Starting phenix.real_space_refine on Sat Aug 23 17:16:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hxz_35083/08_2025/8hxz_35083.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hxz_35083/08_2025/8hxz_35083.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hxz_35083/08_2025/8hxz_35083.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hxz_35083/08_2025/8hxz_35083.map" model { file = "/net/cci-nas-00/data/ceres_data/8hxz_35083/08_2025/8hxz_35083.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hxz_35083/08_2025/8hxz_35083.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 328 5.49 5 S 16 5.16 5 C 7628 2.51 5 N 2563 2.21 5 O 3205 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13740 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 837 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ML3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 843 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 757 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "E" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 818 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 3345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 3345 Classifications: {'DNA': 164} Link IDs: {'rna3p': 163} Chain: "J" Number of atoms: 3379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 3379 Classifications: {'DNA': 164} Link IDs: {'rna3p': 163} Chain: "M" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 915 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain breaks: 1 Time building chain proxies: 3.21, per 1000 atoms: 0.23 Number of scatterers: 13740 At special positions: 0 Unit cell: (75.6, 119.7, 142.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 16 16.00 P 328 15.00 O 3205 8.00 N 2563 7.00 C 7628 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: 1.06 Conformation dependent library (CDL) restraints added in 383.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1644 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 8 sheets defined 66.3% alpha, 6.5% beta 164 base pairs and 294 stacking pairs defined. Time for finding SS restraints: 2.33 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 75 removed outlier: 3.630A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.571A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.907A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.775A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.090A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.538A pdb=" N GLY B 94 " --> pdb=" O LEU B 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.292A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.740A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.784A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.959A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 121 removed outlier: 4.272A pdb=" N HIS D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA D 107 " --> pdb=" O LEU D 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.260A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.892A pdb=" N ALA E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.884A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.224A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 removed outlier: 3.797A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.065A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.562A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 80 Processing helix chain 'H' and resid 87 through 98 removed outlier: 3.978A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 121 removed outlier: 3.944A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 89 Processing helix chain 'M' and resid 101 through 131 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.521A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 77 through 78 removed outlier: 3.525A pdb=" N ILE C 78 " --> pdb=" O GLY D 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA4, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.999A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA6, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA7, first strand: chain 'M' and resid 58 through 59 removed outlier: 6.564A pdb=" N PHE M 78 " --> pdb=" O LEU M 28 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 58 through 59 445 hydrogen bonds defined for protein. 1299 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 416 hydrogen bonds 832 hydrogen bond angles 0 basepair planarities 164 basepair parallelities 294 stacking parallelities Total time for adding SS restraints: 3.03 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2322 1.33 - 1.45: 5135 1.45 - 1.58: 6519 1.58 - 1.70: 654 1.70 - 1.82: 30 Bond restraints: 14660 Sorted by residual: bond pdb=" CA ASN G 73 " pdb=" C ASN G 73 " ideal model delta sigma weight residual 1.523 1.571 -0.048 1.41e-02 5.03e+03 1.16e+01 bond pdb=" CA HIS M 18 " pdb=" C HIS M 18 " ideal model delta sigma weight residual 1.523 1.481 0.042 1.34e-02 5.57e+03 1.00e+01 bond pdb=" SG ML3 A 36 " pdb=" CD ML3 A 36 " ideal model delta sigma weight residual 1.815 1.755 0.060 2.00e-02 2.50e+03 8.99e+00 bond pdb=" CB ML3 A 36 " pdb=" SG ML3 A 36 " ideal model delta sigma weight residual 1.817 1.766 0.051 2.00e-02 2.50e+03 6.46e+00 bond pdb=" CA PHE M 17 " pdb=" C PHE M 17 " ideal model delta sigma weight residual 1.527 1.496 0.031 1.35e-02 5.49e+03 5.27e+00 ... (remaining 14655 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 20831 2.94 - 5.89: 301 5.89 - 8.83: 53 8.83 - 11.78: 7 11.78 - 14.72: 4 Bond angle restraints: 21196 Sorted by residual: angle pdb=" N HIS M 18 " pdb=" CA HIS M 18 " pdb=" C HIS M 18 " ideal model delta sigma weight residual 110.80 96.08 14.72 2.13e+00 2.20e-01 4.78e+01 angle pdb=" N GLY H 101 " pdb=" CA GLY H 101 " pdb=" C GLY H 101 " ideal model delta sigma weight residual 112.64 120.58 -7.94 1.21e+00 6.83e-01 4.30e+01 angle pdb=" N GLU F 63 " pdb=" CA GLU F 63 " pdb=" CB GLU F 63 " ideal model delta sigma weight residual 110.28 119.35 -9.07 1.55e+00 4.16e-01 3.43e+01 angle pdb=" N VAL D 95 " pdb=" CA VAL D 95 " pdb=" C VAL D 95 " ideal model delta sigma weight residual 110.62 104.73 5.89 1.02e+00 9.61e-01 3.34e+01 angle pdb=" CA ASN G 73 " pdb=" C ASN G 73 " pdb=" N LYS G 74 " ideal model delta sigma weight residual 118.32 110.98 7.34 1.35e+00 5.49e-01 2.95e+01 ... (remaining 21191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 6308 35.86 - 71.73: 1647 71.73 - 107.59: 32 107.59 - 143.45: 1 143.45 - 179.32: 4 Dihedral angle restraints: 7992 sinusoidal: 5444 harmonic: 2548 Sorted by residual: dihedral pdb=" CA GLU E 50 " pdb=" C GLU E 50 " pdb=" N ILE E 51 " pdb=" CA ILE E 51 " ideal model delta harmonic sigma weight residual 180.00 150.91 29.09 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA LYS F 79 " pdb=" C LYS F 79 " pdb=" N THR F 80 " pdb=" CA THR F 80 " ideal model delta harmonic sigma weight residual 180.00 151.03 28.97 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA LYS H 31 " pdb=" C LYS H 31 " pdb=" N GLU H 32 " pdb=" CA GLU H 32 " ideal model delta harmonic sigma weight residual -180.00 -155.05 -24.95 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 7989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2054 0.067 - 0.134: 287 0.134 - 0.200: 43 0.200 - 0.267: 5 0.267 - 0.334: 2 Chirality restraints: 2391 Sorted by residual: chirality pdb=" CG LEU E 70 " pdb=" CB LEU E 70 " pdb=" CD1 LEU E 70 " pdb=" CD2 LEU E 70 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CB THR D 112 " pdb=" CA THR D 112 " pdb=" OG1 THR D 112 " pdb=" CG2 THR D 112 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CG LEU A 92 " pdb=" CB LEU A 92 " pdb=" CD1 LEU A 92 " pdb=" CD2 LEU A 92 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 2388 not shown) Planarity restraints: 1543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.055 5.00e-02 4.00e+02 8.39e-02 1.13e+01 pdb=" N PRO G 80 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.050 5.00e-02 4.00e+02 7.55e-02 9.13e+00 pdb=" N PRO C 80 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 88 " -0.011 2.00e-02 2.50e+03 2.02e-02 8.16e+00 pdb=" CG TYR B 88 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR B 88 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR B 88 " 0.042 2.00e-02 2.50e+03 pdb=" CE1 TYR B 88 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR B 88 " -0.017 2.00e-02 2.50e+03 pdb=" CZ TYR B 88 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR B 88 " -0.006 2.00e-02 2.50e+03 ... (remaining 1540 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3364 2.82 - 3.34: 13003 3.34 - 3.86: 29103 3.86 - 4.38: 32268 4.38 - 4.90: 44145 Nonbonded interactions: 121883 Sorted by model distance: nonbonded pdb=" NZ LYS F 79 " pdb=" OP1 DG I 101 " model vdw 2.303 3.120 nonbonded pdb=" N THR H 87 " pdb=" OE2 GLU H 90 " model vdw 2.318 3.120 nonbonded pdb=" O ILE F 50 " pdb=" OG1 THR F 54 " model vdw 2.325 3.040 nonbonded pdb=" NH2 ARG A 42 " pdb=" OP1 DA I 69 " model vdw 2.329 3.120 nonbonded pdb=" NZ LYS G 15 " pdb=" OG SER G 19 " model vdw 2.337 3.120 ... (remaining 121878 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 37 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 23 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 13 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 28 through 121) selection = (chain 'H' and resid 28 through 121) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.640 Find NCS groups from input model: 0.140 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 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 0.067 14660 Z= 0.249 Angle : 0.983 14.720 21196 Z= 0.556 Chirality : 0.050 0.334 2391 Planarity : 0.007 0.084 1543 Dihedral : 29.122 179.316 6348 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.57 (0.26), residues: 856 helix: -0.86 (0.20), residues: 541 sheet: -0.52 (0.90), residues: 30 loop : -1.15 (0.33), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 89 TYR 0.042 0.004 TYR B 88 PHE 0.016 0.003 PHE G 25 TRP 0.010 0.002 TRP M 84 HIS 0.014 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00537 (14660) covalent geometry : angle 0.98261 (21196) hydrogen bonds : bond 0.09779 ( 855) hydrogen bonds : angle 4.87077 ( 2131) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8504 (mt-10) REVERT: B 35 ARG cc_start: 0.9274 (mtp-110) cc_final: 0.8911 (mtp-110) REVERT: B 59 LYS cc_start: 0.9445 (tmmt) cc_final: 0.9058 (ttpp) REVERT: B 63 GLU cc_start: 0.8892 (pp20) cc_final: 0.8632 (pp20) REVERT: B 91 LYS cc_start: 0.9644 (tppp) cc_final: 0.9255 (tppp) REVERT: C 36 LYS cc_start: 0.9435 (mmpt) cc_final: 0.9075 (mmmt) REVERT: C 104 GLN cc_start: 0.9084 (mp10) cc_final: 0.8819 (mp10) REVERT: C 111 ILE cc_start: 0.8572 (mm) cc_final: 0.8360 (mm) REVERT: C 112 GLN cc_start: 0.8565 (mp10) cc_final: 0.7286 (mp10) REVERT: D 80 TYR cc_start: 0.8716 (m-80) cc_final: 0.8444 (m-80) REVERT: D 102 GLU cc_start: 0.9227 (mm-30) cc_final: 0.8953 (tp30) REVERT: E 108 ASN cc_start: 0.9229 (t0) cc_final: 0.8490 (t0) REVERT: E 109 LEU cc_start: 0.9619 (mm) cc_final: 0.9137 (mm) REVERT: F 25 ASN cc_start: 0.9414 (m-40) cc_final: 0.9196 (m110) REVERT: F 27 GLN cc_start: 0.9121 (mp10) cc_final: 0.8764 (mp10) REVERT: F 59 LYS cc_start: 0.9376 (ptmm) cc_final: 0.9167 (ptmm) REVERT: F 63 GLU cc_start: 0.9306 (pm20) cc_final: 0.9068 (pm20) REVERT: F 88 TYR cc_start: 0.8692 (m-10) cc_final: 0.7946 (m-10) REVERT: F 93 GLN cc_start: 0.8450 (tm-30) cc_final: 0.7910 (tm-30) REVERT: G 56 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8276 (mm-30) REVERT: G 92 GLU cc_start: 0.8359 (tt0) cc_final: 0.8066 (tt0) REVERT: G 112 GLN cc_start: 0.9081 (mp10) cc_final: 0.8685 (mp10) REVERT: H 65 ASP cc_start: 0.9349 (t0) cc_final: 0.9049 (t0) REVERT: H 92 GLN cc_start: 0.9212 (tm-30) cc_final: 0.8623 (tm-30) REVERT: H 97 LEU cc_start: 0.9180 (tt) cc_final: 0.8896 (tt) REVERT: H 103 LEU cc_start: 0.9451 (mt) cc_final: 0.8816 (mt) REVERT: M 89 ASP cc_start: 0.7249 (m-30) cc_final: 0.7028 (m-30) outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.1682 time to fit residues: 58.3669 Evaluate side-chains 189 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 20.0000 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.045330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.031133 restraints weight = 101065.690| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 4.06 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 14660 Z= 0.263 Angle : 0.734 9.185 21196 Z= 0.424 Chirality : 0.039 0.160 2391 Planarity : 0.006 0.070 1543 Dihedral : 32.348 177.549 4579 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 18.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.05 % Allowed : 13.25 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.27), residues: 856 helix: 0.05 (0.21), residues: 557 sheet: -0.72 (1.43), residues: 15 loop : -0.71 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 35 TYR 0.049 0.003 TYR B 88 PHE 0.022 0.002 PHE A 84 TRP 0.009 0.001 TRP M 31 HIS 0.009 0.002 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00579 (14660) covalent geometry : angle 0.73445 (21196) hydrogen bonds : bond 0.06221 ( 855) hydrogen bonds : angle 3.82082 ( 2131) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 212 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ASN cc_start: 0.9555 (t0) cc_final: 0.9050 (t0) REVERT: B 59 LYS cc_start: 0.9517 (tmmt) cc_final: 0.9133 (ttpp) REVERT: C 25 PHE cc_start: 0.8976 (m-10) cc_final: 0.8638 (m-10) REVERT: C 36 LYS cc_start: 0.9622 (mmpt) cc_final: 0.9348 (mtmm) REVERT: C 89 ASN cc_start: 0.9801 (m-40) cc_final: 0.9509 (m110) REVERT: C 104 GLN cc_start: 0.9184 (mp10) cc_final: 0.8806 (mp10) REVERT: C 112 GLN cc_start: 0.7884 (mp10) cc_final: 0.7489 (mp10) REVERT: D 56 MET cc_start: 0.9461 (tpp) cc_final: 0.9215 (tpp) REVERT: D 59 MET cc_start: 0.9545 (mmm) cc_final: 0.9206 (mmm) REVERT: D 102 GLU cc_start: 0.9509 (mm-30) cc_final: 0.8945 (tp30) REVERT: E 64 LYS cc_start: 0.9487 (mmtm) cc_final: 0.9098 (mmtm) REVERT: E 84 PHE cc_start: 0.9095 (m-80) cc_final: 0.8741 (m-80) REVERT: E 90 MET cc_start: 0.9402 (mmm) cc_final: 0.9167 (mmp) REVERT: E 108 ASN cc_start: 0.9368 (t0) cc_final: 0.8896 (t0) REVERT: F 27 GLN cc_start: 0.9169 (mp10) cc_final: 0.8836 (mp10) REVERT: G 56 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8396 (mm-30) REVERT: G 61 GLU cc_start: 0.9103 (mm-30) cc_final: 0.8767 (mm-30) REVERT: G 72 ASP cc_start: 0.9300 (m-30) cc_final: 0.9048 (p0) REVERT: G 94 ASN cc_start: 0.8978 (m-40) cc_final: 0.8320 (m110) REVERT: G 112 GLN cc_start: 0.8998 (mp10) cc_final: 0.8450 (mp10) REVERT: H 65 ASP cc_start: 0.9583 (t0) cc_final: 0.9318 (t0) REVERT: H 80 TYR cc_start: 0.8864 (m-80) cc_final: 0.8421 (m-80) REVERT: H 92 GLN cc_start: 0.9339 (tm130) cc_final: 0.9122 (tm-30) outliers start: 15 outliers final: 9 residues processed: 216 average time/residue: 0.1641 time to fit residues: 47.7005 Evaluate side-chains 182 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 173 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain M residue 28 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 95 optimal weight: 8.9990 chunk 84 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 126 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.045891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.031032 restraints weight = 99021.906| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 3.90 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14660 Z= 0.209 Angle : 0.701 9.064 21196 Z= 0.404 Chirality : 0.038 0.173 2391 Planarity : 0.005 0.062 1543 Dihedral : 32.177 179.693 4579 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.78 % Allowed : 17.76 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.28), residues: 856 helix: 0.42 (0.21), residues: 557 sheet: -1.05 (1.39), residues: 15 loop : -0.53 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 129 TYR 0.050 0.002 TYR B 88 PHE 0.013 0.002 PHE A 84 TRP 0.007 0.001 TRP M 31 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00460 (14660) covalent geometry : angle 0.70079 (21196) hydrogen bonds : bond 0.04471 ( 855) hydrogen bonds : angle 3.64152 ( 2131) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 202 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ASN cc_start: 0.9575 (t0) cc_final: 0.9114 (t0) REVERT: B 59 LYS cc_start: 0.9494 (tmmt) cc_final: 0.9200 (ttpp) REVERT: B 63 GLU cc_start: 0.9071 (pp20) cc_final: 0.8844 (pp20) REVERT: C 36 LYS cc_start: 0.9631 (mmpt) cc_final: 0.9362 (mtmm) REVERT: C 89 ASN cc_start: 0.9810 (m-40) cc_final: 0.9457 (m110) REVERT: C 104 GLN cc_start: 0.9213 (mp10) cc_final: 0.8822 (mp10) REVERT: D 31 LYS cc_start: 0.9079 (mmtt) cc_final: 0.8865 (mmtt) REVERT: D 59 MET cc_start: 0.9576 (mmm) cc_final: 0.9338 (mmm) REVERT: D 80 TYR cc_start: 0.8765 (m-80) cc_final: 0.8426 (m-80) REVERT: D 102 GLU cc_start: 0.9489 (mm-30) cc_final: 0.9269 (mp0) REVERT: E 64 LYS cc_start: 0.9438 (mmtm) cc_final: 0.9088 (mmtm) REVERT: E 79 LYS cc_start: 0.9303 (tptp) cc_final: 0.9090 (tptp) REVERT: E 84 PHE cc_start: 0.9148 (m-80) cc_final: 0.8784 (m-80) REVERT: E 97 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8143 (mt-10) REVERT: F 27 GLN cc_start: 0.9050 (mp10) cc_final: 0.8797 (mp10) REVERT: G 61 GLU cc_start: 0.9169 (mm-30) cc_final: 0.8744 (mm-30) REVERT: G 89 ASN cc_start: 0.9529 (m-40) cc_final: 0.9046 (p0) REVERT: G 94 ASN cc_start: 0.8963 (m-40) cc_final: 0.8279 (m110) REVERT: G 112 GLN cc_start: 0.8842 (mp10) cc_final: 0.8260 (mp10) REVERT: H 56 MET cc_start: 0.9349 (tpt) cc_final: 0.9095 (tpt) REVERT: H 65 ASP cc_start: 0.9613 (t0) cc_final: 0.9356 (t0) REVERT: H 92 GLN cc_start: 0.9389 (tm130) cc_final: 0.9145 (tm-30) REVERT: H 96 ARG cc_start: 0.9050 (ptm-80) cc_final: 0.8335 (ttp80) outliers start: 13 outliers final: 8 residues processed: 207 average time/residue: 0.1606 time to fit residues: 44.9140 Evaluate side-chains 188 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 180 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain G residue 114 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 47 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 chunk 84 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 95 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 85 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.042797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.028310 restraints weight = 104380.660| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 3.65 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 14660 Z= 0.360 Angle : 0.777 9.270 21196 Z= 0.447 Chirality : 0.042 0.174 2391 Planarity : 0.006 0.062 1543 Dihedral : 32.422 179.637 4579 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 21.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.28 % Allowed : 19.54 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.27), residues: 856 helix: 0.43 (0.21), residues: 565 sheet: -1.40 (1.37), residues: 15 loop : -0.61 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 76 TYR 0.067 0.003 TYR B 88 PHE 0.017 0.002 PHE D 62 TRP 0.013 0.002 TRP M 84 HIS 0.006 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00788 (14660) covalent geometry : angle 0.77682 (21196) hydrogen bonds : bond 0.08134 ( 855) hydrogen bonds : angle 3.91559 ( 2131) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 196 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ASN cc_start: 0.9604 (t0) cc_final: 0.9085 (t0) REVERT: A 120 MET cc_start: 0.8957 (mmm) cc_final: 0.8117 (mmm) REVERT: A 122 LYS cc_start: 0.9390 (mmtm) cc_final: 0.9141 (ptpp) REVERT: B 59 LYS cc_start: 0.9586 (tmmt) cc_final: 0.9345 (ttpp) REVERT: B 91 LYS cc_start: 0.9663 (tppp) cc_final: 0.9037 (tppp) REVERT: B 95 ARG cc_start: 0.9303 (mmm-85) cc_final: 0.9055 (mmm-85) REVERT: C 104 GLN cc_start: 0.9158 (mp10) cc_final: 0.8828 (mp10) REVERT: C 112 GLN cc_start: 0.8182 (mp10) cc_final: 0.7358 (mp10) REVERT: D 31 LYS cc_start: 0.8986 (mmtt) cc_final: 0.8747 (mmtt) REVERT: D 56 MET cc_start: 0.9442 (tpp) cc_final: 0.9239 (tpp) REVERT: D 76 ARG cc_start: 0.9451 (ttm110) cc_final: 0.9139 (ttp-110) REVERT: D 102 GLU cc_start: 0.9408 (mm-30) cc_final: 0.8979 (tp30) REVERT: E 79 LYS cc_start: 0.9472 (tptp) cc_final: 0.9226 (tptp) REVERT: E 84 PHE cc_start: 0.9259 (m-80) cc_final: 0.9022 (m-80) REVERT: E 108 ASN cc_start: 0.9490 (t0) cc_final: 0.8705 (t0) REVERT: E 112 ILE cc_start: 0.9345 (mt) cc_final: 0.8855 (mt) REVERT: G 38 ASN cc_start: 0.8873 (t0) cc_final: 0.8651 (t0) REVERT: G 56 GLU cc_start: 0.9059 (mt-10) cc_final: 0.8748 (mt-10) REVERT: G 61 GLU cc_start: 0.9255 (mm-30) cc_final: 0.8867 (mm-30) REVERT: G 72 ASP cc_start: 0.9304 (m-30) cc_final: 0.9021 (p0) REVERT: G 112 GLN cc_start: 0.8938 (mp10) cc_final: 0.8385 (mp10) REVERT: H 56 MET cc_start: 0.9464 (tpt) cc_final: 0.9202 (tpt) REVERT: H 65 ASP cc_start: 0.9611 (t0) cc_final: 0.9349 (t0) REVERT: H 76 ARG cc_start: 0.9387 (ttm110) cc_final: 0.9111 (ttp-110) REVERT: H 92 GLN cc_start: 0.9464 (OUTLIER) cc_final: 0.9189 (tm-30) outliers start: 24 outliers final: 10 residues processed: 210 average time/residue: 0.1567 time to fit residues: 44.5105 Evaluate side-chains 180 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 169 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 92 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 66 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 103 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 100 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN F 93 GLN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN G 73 ASN G 110 ASN H 92 GLN M 80 HIS ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 126 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.050803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.037203 restraints weight = 125786.482| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 3.87 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14660 Z= 0.175 Angle : 0.717 10.578 21196 Z= 0.408 Chirality : 0.038 0.182 2391 Planarity : 0.005 0.060 1543 Dihedral : 32.026 179.439 4579 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.55 % Allowed : 23.77 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.28), residues: 856 helix: 0.56 (0.21), residues: 558 sheet: -1.50 (1.37), residues: 15 loop : -0.37 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 92 TYR 0.063 0.003 TYR B 88 PHE 0.013 0.001 PHE A 84 TRP 0.012 0.002 TRP M 88 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00385 (14660) covalent geometry : angle 0.71677 (21196) hydrogen bonds : bond 0.03673 ( 855) hydrogen bonds : angle 3.56459 ( 2131) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 217 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.9467 (tt0) cc_final: 0.8791 (tp40) REVERT: A 108 ASN cc_start: 0.9574 (t0) cc_final: 0.8987 (t0) REVERT: A 122 LYS cc_start: 0.9372 (mmtm) cc_final: 0.9132 (ptpp) REVERT: B 53 GLU cc_start: 0.9188 (pp20) cc_final: 0.8856 (pm20) REVERT: B 59 LYS cc_start: 0.9542 (tmmt) cc_final: 0.9320 (ttpp) REVERT: B 63 GLU cc_start: 0.8961 (pp20) cc_final: 0.8752 (pp20) REVERT: B 84 MET cc_start: 0.9080 (tpp) cc_final: 0.8763 (tpp) REVERT: C 104 GLN cc_start: 0.9024 (mp10) cc_final: 0.8691 (mp10) REVERT: C 112 GLN cc_start: 0.7910 (mp10) cc_final: 0.7117 (mp10) REVERT: D 56 MET cc_start: 0.9302 (tpp) cc_final: 0.9095 (tpp) REVERT: D 102 GLU cc_start: 0.9207 (mm-30) cc_final: 0.8907 (tp30) REVERT: E 64 LYS cc_start: 0.9478 (mmtm) cc_final: 0.9089 (mmtm) REVERT: E 68 GLN cc_start: 0.9070 (OUTLIER) cc_final: 0.8717 (tm-30) REVERT: E 79 LYS cc_start: 0.9477 (tptp) cc_final: 0.9176 (tptp) REVERT: E 84 PHE cc_start: 0.8994 (m-80) cc_final: 0.8762 (m-80) REVERT: E 108 ASN cc_start: 0.9493 (t0) cc_final: 0.8874 (t0) REVERT: E 112 ILE cc_start: 0.9443 (mt) cc_final: 0.9223 (mt) REVERT: F 27 GLN cc_start: 0.8956 (mp10) cc_final: 0.8629 (mp10) REVERT: F 88 TYR cc_start: 0.8957 (m-10) cc_final: 0.8719 (m-80) REVERT: G 38 ASN cc_start: 0.8564 (t0) cc_final: 0.8293 (t0) REVERT: G 56 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8604 (mt-10) REVERT: G 61 GLU cc_start: 0.9082 (mm-30) cc_final: 0.8708 (mm-30) REVERT: G 64 GLU cc_start: 0.9166 (pp20) cc_final: 0.8904 (pp20) REVERT: G 89 ASN cc_start: 0.9537 (m110) cc_final: 0.9124 (p0) REVERT: G 92 GLU cc_start: 0.8592 (tt0) cc_final: 0.8252 (tt0) REVERT: G 112 GLN cc_start: 0.8845 (mp10) cc_final: 0.8258 (mp10) REVERT: H 42 LEU cc_start: 0.9791 (tt) cc_final: 0.9577 (pp) REVERT: H 56 MET cc_start: 0.9291 (tpp) cc_final: 0.9081 (tpt) REVERT: H 65 ASP cc_start: 0.9431 (t0) cc_final: 0.9146 (t0) REVERT: H 92 GLN cc_start: 0.9390 (tm-30) cc_final: 0.9068 (tm-30) outliers start: 26 outliers final: 9 residues processed: 227 average time/residue: 0.1609 time to fit residues: 49.3498 Evaluate side-chains 200 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 190 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 114 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.575 > 50: distance: 3 - 22: 12.346 distance: 8 - 27: 12.372 distance: 12 - 38: 11.551 distance: 19 - 22: 10.023 distance: 22 - 23: 9.911 distance: 23 - 24: 11.102 distance: 23 - 26: 8.821 distance: 24 - 25: 8.086 distance: 24 - 27: 9.097 distance: 27 - 28: 5.225 distance: 28 - 29: 9.469 distance: 28 - 31: 12.204 distance: 29 - 30: 13.287 distance: 29 - 38: 7.977 distance: 31 - 32: 25.057 distance: 32 - 33: 17.091 distance: 33 - 34: 7.949 distance: 34 - 35: 9.789 distance: 35 - 36: 10.683 distance: 35 - 37: 14.902 distance: 38 - 39: 5.481 distance: 39 - 40: 12.731 distance: 39 - 42: 15.583 distance: 40 - 41: 10.714 distance: 40 - 46: 19.966 distance: 42 - 43: 21.498 distance: 43 - 44: 20.585 distance: 43 - 45: 22.592 distance: 46 - 47: 6.330 distance: 47 - 50: 7.499 distance: 48 - 49: 7.167 distance: 48 - 54: 7.532 distance: 50 - 51: 16.109 distance: 51 - 52: 34.917 distance: 51 - 53: 16.992 distance: 54 - 55: 10.994 distance: 55 - 56: 8.949 distance: 55 - 58: 3.106 distance: 56 - 57: 11.541 distance: 56 - 63: 10.860 distance: 58 - 59: 18.783 distance: 59 - 60: 24.431 distance: 60 - 61: 20.990 distance: 61 - 62: 16.970 distance: 63 - 64: 4.400 distance: 64 - 65: 11.087 distance: 64 - 67: 8.318 distance: 65 - 66: 19.084 distance: 67 - 68: 17.259 distance: 68 - 69: 28.123 distance: 69 - 70: 10.867 distance: 70 - 71: 13.635 distance: 72 - 73: 11.510 distance: 73 - 74: 4.045 distance: 73 - 76: 16.957 distance: 74 - 75: 6.844 distance: 74 - 79: 8.998 distance: 76 - 77: 26.447 distance: 76 - 78: 30.072 distance: 80 - 81: 13.491 distance: 80 - 83: 10.733 distance: 81 - 82: 9.737 distance: 81 - 90: 7.969 distance: 83 - 84: 16.270 distance: 84 - 85: 15.397 distance: 85 - 86: 12.778 distance: 86 - 87: 3.308 distance: 87 - 88: 7.040 distance: 87 - 89: 11.433 distance: 90 - 91: 15.553 distance: 91 - 92: 7.783 distance: 91 - 94: 4.611 distance: 92 - 93: 13.958 distance: 92 - 98: 21.870 distance: 94 - 95: 11.748 distance: 94 - 96: 21.164 distance: 95 - 97: 18.619 distance: 98 - 99: 42.605 distance: 99 - 100: 16.838 distance: 99 - 102: 46.055 distance: 100 - 101: 53.594 distance: 100 - 106: 24.435 distance: 101 - 129: 29.650 distance: 102 - 103: 23.467 distance: 102 - 104: 27.762 distance: 103 - 105: 22.030