Starting phenix.real_space_refine on Fri Jul 3 12:34:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8b9g_15931/07_2026/8b9g_15931.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b9g_15931/07_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_15931/07_2026/8b9g_15931.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b9g_15931/07_2026/8b9g_15931.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8b9g_15931/07_2026/8b9g_15931.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8b9g_15931/07_2026/8b9g_15931.cif" model { file = "/net/cci-nas-00/data/ceres_data/8b9g_15931/07_2026/8b9g_15931.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b9g_15931/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'RNA': 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: 2.53, per 1000 atoms: 0.33 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: 0.68 Conformation dependent library (CDL) restraints added in 444.5 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: 0.66 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: 1.00 Time building geometry restraints manager: 0.88 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 - 32.93: 4659 32.93 - 65.86: 167 65.86 - 98.79: 17 98.79 - 131.73: 1 131.73 - 164.66: 1 Dihedral angle restraints: 4845 sinusoidal: 2047 harmonic: 2798 Sorted by residual: dihedral pdb=" O4' U C 6 " pdb=" C1' U C 6 " pdb=" N1 U C 6 " pdb=" C2 U C 6 " ideal model delta sinusoidal sigma weight residual -160.00 4.66 -164.66 1 1.50e+01 4.44e-03 8.38e+01 dihedral pdb=" C5' ADP A1201 " pdb=" O5' ADP A1201 " pdb=" PA ADP A1201 " pdb=" O2A ADP A1201 " ideal model delta sinusoidal sigma weight residual -60.00 -164.32 104.33 1 2.00e+01 2.50e-03 2.99e+01 dihedral pdb=" CA THR A 722 " pdb=" C THR A 722 " pdb=" N SER A 723 " pdb=" CA SER A 723 " ideal model delta harmonic sigma weight residual 180.00 156.00 24.00 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 4842 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 805 0.035 - 0.071: 299 0.071 - 0.106: 98 0.106 - 0.141: 45 0.141 - 0.176: 2 Chirality restraints: 1249 Sorted by residual: chirality pdb=" CA GLU A1134 " pdb=" N GLU A1134 " pdb=" C GLU A1134 " pdb=" CB GLU A1134 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.78e-01 chirality pdb=" CB ILE A 719 " pdb=" CA ILE A 719 " pdb=" CG1 ILE A 719 " pdb=" CG2 ILE A 719 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.18e-01 chirality pdb=" CB THR A 414 " pdb=" CA THR A 414 " pdb=" OG1 THR A 414 " pdb=" CG2 THR A 414 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.53e-01 ... (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: 0.000 Normalize map: mean=0, sd=1: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.150 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.760 ------------------------------------------------------------------------------- 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= 0.241 Angle : 1.198 70.010 10811 Z= 0.470 Chirality : 0.045 0.176 1249 Planarity : 0.005 0.049 1358 Dihedral : 16.623 164.658 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 0.00503 / 0.24 ( 7944) covalent geometry : angle 1.19771 / 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 : 0.221 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 48 average time/residue: 0.6279 time to fit residues: 31.7927 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 : 0.216 ------------------------------------------------------------------------------- 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 = 0.3375 r_free = 0.3375 target = 0.064638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.049642 restraints weight = 46972.576| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 4.75 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 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 = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7944 Z= 0.119 Angle : 0.603 9.298 10811 Z= 0.299 Chirality : 0.043 0.167 1249 Planarity : 0.004 0.049 1358 Dihedral : 8.302 156.618 1167 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.09 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: 0.34 (0.42), residues: 159 loop : 0.17 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 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 0.004 0.001 HIS A 646 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 7944) covalent geometry : angle 0.60330 / 0.30 (10811) hydrogen bonds : bond 0.03425 / 2.46 ( 377) hydrogen bonds : angle 4.09672 / 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 45 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 29 time to evaluate : 0.295 Fit side-chains REVERT: A 865 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7311 (mp0) REVERT: A 942 MET cc_start: 0.8314 (mmm) cc_final: 0.7838 (mtp) REVERT: A 950 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7870 (tppp) REVERT: A 954 MET cc_start: 0.7983 (ttm) cc_final: 0.7736 (ttm) outliers start: 16 outliers final: 2 residues processed: 44 average time/residue: 0.5052 time to fit residues: 23.8513 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 : 0.235 ------------------------------------------------------------------------------- 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: 1.9990 chunk 4 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 56 optimal weight: 0.0010 chunk 25 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 overall best weight: 1.1590 ------------------------------------------------------------------------------- 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 = 0.3342 r_free = 0.3342 target = 0.063061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.048874 restraints weight = 38018.773| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 4.27 r_work: 0.2816 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2821 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 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: 0.2821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7944 Z= 0.119 Angle : 0.560 8.101 10811 Z= 0.275 Chirality : 0.042 0.161 1249 Planarity : 0.004 0.051 1358 Dihedral : 7.919 156.210 1163 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.80 % Favored : 98.10 % Rotamer: Outliers : 1.31 % Allowed : 16.57 % 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: 1.72 (0.28), residues: 947 helix: 2.16 (0.24), residues: 452 sheet: 0.35 (0.43), residues: 159 loop : 0.22 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 375 TYR 0.005 0.001 TYR A 467 PHE 0.016 0.001 PHE A 667 TRP 0.010 0.001 TRP A 663 HIS 0.005 0.001 HIS A 746 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 7944) covalent geometry : angle 0.55988 / 0.28 (10811) hydrogen bonds : bond 0.03394 / 2.41 ( 377) hydrogen bonds : angle 4.00849 / 2.92 ( 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 : 0.278 Fit side-chains REVERT: A 843 MET cc_start: 0.8350 (ttm) cc_final: 0.8090 (ttp) REVERT: A 942 MET cc_start: 0.8451 (mmm) cc_final: 0.7961 (mtp) REVERT: A 950 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7945 (tppp) outliers start: 10 outliers final: 1 residues processed: 34 average time/residue: 0.5408 time to fit residues: 19.7387 Evaluate side-chains 28 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 9 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 28 optimal weight: 0.0970 chunk 4 optimal weight: 9.9990 chunk 78 optimal weight: 0.0170 chunk 85 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 overall best weight: 0.5416 ------------------------------------------------------------------------------- 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 = 0.3366 r_free = 0.3366 target = 0.063936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.049326 restraints weight = 50178.828| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 4.86 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3002 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3002 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2140 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= 0.093 Angle : 0.537 8.548 10811 Z= 0.262 Chirality : 0.041 0.161 1249 Planarity : 0.004 0.050 1358 Dihedral : 7.714 152.085 1163 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.69 % Favored : 98.20 % Rotamer: Outliers : 1.31 % Allowed : 16.57 % 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 (0.28), residues: 947 helix: 2.22 (0.24), residues: 453 sheet: 0.38 (0.43), residues: 159 loop : 0.31 (0.36), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 375 TYR 0.004 0.001 TYR A 619 PHE 0.015 0.001 PHE A 667 TRP 0.010 0.001 TRP A 663 HIS 0.004 0.001 HIS A 646 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.09 ( 7944) covalent geometry : angle 0.53719 / 0.26 (10811) hydrogen bonds : bond 0.02973 / 2.11 ( 377) hydrogen bonds : angle 3.87535 / 2.82 ( 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: 10 poor density : 27 time to evaluate : 0.297 Fit side-chains REVERT: A 865 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7357 (mp0) REVERT: A 942 MET cc_start: 0.8322 (mmm) cc_final: 0.7797 (mtp) outliers start: 10 outliers final: 2 residues processed: 35 average time/residue: 0.5868 time to fit residues: 21.9219 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 : 0.215 ------------------------------------------------------------------------------- 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 1092 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 26 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 64 optimal weight: 0.1980 chunk 67 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 = 0.3297 r_free = 0.3297 target = 0.061167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.046865 restraints weight = 39033.461| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 4.28 r_work: 0.2757 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2769 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2769 r_free = 0.2769 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2769 r_free = 0.2769 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2769 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2300 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= 0.167 Angle : 0.594 9.608 10811 Z= 0.288 Chirality : 0.043 0.154 1249 Planarity : 0.004 0.051 1358 Dihedral : 7.907 158.799 1163 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.01 % Favored : 97.88 % Rotamer: Outliers : 1.07 % Allowed : 16.92 % Favored : 82.00 % 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: 1.73 (0.28), residues: 947 helix: 2.15 (0.24), residues: 451 sheet: 0.22 (0.45), residues: 150 loop : 0.35 (0.36), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 375 TYR 0.009 0.001 TYR A 187 PHE 0.015 0.001 PHE A 667 TRP 0.015 0.001 TRP A 949 HIS 0.003 0.001 HIS A 746 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 ( 7944) covalent geometry : angle 0.59428 / 0.29 (10811) hydrogen bonds : bond 0.03647 / 2.57 ( 377) hydrogen bonds : angle 4.04690 / 2.94 ( 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 34 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 26 time to evaluate : 0.190 Fit side-chains REVERT: A 865 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7724 (mp0) REVERT: A 942 MET cc_start: 0.8441 (mmm) cc_final: 0.7919 (mtm) outliers start: 8 outliers final: 1 residues processed: 32 average time/residue: 0.6459 time to fit residues: 21.9136 Evaluate side-chains 28 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 865 GLU 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: 0.8980 chunk 59 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 69 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 = 0.3310 r_free = 0.3310 target = 0.061642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.046392 restraints weight = 71796.427| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 5.60 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7944 Z= 0.130 Angle : 0.571 9.958 10811 Z= 0.274 Chirality : 0.042 0.155 1249 Planarity : 0.004 0.050 1358 Dihedral : 7.809 156.052 1163 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.69 % Favored : 98.20 % 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: 1.79 (0.29), residues: 947 helix: 2.20 (0.24), residues: 451 sheet: 0.27 (0.45), residues: 149 loop : 0.35 (0.36), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 375 TYR 0.006 0.001 TYR A 467 PHE 0.014 0.001 PHE A 667 TRP 0.009 0.001 TRP A 663 HIS 0.003 0.001 HIS A 746 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 7944) covalent geometry : angle 0.57073 / 0.27 (10811) hydrogen bonds : bond 0.03304 / 2.33 ( 377) hydrogen bonds : angle 3.92819 / 2.86 ( 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 34 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 26 time to evaluate : 0.223 Fit side-chains REVERT: A 865 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7529 (mp0) REVERT: A 942 MET cc_start: 0.8401 (mmm) cc_final: 0.7861 (mtm) outliers start: 8 outliers final: 2 residues processed: 33 average time/residue: 0.5938 time to fit residues: 20.8422 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 : 0.213 ------------------------------------------------------------------------------- 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 1092 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.5804 > 50: distance: 46 - 140: 27.908 distance: 95 - 132: 33.311 distance: 101 - 135: 30.930 distance: 127 - 132: 35.668 distance: 132 - 133: 50.370 distance: 133 - 134: 11.326 distance: 133 - 136: 40.140 distance: 134 - 135: 43.820 distance: 134 - 140: 39.616 distance: 136 - 137: 54.888 distance: 137 - 138: 20.303 distance: 137 - 139: 48.705 distance: 140 - 141: 15.354 distance: 141 - 142: 38.287 distance: 141 - 144: 35.462 distance: 142 - 143: 30.822 distance: 142 - 146: 35.271 distance: 144 - 145: 5.161 distance: 146 - 147: 31.366 distance: 147 - 148: 37.304 distance: 147 - 150: 27.067 distance: 148 - 149: 12.191 distance: 148 - 153: 11.710 distance: 150 - 152: 8.597 distance: 153 - 154: 20.258 distance: 154 - 155: 69.195 distance: 154 - 157: 28.402 distance: 155 - 156: 58.504 distance: 155 - 161: 69.580 distance: 156 - 174: 13.214 distance: 157 - 158: 17.964 distance: 158 - 159: 20.796 distance: 158 - 160: 15.038 distance: 161 - 162: 68.504 distance: 162 - 165: 41.366 distance: 163 - 164: 56.184 distance: 163 - 169: 43.522 distance: 165 - 166: 44.780 distance: 165 - 167: 11.904 distance: 166 - 168: 7.379 distance: 169 - 170: 40.985 distance: 170 - 171: 27.657 distance: 170 - 173: 26.604 distance: 171 - 172: 41.820 distance: 171 - 174: 10.934 distance: 174 - 175: 30.299 distance: 175 - 176: 40.291 distance: 175 - 178: 35.696 distance: 176 - 177: 60.198 distance: 176 - 183: 21.414 distance: 178 - 179: 49.448 distance: 179 - 180: 15.867 distance: 180 - 181: 22.231 distance: 180 - 182: 13.614 distance: 183 - 184: 18.190 distance: 184 - 185: 25.686 distance: 184 - 187: 7.573 distance: 185 - 186: 10.686 distance: 185 - 190: 34.361 distance: 187 - 189: 40.650 distance: 190 - 191: 25.358 distance: 191 - 192: 7.826 distance: 191 - 194: 19.883 distance: 192 - 193: 48.688 distance: 192 - 196: 22.672 distance: 194 - 195: 38.565 distance: 196 - 197: 35.402 distance: 197 - 198: 31.853 distance: 197 - 200: 40.583 distance: 198 - 199: 17.994 distance: 198 - 204: 30.255 distance: 200 - 201: 38.359 distance: 200 - 202: 6.382 distance: 201 - 203: 38.838