Starting phenix.real_space_refine on Wed Feb 4 15:27:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i7s_52660/02_2026/9i7s_52660.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i7s_52660/02_2026/9i7s_52660.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9i7s_52660/02_2026/9i7s_52660.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i7s_52660/02_2026/9i7s_52660.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9i7s_52660/02_2026/9i7s_52660.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i7s_52660/02_2026/9i7s_52660.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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 11 5.49 5 S 34 5.16 5 C 7316 2.51 5 N 1817 2.21 5 O 2160 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11338 Number of models: 1 Model: "" Number of chains: 18 Chain: "C" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 718 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "E" Number of atoms: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 326 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 39} Chain: "G" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 298 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Chain: "I" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 410 Classifications: {'peptide': 51} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 46} Chain: "K" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1093 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 5, 'TRANS': 129} Chain: "A" Number of atoms: 2466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2466 Classifications: {'peptide': 318} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 305} Chain breaks: 1 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 718 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "F" Number of atoms: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 326 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 39} Chain: "H" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 298 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Chain: "J" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 410 Classifications: {'peptide': 51} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 46} Chain: "L" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1093 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 5, 'TRANS': 129} Chain: "B" Number of atoms: 2466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2466 Classifications: {'peptide': 318} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 305} Chain breaks: 1 Chain: "C" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 167 Unusual residues: {'DU0': 1, 'PC1': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 32 Chain: "G" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'DU0': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 175 Unusual residues: {'DU0': 2, 'PC1': 2, 'PLC': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 49 Chain: "D" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 167 Unusual residues: {'DU0': 1, 'PC1': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 32 Chain: "H" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'DU0': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 133 Unusual residues: {'DU0': 2, 'PC1': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 49 Time building chain proxies: 2.10, per 1000 atoms: 0.19 Number of scatterers: 11338 At special positions: 0 Unit cell: (128.925, 148.407, 107.724, 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 34 16.00 P 11 15.00 O 2160 8.00 N 1817 7.00 C 7316 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 357.4 milliseconds 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2552 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 2 sheets defined 51.8% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 45 through 56 removed outlier: 3.716A pdb=" N LEU C 53 " --> pdb=" O ARG C 49 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG C 54 " --> pdb=" O LEU C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 117 Proline residue: C 100 - end of helix Processing helix chain 'E' and resid 11 through 50 Proline residue: E 40 - end of helix removed outlier: 4.036A pdb=" N PHE E 50 " --> pdb=" O VAL E 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 26 removed outlier: 3.636A pdb=" N ASN G 22 " --> pdb=" O THR G 18 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ALA G 23 " --> pdb=" O GLY G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 48 Processing helix chain 'G' and resid 49 through 56 Processing helix chain 'I' and resid 23 through 57 removed outlier: 5.496A pdb=" N LEU I 46 " --> pdb=" O HIS I 42 " (cutoff:3.500A) Proline residue: I 47 - end of helix Processing helix chain 'I' and resid 64 through 68 removed outlier: 3.577A pdb=" N LEU I 67 " --> pdb=" O ILE I 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 23 through 36 Processing helix chain 'K' and resid 36 through 80 removed outlier: 3.551A pdb=" N GLU K 78 " --> pdb=" O ASP K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 104 removed outlier: 3.502A pdb=" N ALA K 104 " --> pdb=" O GLU K 100 " (cutoff:3.500A) Processing helix chain 'K' and resid 105 through 107 No H-bonds generated for 'chain 'K' and resid 105 through 107' Processing helix chain 'K' and resid 108 through 123 Processing helix chain 'K' and resid 125 through 137 Processing helix chain 'K' and resid 138 through 152 removed outlier: 3.709A pdb=" N ILE K 144 " --> pdb=" O PRO K 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 34 Processing helix chain 'A' and resid 42 through 46 Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 331 through 335 removed outlier: 4.299A pdb=" N GLU A 335 " --> pdb=" O ALA A 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 331 through 335' Processing helix chain 'D' and resid 29 through 34 Processing helix chain 'D' and resid 45 through 56 removed outlier: 3.716A pdb=" N LEU D 53 " --> pdb=" O ARG D 49 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG D 54 " --> pdb=" O LEU D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 117 Proline residue: D 100 - end of helix Processing helix chain 'F' and resid 11 through 50 Proline residue: F 40 - end of helix removed outlier: 4.036A pdb=" N PHE F 50 " --> pdb=" O VAL F 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 26 removed outlier: 3.636A pdb=" N ASN H 22 " --> pdb=" O THR H 18 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ALA H 23 " --> pdb=" O GLY H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 48 Processing helix chain 'H' and resid 49 through 56 Processing helix chain 'J' and resid 23 through 57 removed outlier: 5.496A pdb=" N LEU J 46 " --> pdb=" O HIS J 42 " (cutoff:3.500A) Proline residue: J 47 - end of helix Processing helix chain 'J' and resid 64 through 68 removed outlier: 3.577A pdb=" N LEU J 67 " --> pdb=" O ILE J 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 23 through 36 Processing helix chain 'L' and resid 36 through 80 removed outlier: 3.551A pdb=" N GLU L 78 " --> pdb=" O ASP L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 104 removed outlier: 3.502A pdb=" N ALA L 104 " --> pdb=" O GLU L 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 107 No H-bonds generated for 'chain 'L' and resid 105 through 107' Processing helix chain 'L' and resid 108 through 123 Processing helix chain 'L' and resid 125 through 137 Processing helix chain 'L' and resid 138 through 152 removed outlier: 3.709A pdb=" N ILE L 144 " --> pdb=" O PRO L 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 34 Processing helix chain 'B' and resid 42 through 46 Processing helix chain 'B' and resid 47 through 52 Processing helix chain 'B' and resid 331 through 335 removed outlier: 4.299A pdb=" N GLU B 335 " --> pdb=" O ALA B 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 331 through 335' Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 73 removed outlier: 6.357A pdb=" N PHE A 78 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N PHE A 128 " --> pdb=" O TRP A 124 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ALA A 146 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N THR A 174 " --> pdb=" O PRO A 166 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS A 293 " --> pdb=" O ASP A 289 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 63 through 73 removed outlier: 6.357A pdb=" N PHE B 78 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N PHE B 128 " --> pdb=" O TRP B 124 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ALA B 146 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N THR B 174 " --> pdb=" O PRO B 166 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS B 293 " --> pdb=" O ASP B 289 " (cutoff:3.500A) 808 hydrogen bonds defined for protein. 2358 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.46 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1860 1.32 - 1.44: 3000 1.44 - 1.56: 6631 1.56 - 1.69: 28 1.69 - 1.81: 64 Bond restraints: 11583 Sorted by residual: bond pdb=" CB PRO E 8 " pdb=" CG PRO E 8 " ideal model delta sigma weight residual 1.492 1.584 -0.092 5.00e-02 4.00e+02 3.40e+00 bond pdb=" CB PRO F 8 " pdb=" CG PRO F 8 " ideal model delta sigma weight residual 1.492 1.584 -0.092 5.00e-02 4.00e+02 3.40e+00 bond pdb=" CB PRO E 10 " pdb=" CG PRO E 10 " ideal model delta sigma weight residual 1.492 1.570 -0.078 5.00e-02 4.00e+02 2.43e+00 bond pdb=" CB PRO F 10 " pdb=" CG PRO F 10 " ideal model delta sigma weight residual 1.492 1.570 -0.078 5.00e-02 4.00e+02 2.43e+00 bond pdb=" CB PRO G 16 " pdb=" CG PRO G 16 " ideal model delta sigma weight residual 1.492 1.560 -0.068 5.00e-02 4.00e+02 1.86e+00 ... (remaining 11578 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 15308 2.25 - 4.49: 343 4.49 - 6.74: 46 6.74 - 8.98: 0 8.98 - 11.23: 4 Bond angle restraints: 15701 Sorted by residual: angle pdb=" CA PRO F 40 " pdb=" N PRO F 40 " pdb=" CD PRO F 40 " ideal model delta sigma weight residual 112.00 106.55 5.45 1.40e+00 5.10e-01 1.51e+01 angle pdb=" CA PRO E 40 " pdb=" N PRO E 40 " pdb=" CD PRO E 40 " ideal model delta sigma weight residual 112.00 106.55 5.45 1.40e+00 5.10e-01 1.51e+01 angle pdb=" N ASP A 338 " pdb=" CA ASP A 338 " pdb=" C ASP A 338 " ideal model delta sigma weight residual 112.38 117.06 -4.68 1.22e+00 6.72e-01 1.47e+01 angle pdb=" N ASP B 338 " pdb=" CA ASP B 338 " pdb=" C ASP B 338 " ideal model delta sigma weight residual 112.38 117.06 -4.68 1.22e+00 6.72e-01 1.47e+01 angle pdb=" CA PRO F 12 " pdb=" N PRO F 12 " pdb=" CD PRO F 12 " ideal model delta sigma weight residual 112.00 107.32 4.68 1.40e+00 5.10e-01 1.12e+01 ... (remaining 15696 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.33: 7222 24.33 - 48.65: 247 48.65 - 72.98: 88 72.98 - 97.31: 32 97.31 - 121.63: 32 Dihedral angle restraints: 7621 sinusoidal: 3667 harmonic: 3954 Sorted by residual: dihedral pdb=" C09 DU0 B 403 " pdb=" C11 DU0 B 403 " pdb=" O10 DU0 B 403 " pdb=" C12 DU0 B 403 " ideal model delta sinusoidal sigma weight residual 58.49 -63.14 121.63 1 3.00e+01 1.11e-03 1.63e+01 dihedral pdb=" C09 DU0 A 403 " pdb=" C11 DU0 A 403 " pdb=" O10 DU0 A 403 " pdb=" C12 DU0 A 403 " ideal model delta sinusoidal sigma weight residual 58.49 -63.14 121.63 1 3.00e+01 1.11e-03 1.63e+01 dihedral pdb=" C09 DU0 H 101 " pdb=" C11 DU0 H 101 " pdb=" O10 DU0 H 101 " pdb=" C12 DU0 H 101 " ideal model delta sinusoidal sigma weight residual 58.49 -61.95 120.44 1 3.00e+01 1.11e-03 1.61e+01 ... (remaining 7618 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1241 0.048 - 0.095: 362 0.095 - 0.143: 98 0.143 - 0.190: 18 0.190 - 0.238: 8 Chirality restraints: 1727 Sorted by residual: chirality pdb=" CA PRO E 40 " pdb=" N PRO E 40 " pdb=" C PRO E 40 " pdb=" CB PRO E 40 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA PRO F 40 " pdb=" N PRO F 40 " pdb=" C PRO F 40 " pdb=" CB PRO F 40 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA ASP B 338 " pdb=" N ASP B 338 " pdb=" C ASP B 338 " pdb=" CB ASP B 338 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 1724 not shown) Planarity restraints: 1930 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA E 39 " 0.078 5.00e-02 4.00e+02 1.15e-01 2.12e+01 pdb=" N PRO E 40 " -0.199 5.00e-02 4.00e+02 pdb=" CA PRO E 40 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO E 40 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 39 " -0.078 5.00e-02 4.00e+02 1.15e-01 2.12e+01 pdb=" N PRO F 40 " 0.199 5.00e-02 4.00e+02 pdb=" CA PRO F 40 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO F 40 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 11 " -0.070 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO E 12 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO E 12 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO E 12 " -0.057 5.00e-02 4.00e+02 ... (remaining 1927 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 276 2.71 - 3.26: 10783 3.26 - 3.80: 16975 3.80 - 4.35: 21831 4.35 - 4.90: 38539 Nonbonded interactions: 88404 Sorted by model distance: nonbonded pdb=" NE2 GLN A 147 " pdb=" OE2 GLU A 149 " model vdw 2.160 3.120 nonbonded pdb=" NE2 GLN B 147 " pdb=" OE2 GLU B 149 " model vdw 2.160 3.120 nonbonded pdb=" NH2 ARG B 301 " pdb=" O ALA B 304 " model vdw 2.221 3.120 nonbonded pdb=" NH2 ARG A 301 " pdb=" O ALA A 304 " model vdw 2.221 3.120 nonbonded pdb=" OH TYR D 105 " pdb=" O14 PC1 D 403 " model vdw 2.245 3.040 ... (remaining 88399 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 21 through 403) selection = (chain 'B' and resid 21 through 403) } ncs_group { reference = (chain 'C' and (resid 28 through 118 or (resid 201 and (name N or name C1 or nam \ e C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name C2A or name C2B or name C2C or name C2D or name C2E or name \ C2F or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or n \ ame C36 or name C37 or name C38 or name C39 or name C3A or name C3B or name O11 \ or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name \ O32 or name P )) or (resid 203 and (name N or name C1 or name C11 or name C12 or \ name C13 or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 \ or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name \ C2A or name C2B or name C2C or name C2D or name C2E or name C2F or name C3 or n \ ame C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name C3A or name C3B or name O11 or name O12 or name \ O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P )))) selection = (chain 'D' and (resid 28 through 118 or (resid 401 and (name N or name C1 or nam \ e C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name C2A or name C2B or name C2C or name C2D or name C2E or name \ C2F or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or n \ ame C36 or name C37 or name C38 or name C39 or name C3A or name C3B or name O11 \ or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name \ O32 or name P )) or (resid 403 and (name N or name C1 or name C11 or name C12 or \ name C13 or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 \ or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name \ C2A or name C2B or name C2C or name C2D or name C2E or name C2F or name C3 or n \ ame C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name C3A or name C3B or name O11 or name O12 or name \ O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P )))) } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 17.900 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: 0.360 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.010 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6484 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 : 0.006 0.092 11585 Z= 0.265 Angle : 0.779 11.228 15701 Z= 0.404 Chirality : 0.051 0.238 1727 Planarity : 0.010 0.115 1930 Dihedral : 17.287 121.631 5069 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.54 % Allowed : 1.26 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.54 (0.23), residues: 1330 helix: 1.60 (0.19), residues: 642 sheet: 0.99 (0.26), residues: 400 loop : -0.08 (0.40), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.003 ARG L 44 TYR 0.016 0.002 TYR B 237 PHE 0.017 0.002 PHE K 91 TRP 0.020 0.003 TRP A 197 HIS 0.006 0.002 HIS B 316 Details of bonding type rmsd covalent geometry : bond 0.00635 (11583) covalent geometry : angle 0.77874 (15701) hydrogen bonds : bond 0.18761 ( 808) hydrogen bonds : angle 7.04566 ( 2358) Misc. bond : bond 0.00125 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 196 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 48 SER cc_start: 0.9178 (p) cc_final: 0.8913 (p) REVERT: I 56 ARG cc_start: 0.8235 (mtt-85) cc_final: 0.7976 (mtt90) REVERT: A 111 ASP cc_start: 0.7817 (m-30) cc_final: 0.7591 (m-30) REVERT: A 143 GLN cc_start: 0.7125 (OUTLIER) cc_final: 0.6919 (mp10) REVERT: A 156 ASP cc_start: 0.8728 (p0) cc_final: 0.8063 (p0) REVERT: A 217 LYS cc_start: 0.8592 (tttp) cc_final: 0.8341 (ttmt) REVERT: A 289 ASP cc_start: 0.8335 (p0) cc_final: 0.8070 (p0) REVERT: A 307 MET cc_start: 0.8452 (ttp) cc_final: 0.8233 (ttm) REVERT: A 328 SER cc_start: 0.8472 (m) cc_final: 0.8243 (t) REVERT: H 48 SER cc_start: 0.9178 (p) cc_final: 0.8914 (p) REVERT: J 56 ARG cc_start: 0.8236 (mtt-85) cc_final: 0.7975 (mtt90) REVERT: B 111 ASP cc_start: 0.7819 (m-30) cc_final: 0.7592 (m-30) REVERT: B 143 GLN cc_start: 0.7123 (OUTLIER) cc_final: 0.6914 (mp10) REVERT: B 156 ASP cc_start: 0.8725 (p0) cc_final: 0.8058 (p0) REVERT: B 217 LYS cc_start: 0.8589 (tttp) cc_final: 0.8341 (ttmt) REVERT: B 289 ASP cc_start: 0.8337 (p0) cc_final: 0.8070 (p0) REVERT: B 307 MET cc_start: 0.8458 (ttp) cc_final: 0.8238 (ttm) REVERT: B 328 SER cc_start: 0.8474 (m) cc_final: 0.8244 (t) outliers start: 6 outliers final: 0 residues processed: 200 average time/residue: 0.1189 time to fit residues: 31.4808 Evaluate side-chains 110 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 108 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain B residue 143 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 20.0000 chunk 55 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 27 GLN ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 27 GLN ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.214453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.134012 restraints weight = 12111.115| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.07 r_work: 0.3395 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11585 Z= 0.164 Angle : 0.677 11.777 15701 Z= 0.333 Chirality : 0.043 0.179 1727 Planarity : 0.005 0.056 1930 Dihedral : 13.436 102.697 2587 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 0.90 % Allowed : 6.59 % Favored : 92.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.53 (0.24), residues: 1330 helix: 2.56 (0.19), residues: 654 sheet: 1.01 (0.26), residues: 398 loop : 0.60 (0.46), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 66 TYR 0.024 0.001 TYR K 117 PHE 0.012 0.001 PHE L 91 TRP 0.011 0.001 TRP A 197 HIS 0.003 0.001 HIS B 150 Details of bonding type rmsd covalent geometry : bond 0.00367 (11583) covalent geometry : angle 0.67657 (15701) hydrogen bonds : bond 0.04906 ( 808) hydrogen bonds : angle 4.88271 ( 2358) Misc. bond : bond 0.00013 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 54 TYR cc_start: 0.8725 (t80) cc_final: 0.8524 (t80) REVERT: K 147 GLU cc_start: 0.6809 (OUTLIER) cc_final: 0.6471 (pm20) REVERT: K 148 MET cc_start: 0.4222 (tmm) cc_final: 0.3239 (ttm) REVERT: A 143 GLN cc_start: 0.6840 (OUTLIER) cc_final: 0.6191 (tp40) REVERT: L 147 GLU cc_start: 0.6794 (OUTLIER) cc_final: 0.6461 (pm20) REVERT: L 148 MET cc_start: 0.4209 (tmm) cc_final: 0.3229 (ttm) REVERT: B 143 GLN cc_start: 0.6843 (OUTLIER) cc_final: 0.6189 (tp40) outliers start: 10 outliers final: 6 residues processed: 112 average time/residue: 0.0886 time to fit residues: 14.4530 Evaluate side-chains 104 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain D residue 109 GLN Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain L residue 147 GLU Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 208 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 0 optimal weight: 30.0000 chunk 75 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 89 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 126 optimal weight: 0.8980 chunk 83 optimal weight: 10.0000 chunk 65 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 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 = 0.4481 r_free = 0.4481 target = 0.217561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.134199 restraints weight = 12470.066| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.34 r_work: 0.3374 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11585 Z= 0.146 Angle : 0.572 8.655 15701 Z= 0.292 Chirality : 0.041 0.148 1727 Planarity : 0.005 0.043 1930 Dihedral : 11.704 99.091 2587 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.44 % Allowed : 9.03 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.57 (0.24), residues: 1330 helix: 2.71 (0.19), residues: 654 sheet: 0.86 (0.26), residues: 398 loop : 0.63 (0.45), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 56 TYR 0.021 0.001 TYR K 123 PHE 0.008 0.001 PHE A 134 TRP 0.011 0.001 TRP D 64 HIS 0.002 0.001 HIS B 150 Details of bonding type rmsd covalent geometry : bond 0.00336 (11583) covalent geometry : angle 0.57228 (15701) hydrogen bonds : bond 0.04080 ( 808) hydrogen bonds : angle 4.51137 ( 2358) Misc. bond : bond 0.00026 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 147 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.6541 (pm20) REVERT: K 148 MET cc_start: 0.4276 (tmm) cc_final: 0.3153 (ttp) REVERT: A 143 GLN cc_start: 0.6942 (OUTLIER) cc_final: 0.6204 (tp40) REVERT: L 147 GLU cc_start: 0.6888 (OUTLIER) cc_final: 0.6537 (pm20) REVERT: L 148 MET cc_start: 0.4266 (tmm) cc_final: 0.3135 (ttp) REVERT: B 143 GLN cc_start: 0.6946 (OUTLIER) cc_final: 0.6212 (tp40) outliers start: 16 outliers final: 4 residues processed: 124 average time/residue: 0.0835 time to fit residues: 15.6880 Evaluate side-chains 106 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain L residue 147 GLU Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 208 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 57 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 118 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 chunk 116 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 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 = 0.4479 r_free = 0.4479 target = 0.217499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.134347 restraints weight = 12538.964| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.95 r_work: 0.3411 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11585 Z= 0.139 Angle : 0.576 11.721 15701 Z= 0.289 Chirality : 0.040 0.144 1727 Planarity : 0.004 0.046 1930 Dihedral : 11.008 95.738 2587 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.62 % Allowed : 9.30 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.50 (0.24), residues: 1330 helix: 2.83 (0.19), residues: 658 sheet: 0.65 (0.26), residues: 404 loop : 0.33 (0.46), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 56 TYR 0.018 0.001 TYR H 21 PHE 0.009 0.001 PHE L 39 TRP 0.010 0.001 TRP D 64 HIS 0.003 0.001 HIS D 51 Details of bonding type rmsd covalent geometry : bond 0.00319 (11583) covalent geometry : angle 0.57637 (15701) hydrogen bonds : bond 0.03727 ( 808) hydrogen bonds : angle 4.34127 ( 2358) Misc. bond : bond 0.00030 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 147 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6606 (pm20) REVERT: K 148 MET cc_start: 0.4240 (tmm) cc_final: 0.2989 (ttp) REVERT: A 143 GLN cc_start: 0.7149 (OUTLIER) cc_final: 0.6293 (tp40) REVERT: L 147 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.6602 (pm20) REVERT: L 148 MET cc_start: 0.4227 (tmm) cc_final: 0.2977 (ttp) REVERT: B 143 GLN cc_start: 0.7156 (OUTLIER) cc_final: 0.6304 (tp40) outliers start: 18 outliers final: 8 residues processed: 102 average time/residue: 0.0840 time to fit residues: 12.8036 Evaluate side-chains 100 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain L residue 147 GLU Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 208 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 20.0000 chunk 5 optimal weight: 0.7980 chunk 36 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 51 optimal weight: 0.0980 chunk 115 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 102 optimal weight: 7.9990 chunk 114 optimal weight: 0.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.211536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.130298 restraints weight = 12121.416| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.11 r_work: 0.3374 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11585 Z= 0.212 Angle : 0.622 9.919 15701 Z= 0.311 Chirality : 0.042 0.149 1727 Planarity : 0.005 0.046 1930 Dihedral : 10.963 93.481 2587 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.17 % Allowed : 9.93 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.24), residues: 1330 helix: 2.73 (0.19), residues: 660 sheet: 0.49 (0.26), residues: 402 loop : -0.07 (0.44), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 56 TYR 0.019 0.001 TYR H 21 PHE 0.010 0.001 PHE A 134 TRP 0.009 0.001 TRP A 221 HIS 0.003 0.001 HIS B 316 Details of bonding type rmsd covalent geometry : bond 0.00507 (11583) covalent geometry : angle 0.62184 (15701) hydrogen bonds : bond 0.03812 ( 808) hydrogen bonds : angle 4.44985 ( 2358) Misc. bond : bond 0.00094 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 147 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6568 (pm20) REVERT: K 148 MET cc_start: 0.4073 (tmm) cc_final: 0.3087 (ttp) REVERT: A 143 GLN cc_start: 0.7278 (OUTLIER) cc_final: 0.6479 (tp40) REVERT: A 145 MET cc_start: 0.8228 (mtp) cc_final: 0.7547 (mmt) REVERT: L 147 GLU cc_start: 0.6976 (OUTLIER) cc_final: 0.6570 (pm20) REVERT: L 148 MET cc_start: 0.4072 (tmm) cc_final: 0.3090 (ttp) REVERT: B 143 GLN cc_start: 0.7280 (OUTLIER) cc_final: 0.6486 (tp40) REVERT: B 145 MET cc_start: 0.8227 (mtp) cc_final: 0.7544 (mmt) outliers start: 24 outliers final: 18 residues processed: 108 average time/residue: 0.0825 time to fit residues: 13.1973 Evaluate side-chains 104 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain K residue 101 MET Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain L residue 101 MET Chi-restraints excluded: chain L residue 147 GLU Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 328 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 112 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 130 optimal weight: 0.6980 chunk 126 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.212259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.131153 restraints weight = 12237.878| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.08 r_work: 0.3380 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11585 Z= 0.162 Angle : 0.560 8.895 15701 Z= 0.285 Chirality : 0.040 0.144 1727 Planarity : 0.004 0.051 1930 Dihedral : 10.637 90.500 2587 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.53 % Allowed : 9.03 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.24), residues: 1330 helix: 2.91 (0.19), residues: 660 sheet: 0.45 (0.26), residues: 406 loop : -0.18 (0.45), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 56 TYR 0.019 0.001 TYR H 21 PHE 0.008 0.001 PHE A 134 TRP 0.008 0.001 TRP A 197 HIS 0.002 0.001 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00383 (11583) covalent geometry : angle 0.56008 (15701) hydrogen bonds : bond 0.03446 ( 808) hydrogen bonds : angle 4.32718 ( 2358) Misc. bond : bond 0.00055 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 88 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 147 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6564 (pm20) REVERT: K 148 MET cc_start: 0.4244 (tmm) cc_final: 0.3117 (ttp) REVERT: A 143 GLN cc_start: 0.7256 (OUTLIER) cc_final: 0.6428 (tp40) REVERT: A 145 MET cc_start: 0.8148 (mtp) cc_final: 0.7534 (mmt) REVERT: A 156 ASP cc_start: 0.8946 (p0) cc_final: 0.8629 (p0) REVERT: L 147 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6564 (pm20) REVERT: L 148 MET cc_start: 0.4241 (tmm) cc_final: 0.3114 (ttp) REVERT: B 143 GLN cc_start: 0.7253 (OUTLIER) cc_final: 0.6427 (tp40) REVERT: B 145 MET cc_start: 0.8152 (mtp) cc_final: 0.7541 (mmt) REVERT: B 156 ASP cc_start: 0.8945 (p0) cc_final: 0.8626 (p0) outliers start: 28 outliers final: 16 residues processed: 112 average time/residue: 0.0756 time to fit residues: 13.0395 Evaluate side-chains 100 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain K residue 110 LEU Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain L residue 147 GLU Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 328 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 8 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 91 optimal weight: 20.0000 chunk 5 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 85 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 104 optimal weight: 0.0970 chunk 124 optimal weight: 4.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.214325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.133388 restraints weight = 12198.468| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.02 r_work: 0.3408 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11585 Z= 0.116 Angle : 0.527 9.481 15701 Z= 0.269 Chirality : 0.038 0.140 1727 Planarity : 0.004 0.051 1930 Dihedral : 10.122 87.914 2587 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.99 % Allowed : 10.11 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.55 (0.24), residues: 1330 helix: 3.11 (0.19), residues: 658 sheet: 0.55 (0.26), residues: 404 loop : -0.15 (0.43), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 56 TYR 0.019 0.001 TYR H 21 PHE 0.008 0.001 PHE E 41 TRP 0.009 0.001 TRP B 197 HIS 0.002 0.000 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00264 (11583) covalent geometry : angle 0.52651 (15701) hydrogen bonds : bond 0.03139 ( 808) hydrogen bonds : angle 4.14228 ( 2358) Misc. bond : bond 0.00013 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 120 LEU cc_start: 0.4968 (tp) cc_final: 0.4510 (pp) REVERT: K 147 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6539 (pm20) REVERT: K 148 MET cc_start: 0.4222 (tmm) cc_final: 0.2954 (ttp) REVERT: A 143 GLN cc_start: 0.7079 (OUTLIER) cc_final: 0.6310 (tp40) REVERT: A 145 MET cc_start: 0.8097 (mtp) cc_final: 0.7621 (mmt) REVERT: L 120 LEU cc_start: 0.4980 (tp) cc_final: 0.4521 (pp) REVERT: L 147 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.6540 (pm20) REVERT: L 148 MET cc_start: 0.4226 (tmm) cc_final: 0.2962 (ttp) REVERT: B 143 GLN cc_start: 0.7077 (OUTLIER) cc_final: 0.6311 (tp40) REVERT: B 145 MET cc_start: 0.8107 (mtp) cc_final: 0.7625 (mmt) outliers start: 22 outliers final: 14 residues processed: 104 average time/residue: 0.0725 time to fit residues: 11.5812 Evaluate side-chains 105 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain L residue 147 GLU Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 328 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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: 66.4497 > 50: distance: 2 - 11: 3.260 distance: 79 - 130: 36.972 distance: 82 - 127: 14.054 distance: 90 - 109: 36.919 distance: 93 - 106: 27.586 distance: 104 - 106: 30.855 distance: 106 - 107: 38.417 distance: 107 - 108: 11.093 distance: 107 - 110: 40.214 distance: 108 - 109: 24.258 distance: 108 - 115: 22.540 distance: 110 - 111: 30.069 distance: 112 - 113: 30.202 distance: 112 - 114: 9.147 distance: 115 - 116: 6.333 distance: 115 - 210: 29.494 distance: 116 - 117: 33.233 distance: 116 - 119: 13.788 distance: 117 - 118: 8.207 distance: 117 - 127: 18.108 distance: 118 - 207: 19.193 distance: 119 - 120: 10.805 distance: 120 - 122: 7.296 distance: 121 - 123: 10.383 distance: 122 - 124: 13.035 distance: 123 - 125: 12.232 distance: 124 - 125: 11.864 distance: 125 - 126: 9.429 distance: 127 - 128: 9.846 distance: 128 - 129: 42.279 distance: 128 - 131: 16.156 distance: 129 - 130: 33.472 distance: 129 - 135: 35.491 distance: 131 - 132: 17.739 distance: 132 - 133: 14.664 distance: 132 - 134: 10.057 distance: 135 - 136: 21.784 distance: 135 - 198: 30.538 distance: 136 - 137: 26.025 distance: 136 - 139: 20.314 distance: 137 - 138: 18.195 distance: 137 - 144: 21.651 distance: 138 - 195: 35.027 distance: 139 - 140: 21.441 distance: 140 - 141: 25.952 distance: 141 - 142: 27.551 distance: 141 - 143: 9.021 distance: 144 - 145: 25.243 distance: 145 - 146: 23.132 distance: 145 - 148: 25.475 distance: 146 - 150: 27.580 distance: 148 - 149: 38.683 distance: 150 - 151: 35.192 distance: 151 - 152: 13.832 distance: 151 - 154: 48.903 distance: 152 - 153: 33.371 distance: 152 - 158: 16.395 distance: 154 - 155: 38.802 distance: 154 - 156: 6.003 distance: 155 - 157: 3.623 distance: 158 - 159: 8.617 distance: 159 - 160: 16.013 distance: 159 - 162: 27.058 distance: 160 - 161: 51.971 distance: 160 - 165: 42.344 distance: 162 - 163: 40.395 distance: 162 - 164: 48.457 distance: 165 - 166: 46.917 distance: 165 - 171: 39.623 distance: 166 - 167: 37.397 distance: 166 - 169: 43.774 distance: 167 - 168: 11.604 distance: 167 - 172: 16.352 distance: 169 - 170: 27.607 distance: 170 - 171: 25.329 distance: 172 - 173: 19.885 distance: 173 - 174: 9.155 distance: 173 - 176: 24.289 distance: 174 - 175: 7.303 distance: 174 - 181: 13.030 distance: 176 - 177: 26.408 distance: 178 - 179: 39.643 distance: 181 - 182: 24.849 distance: 182 - 183: 36.584 distance: 182 - 185: 25.906 distance: 183 - 184: 40.590 distance: 183 - 189: 21.578 distance: 185 - 186: 34.805 distance: 186 - 187: 9.862 distance: 186 - 188: 14.025