 (ttm) cc_final: 0.7697 (ttm) outliers start: 16 outliers final: 2 residues processed: 45 average time/residue: 0.5656 time to fit residues: 27.2272 Evaluate side-chains 30 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 950 LYS Chi-restraints excluded: chain A residue 1092 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 84 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 56 optimal weight: 0.0980 chunk 25 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 972 GLN ** 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 = 0.3337 r_free = 0.3337 target = 0.062945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.048548 restraints weight = 38070.996| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 4.28 r_work: 0.2804 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2810 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7944 Z= 0.131 Angle : 0.598 8.097 10811 Z= 0.284 Chirality : 0.048 0.430 1249 Planarity : 0.004 0.051 1358 Dihedral : 7.023 65.520 1163 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.69 % Favored : 98.20 % Rotamer: Outliers : 1.31 % Allowed : 16.81 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.28), residues: 947 helix: 2.14 (0.24), residues: 452 sheet: 0.31 (0.43), residues: 159 loop : 0.19 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 375 TYR 0.010 0.001 TYR A 187 PHE 0.017 0.001 PHE A 667 TRP 0.010 0.001 TRP A 663 HIS 0.004 0.001 HIS A 746 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 7944) covalent geometry : angle 0.59801 / 0.28 (10811) hydrogen bonds : bond 0.03492 / 2.47 ( 377) hydrogen bonds : angle 4.04167 / 2.94 ( 1080) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 27 time to evaluate : 0.308 Fit side-chains REVERT: A 865 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7530 (mp0) REVERT: A 942 MET cc_start: 0.8460 (mmm) cc_final: 0.7990 (mtp) REVERT: A 950 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7950 (tppp) outliers start: 10 outliers final: 1 residues processed: 34 average time/residue: 0.6823 time to fit residues: 24.7037 Evaluate side-chains 29 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 950 LYS Chi-restraints excluded: chain A residue 1092 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 45 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 4 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 621 GLN A 625 ASN ** A 972 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.061074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.045977 restraints weight = 50657.873| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 4.70 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2925 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2925 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7944 Z= 0.211 Angle : 0.655 9.462 10811 Z= 0.309 Chirality : 0.049 0.479 1249 Planarity : 0.004 0.051 1358 Dihedral : 6.970 74.938 1163 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.90 % Favored : 97.99 % Rotamer: Outliers : 1.43 % Allowed : 16.81 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.28), residues: 947 helix: 1.99 (0.24), residues: 449 sheet: 0.07 (0.43), residues: 160 loop : 0.13 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 739 TYR 0.009 0.001 TYR A1009 PHE 0.016 0.002 PHE A 667 TRP 0.009 0.001 TRP A 663 HIS 0.003 0.001 HIS A 691 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.21 ( 7944) covalent geometry : angle 0.65475 / 0.31 (10811) hydrogen bonds : bond 0.04026 / 2.82 ( 377) hydrogen bonds : angle 4.20287 / 3.05 ( 1080) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 26 time to evaluate : 0.277 Fit side-chains REVERT: A 494 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.9009 (mm) REVERT: A 865 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7778 (mp0) REVERT: A 942 MET cc_start: 0.8474 (mmm) cc_final: 0.7946 (mtm) REVERT: A 950 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8290 (tppp) outliers start: 11 outliers final: 1 residues processed: 35 average time/residue: 0.6998 time to fit residues: 25.9275 Evaluate side-chains 30 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 950 LYS Chi-restraints excluded: chain A residue 1092 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 26 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 74 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 40 optimal weight: 0.0270 chunk 7 optimal weight: 5.9990 overall best weight: 1.1444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 972 GLN ** 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 = 0.3353 r_free = 0.3353 target = 0.062600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.048174 restraints weight = 38529.895| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 4.17 r_work: 0.2816 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2825 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2825 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7944 Z= 0.112 Angle : 0.578 9.231 10811 Z= 0.273 Chirality : 0.046 0.453 1249 Planarity : 0.004 0.050 1358 Dihedral : 6.722 69.077 1163 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.80 % Favored : 98.10 % Rotamer: Outliers : 1.31 % Allowed : 16.33 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.28), residues: 947 helix: 2.14 (0.24), residues: 450 sheet: 0.10 (0.44), residues: 160 loop : 0.25 (0.36), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 375 TYR 0.007 0.001 TYR A 187 PHE 0.015 0.001 PHE A 667 TRP 0.008 0.001 TRP A 663 HIS 0.003 0.001 HIS A 746 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 7944) covalent geometry : angle 0.57780 / 0.27 (10811) hydrogen bonds : bond 0.03237 / 2.29 ( 377) hydrogen bonds : angle 3.93096 / 2.86 ( 1080) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 26 time to evaluate : 0.360 Fit side-chains REVERT: A 494 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8988 (mm) REVERT: A 865 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7804 (mp0) REVERT: A 942 MET cc_start: 0.8545 (mmm) cc_final: 0.8038 (mtm) outliers start: 10 outliers final: 3 residues processed: 32 average time/residue: 0.4627 time to fit residues: 15.9134 Evaluate side-chains 31 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 955 SER Chi-restraints excluded: chain A residue 1092 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 71 optimal weight: 0.5980 chunk 59 optimal weight: 6.9990 chunk 47 optimal weight: 0.1980 chunk 35 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 972 GLN ** 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 = 0.3319 r_free = 0.3319 target = 0.061222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.045588 restraints weight = 71489.390| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 5.48 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2911 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2911 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7944 Z= 0.185 Angle : 0.629 10.590 10811 Z= 0.295 Chirality : 0.048 0.486 1249 Planarity : 0.004 0.049 1358 Dihedral : 6.730 71.935 1163 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.90 % Favored : 97.99 % Rotamer: Outliers : 1.55 % Allowed : 16.21 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.28), residues: 947 helix: 2.08 (0.24), residues: 449 sheet: 0.03 (0.45), residues: 149 loop : 0.26 (0.36), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 375 TYR 0.008 0.001 TYR A 467 PHE 0.016 0.001 PHE A 667 TRP 0.010 0.001 TRP A 663 HIS 0.003 0.001 HIS A 691 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 ( 7944) covalent geometry : angle 0.62857 / 0.29 (10811) hydrogen bonds : bond 0.03785 / 2.65 ( 377) hydrogen bonds : angle 4.06798 / 2.95 ( 1080) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 26 time to evaluate : 0.318 Fit side-chains REVERT: A 494 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8977 (mm) REVERT: A 865 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7800 (mp0) REVERT: A 942 MET cc_start: 0.8557 (mmm) cc_final: 0.8007 (mtm) REVERT: A 950 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8429 (tppp) outliers start: 12 outliers final: 4 residues processed: 37 average time/residue: 0.4813 time to fit residues: 19.1194 Evaluate side-chains 33 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 26 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 950 LYS Chi-restraints excluded: chain A residue 955 SER Chi-restraints excluded: chain A residue 1092 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 84 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 4 optimal weight: 0.0000 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 972 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.062980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.048193 restraints weight = 47261.773| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 4.63 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7944 Z= 0.098 Angle : 0.577 14.293 10811 Z= 0.268 Chirality : 0.045 0.454 1249 Planarity : 0.004 0.051 1358 Dihedral : 6.532 67.371 1163 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.59 % Favored : 98.31 % Rotamer: Outliers : 1.07 % Allowed : 16.81 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.29), residues: 947 helix: 2.25 (0.24), residues: 451 sheet: 0.14 (0.45), residues: 149 loop : 0.40 (0.37), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 375 TYR 0.007 0.001 TYR A 187 PHE 0.013 0.001 PHE A 667 TRP 0.008 0.001 TRP A 663 HIS 0.003 0.001 HIS A 746 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 ( 7944) covalent geometry : angle 0.57716 / 0.27 (10811) hydrogen bonds : bond 0.03041 / 2.16 ( 377) hydrogen bonds : angle 3.84426 / 2.80 ( 1080) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.359 Fit side-chains REVERT: A 494 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8947 (mm) REVERT: A 865 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7682 (mp0) REVERT: A 942 MET cc_start: 0.8539 (mmm) cc_final: 0.7996 (mtm) outliers start: 8 outliers final: 3 residues processed: 33 average time/residue: 0.6409 time to fit residues: 22.5626 Evaluate side-chains 31 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 627 MET Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 1092 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 60 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 16 optimal weight: 7.9990 chunk 49 optimal weight: 0.7980 chunk 58 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.062774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.047960 restraints weight = 48108.744| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 4.66 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7944 Z= 0.107 Angle : 0.585 14.629 10811 Z= 0.271 Chirality : 0.045 0.463 1249 Planarity : 0.004 0.050 1358 Dihedral : 6.445 66.833 1163 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.59 % Favored : 98.31 % Rotamer: Outliers : 0.72 % Allowed : 17.52 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.29), residues: 947 helix: 2.28 (0.24), residues: 451 sheet: 0.18 (0.45), residues: 149 loop : 0.43 (0.37), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 375 TYR 0.006 0.001 TYR A 187 PHE 0.015 0.001 PHE A 667 TRP 0.010 0.001 TRP A 663 HIS 0.003 0.001 HIS A 746 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 7944) covalent geometry : angle 0.58513 / 0.27 (10811) hydrogen bonds : bond 0.03125 / 2.21 ( 377) hydrogen bonds : angle 3.83960 / 2.81 ( 1080) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.269 Fit side-chains REVERT: A 494 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8950 (mm) REVERT: A 865 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7751 (mp0) REVERT: A 942 MET cc_start: 0.8516 (mmm) cc_final: 0.7945 (mtm) outliers start: 5 outliers final: 3 residues processed: 30 average time/residue: 0.5948 time to fit residues: 19.0529 Evaluate side-chains 31 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 627 MET Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 1092 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 87 optimal weight: 5.9990 chunk 41 optimal weight: 0.1980 chunk 77 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 81 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 11 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.062465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.047444 restraints weight = 54049.670| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 4.89 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7944 Z= 0.121 Angle : 0.583 14.201 10811 Z= 0.271 Chirality : 0.045 0.476 1249 Planarity : 0.004 0.049 1358 Dihedral : 6.428 67.401 1163 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.69 % Favored : 98.20 % Rotamer: Outliers : 0.83 % Allowed : 17.40 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.29), residues: 947 helix: 2.30 (0.24), residues: 452 sheet: 0.19 (0.46), residues: 149 loop : 0.41 (0.37), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 375 TYR 0.006 0.001 TYR A 187 PHE 0.015 0.001 PHE A 667 TRP 0.010 0.001 TRP A 663 HIS 0.003 0.001 HIS A 746 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 7944) covalent geometry : angle 0.58300 / 0.27 (10811) hydrogen bonds : bond 0.03193 / 2.25 ( 377) hydrogen bonds : angle 3.85089 / 2.81 ( 1080) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.308 Fit side-chains REVERT: A 494 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8934 (mm) REVERT: A 865 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7825 (mp0) REVERT: A 942 MET cc_start: 0.8588 (mmm) cc_final: 0.7994 (mtm) outliers start: 6 outliers final: 2 residues processed: 31 average time/residue: 0.5935 time to fit residues: 19.6541 Evaluate side-chains 30 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 1092 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 58 optimal weight: 0.0670 chunk 29 optimal weight: 0.0370 chunk 45 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 55 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 56 optimal weight: 0.1980 chunk 21 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.063987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.049362 restraints weight = 46411.190| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 4.61 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3029 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3029 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7944 Z= 0.086 Angle : 0.566 13.743 10811 Z= 0.262 Chirality : 0.044 0.452 1249 Planarity : 0.004 0.050 1358 Dihedral : 6.331 63.732 1163 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.48 % Favored : 98.41 % Rotamer: Outliers : 0.60 % Allowed : 17.76 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.29), residues: 947 helix: 2.41 (0.24), residues: 452 sheet: 0.25 (0.44), residues: 159 loop : 0.36 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 375 TYR 0.009 0.001 TYR A 187 PHE 0.015 0.001 PHE A 667 TRP 0.009 0.001 TRP A 663 HIS 0.003 0.000 HIS A 746 Details of bonding type rmsd/Z covalent geometry : bond 0.00188 / 0.09 ( 7944) covalent geometry : angle 0.56615 / 0.26 (10811) hydrogen bonds : bond 0.02786 / 1.98 ( 377) hydrogen bonds : angle 3.73867 / 2.74 ( 1080) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.239 Fit side-chains REVERT: A 494 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8905 (mm) REVERT: A 865 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7737 (mp0) REVERT: A 942 MET cc_start: 0.8494 (mmm) cc_final: 0.7910 (mtm) outliers start: 4 outliers final: 2 residues processed: 32 average time/residue: 0.5536 time to fit residues: 19.0355 Evaluate side-chains 31 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 1092 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 95 optimal weight: 10.0000 chunk 87 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 62 optimal weight: 0.0570 chunk 85 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.063749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.048361 restraints weight = 70556.074| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 5.49 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2999 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2999 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7944 Z= 0.093 Angle : 0.562 12.120 10811 Z= 0.262 Chirality : 0.044 0.456 1249 Planarity : 0.004 0.049 1358 Dihedral : 6.277 63.230 1163 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.59 % Favored : 98.31 % Rotamer: Outliers : 0.60 % Allowed : 17.76 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.29), residues: 947 helix: 2.45 (0.24), residues: 452 sheet: 0.31 (0.44), residues: 159 loop : 0.38 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 375 TYR 0.008 0.001 TYR A 187 PHE 0.015 0.001 PHE A 667 TRP 0.010 0.001 TRP A 663 HIS 0.003 0.000 HIS A 746 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.09 ( 7944) covalent geometry : angle 0.56161 / 0.26 (10811) hydrogen bonds : bond 0.02901 / 2.06 ( 377) hydrogen bonds : angle 3.76311 / 2.75 ( 1080) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1917.25 seconds wall clock time: 33 minutes 29.58 seconds (2009.58 seconds total)