Starting phenix.real_space_refine on Fri Aug 22 16:04:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w5m_37297/08_2025/8w5m_37297.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w5m_37297/08_2025/8w5m_37297.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8w5m_37297/08_2025/8w5m_37297.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w5m_37297/08_2025/8w5m_37297.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8w5m_37297/08_2025/8w5m_37297.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w5m_37297/08_2025/8w5m_37297.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.078 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: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 3519 2.51 5 N 995 2.21 5 O 1116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 5645 Number of models: 1 Model: "" Number of chains: 6 Chain: "L" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 777 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "H" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 924 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "A" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 980 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "b" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 992 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 8, 'TRANS': 123} Chain: "B" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 992 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 8, 'TRANS': 123} Chain: "C" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 980 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Time building chain proxies: 1.61, per 1000 atoms: 0.29 Number of scatterers: 5645 At special positions: 0 Unit cell: (101.64, 109.56, 89.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 1116 8.00 N 995 7.00 C 3519 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS L 25 " - pdb=" SG CYS L 93 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.30 Conformation dependent library (CDL) restraints added in 255.0 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1388 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 9 sheets defined 12.8% alpha, 34.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 101 through 116 removed outlier: 3.583A pdb=" N ARG A 105 " --> pdb=" O THR A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 125 Processing helix chain 'b' and resid 101 through 116 removed outlier: 3.583A pdb=" N ARG b 105 " --> pdb=" O THR b 101 " (cutoff:3.500A) Processing helix chain 'b' and resid 118 through 125 Processing helix chain 'B' and resid 101 through 116 removed outlier: 3.584A pdb=" N ARG B 105 " --> pdb=" O THR B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 125 Processing helix chain 'C' and resid 101 through 116 removed outlier: 3.584A pdb=" N ARG C 105 " --> pdb=" O THR C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 125 Processing sheet with id=AA1, first strand: chain 'L' and resid 8 through 9 Processing sheet with id=AA2, first strand: chain 'L' and resid 21 through 22 Processing sheet with id=AA3, first strand: chain 'L' and resid 48 through 53 removed outlier: 6.584A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 94 through 96 Processing sheet with id=AA5, first strand: chain 'H' and resid 7 through 10 removed outlier: 3.842A pdb=" N LEU H 7 " --> pdb=" O ALA H 26 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU H 9 " --> pdb=" O SER H 24 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N SER H 24 " --> pdb=" O GLU H 9 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER H 74 " --> pdb=" O PHE H 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 50 through 54 removed outlier: 6.874A pdb=" N TRP H 39 " --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N TYR H 53 " --> pdb=" O MET H 37 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N MET H 37 " --> pdb=" O TYR H 53 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG H 42 " --> pdb=" O MET H 96 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N MET H 96 " --> pdb=" O ARG H 42 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA H 95 " --> pdb=" O LEU H 119 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR H 117 " --> pdb=" O TYR H 97 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 6 through 11 removed outlier: 5.243A pdb=" N THR A 7 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU A 21 " --> pdb=" O THR A 7 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLY A 9 " --> pdb=" O LEU A 19 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU A 19 " --> pdb=" O GLY A 9 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N SER A 34 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N VAL A 26 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL A 32 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG A 86 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N CYS A 74 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL A 84 " --> pdb=" O CYS A 74 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER b 95 " --> pdb=" O TYR A 89 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL b 84 " --> pdb=" O CYS b 74 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N CYS b 74 " --> pdb=" O VAL b 84 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG b 86 " --> pdb=" O THR b 72 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N VAL b 32 " --> pdb=" O VAL b 26 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N VAL b 26 " --> pdb=" O VAL b 32 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N SER b 34 " --> pdb=" O ARG b 24 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU b 19 " --> pdb=" O GLY b 9 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLY b 9 " --> pdb=" O LEU b 19 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU b 21 " --> pdb=" O THR b 7 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N THR b 7 " --> pdb=" O LEU b 21 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 6 through 11 removed outlier: 5.243A pdb=" N THR B 7 " --> pdb=" O LEU B 21 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU B 21 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLY B 9 " --> pdb=" O LEU B 19 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU B 19 " --> pdb=" O GLY B 9 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N SER B 34 " --> pdb=" O ARG B 24 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N VAL B 26 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL B 32 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG B 86 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N CYS B 74 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL B 84 " --> pdb=" O CYS B 74 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 6 through 11 removed outlier: 5.244A pdb=" N THR C 7 " --> pdb=" O LEU C 21 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU C 21 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLY C 9 " --> pdb=" O LEU C 19 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU C 19 " --> pdb=" O GLY C 9 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N SER C 34 " --> pdb=" O ARG C 24 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N VAL C 26 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N VAL C 32 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG C 86 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N CYS C 74 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL C 84 " --> pdb=" O CYS C 74 " (cutoff:3.500A) 211 hydrogen bonds defined for protein. 582 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: 0.78 Time building geometry restraints manager: 0.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 958 1.29 - 1.42: 1378 1.42 - 1.55: 3372 1.55 - 1.68: 14 1.68 - 1.81: 18 Bond restraints: 5740 Sorted by residual: bond pdb=" C VAL A 6 " pdb=" O VAL A 6 " ideal model delta sigma weight residual 1.236 1.156 0.081 1.20e-02 6.94e+03 4.53e+01 bond pdb=" C LEU A 3 " pdb=" O LEU A 3 " ideal model delta sigma weight residual 1.235 1.169 0.066 1.20e-02 6.94e+03 2.99e+01 bond pdb=" C THR A 5 " pdb=" O THR A 5 " ideal model delta sigma weight residual 1.234 1.171 0.063 1.20e-02 6.94e+03 2.76e+01 bond pdb=" CB THR A 5 " pdb=" CG2 THR A 5 " ideal model delta sigma weight residual 1.521 1.377 0.144 3.30e-02 9.18e+02 1.90e+01 bond pdb=" CA THR A 5 " pdb=" CB THR A 5 " ideal model delta sigma weight residual 1.529 1.461 0.068 1.64e-02 3.72e+03 1.70e+01 ... (remaining 5735 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 7509 2.20 - 4.39: 249 4.39 - 6.59: 35 6.59 - 8.79: 13 8.79 - 10.98: 7 Bond angle restraints: 7813 Sorted by residual: angle pdb=" C SER C 53 " pdb=" N GLN C 54 " pdb=" CA GLN C 54 " ideal model delta sigma weight residual 120.86 130.18 -9.32 1.60e+00 3.91e-01 3.39e+01 angle pdb=" C SER b 53 " pdb=" N GLN b 54 " pdb=" CA GLN b 54 " ideal model delta sigma weight residual 120.86 130.16 -9.30 1.60e+00 3.91e-01 3.38e+01 angle pdb=" C SER B 53 " pdb=" N GLN B 54 " pdb=" CA GLN B 54 " ideal model delta sigma weight residual 120.86 130.15 -9.29 1.60e+00 3.91e-01 3.37e+01 angle pdb=" C SER A 53 " pdb=" N GLN A 54 " pdb=" CA GLN A 54 " ideal model delta sigma weight residual 120.86 130.13 -9.27 1.60e+00 3.91e-01 3.36e+01 angle pdb=" N VAL A 6 " pdb=" CA VAL A 6 " pdb=" CB VAL A 6 " ideal model delta sigma weight residual 111.83 105.69 6.14 1.23e+00 6.61e-01 2.49e+01 ... (remaining 7808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.03: 3316 14.03 - 28.06: 123 28.06 - 42.09: 29 42.09 - 56.12: 0 56.12 - 70.15: 4 Dihedral angle restraints: 3472 sinusoidal: 1315 harmonic: 2157 Sorted by residual: dihedral pdb=" CA GLY L 18 " pdb=" C GLY L 18 " pdb=" N GLU L 19 " pdb=" CA GLU L 19 " ideal model delta harmonic sigma weight residual 180.00 141.49 38.51 0 5.00e+00 4.00e-02 5.93e+01 dihedral pdb=" CA ASP H 65 " pdb=" C ASP H 65 " pdb=" N THR H 66 " pdb=" CA THR H 66 " ideal model delta harmonic sigma weight residual 180.00 151.56 28.44 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA CYS H 99 " pdb=" C CYS H 99 " pdb=" N ALA H 100 " pdb=" CA ALA H 100 " ideal model delta harmonic sigma weight residual -180.00 -151.88 -28.12 0 5.00e+00 4.00e-02 3.16e+01 ... (remaining 3469 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 599 0.050 - 0.101: 217 0.101 - 0.151: 74 0.151 - 0.201: 20 0.201 - 0.251: 11 Chirality restraints: 921 Sorted by residual: chirality pdb=" CA VAL A 6 " pdb=" N VAL A 6 " pdb=" C VAL A 6 " pdb=" CB VAL A 6 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CG LEU b 128 " pdb=" CB LEU b 128 " pdb=" CD1 LEU b 128 " pdb=" CD2 LEU b 128 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CG LEU C 128 " pdb=" CB LEU C 128 " pdb=" CD1 LEU C 128 " pdb=" CD2 LEU C 128 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 918 not shown) Planarity restraints: 1021 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY L 18 " -0.013 2.00e-02 2.50e+03 2.66e-02 7.09e+00 pdb=" C GLY L 18 " 0.046 2.00e-02 2.50e+03 pdb=" O GLY L 18 " -0.017 2.00e-02 2.50e+03 pdb=" N GLU L 19 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL H 67 " -0.013 2.00e-02 2.50e+03 2.51e-02 6.30e+00 pdb=" C VAL H 67 " 0.043 2.00e-02 2.50e+03 pdb=" O VAL H 67 " -0.016 2.00e-02 2.50e+03 pdb=" N LYS H 68 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL b 41 " 0.040 5.00e-02 4.00e+02 6.13e-02 6.01e+00 pdb=" N PRO b 42 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO b 42 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO b 42 " 0.033 5.00e-02 4.00e+02 ... (remaining 1018 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1364 2.80 - 3.32: 4481 3.32 - 3.85: 8661 3.85 - 4.37: 9553 4.37 - 4.90: 17345 Nonbonded interactions: 41404 Sorted by model distance: nonbonded pdb=" N ALA A 1 " pdb=" OD2 ASP b 123 " model vdw 2.272 3.120 nonbonded pdb=" OG1 THR H 72 " pdb=" O GLN H 85 " model vdw 2.329 3.040 nonbonded pdb=" O ASP H 105 " pdb=" OH TYR H 109 " model vdw 2.369 3.040 nonbonded pdb=" OE1 GLN B 87 " pdb=" OH TYR B 89 " model vdw 2.402 3.040 nonbonded pdb=" OE1 GLN A 87 " pdb=" OH TYR A 89 " model vdw 2.402 3.040 ... (remaining 41399 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' selection = (chain 'B' and resid 1 through 131) selection = chain 'C' selection = (chain 'b' and resid 1 through 131) } 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: 0.620 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: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.360 Find NCS groups from input model: 0.080 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 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 0.144 5741 Z= 0.309 Angle : 0.981 10.984 7815 Z= 0.546 Chirality : 0.063 0.251 921 Planarity : 0.008 0.061 1021 Dihedral : 8.719 70.155 2081 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.16 % Allowed : 4.38 % Favored : 95.45 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -3.59 (0.26), residues: 739 helix: -2.05 (0.44), residues: 92 sheet: -1.48 (0.29), residues: 301 loop : -3.34 (0.22), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG H 102 TYR 0.021 0.003 TYR b 62 PHE 0.024 0.003 PHE H 71 TRP 0.028 0.002 TRP H 113 HIS 0.008 0.003 HIS H 107 Details of bonding type rmsd covalent geometry : bond 0.00578 ( 5740) covalent geometry : angle 0.98160 ( 7813) SS BOND : bond 0.00060 ( 1) SS BOND : angle 0.41650 ( 2) hydrogen bonds : bond 0.14308 ( 211) hydrogen bonds : angle 6.66526 ( 582) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 162 time to evaluate : 0.250 Fit side-chains REVERT: L 72 ILE cc_start: 0.9129 (mt) cc_final: 0.8779 (pt) REVERT: L 102 VAL cc_start: 0.8596 (t) cc_final: 0.8395 (m) REVERT: H 21 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.7021 (tm) REVERT: H 74 SER cc_start: 0.8886 (t) cc_final: 0.8254 (p) REVERT: A 53 SER cc_start: 0.8085 (m) cc_final: 0.7660 (t) REVERT: b 2 LYS cc_start: 0.7997 (tttt) cc_final: 0.7516 (mmtt) REVERT: b 24 ARG cc_start: 0.8211 (mtp180) cc_final: 0.6545 (tpt170) REVERT: b 53 SER cc_start: 0.8613 (m) cc_final: 0.8399 (t) REVERT: b 60 LYS cc_start: 0.8426 (pttm) cc_final: 0.8221 (ptpp) REVERT: b 102 ASP cc_start: 0.8366 (p0) cc_final: 0.8134 (p0) REVERT: C 34 SER cc_start: 0.8797 (m) cc_final: 0.8546 (t) outliers start: 1 outliers final: 0 residues processed: 162 average time/residue: 0.0993 time to fit residues: 20.0902 Evaluate side-chains 111 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.0040 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 overall best weight: 2.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 36 ASN L 57 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN b 61 ASN b 77 ASN B 61 ASN C 61 ASN C 70 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.136661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.103732 restraints weight = 7348.629| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.74 r_work: 0.3119 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5741 Z= 0.169 Angle : 0.626 7.812 7815 Z= 0.331 Chirality : 0.048 0.145 921 Planarity : 0.006 0.050 1021 Dihedral : 5.219 38.536 808 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.60 % Allowed : 9.58 % Favored : 87.82 % 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: -2.69 (0.28), residues: 739 helix: -0.51 (0.53), residues: 94 sheet: -0.98 (0.28), residues: 323 loop : -3.06 (0.25), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 57 TYR 0.015 0.002 TYR H 63 PHE 0.018 0.002 PHE H 71 TRP 0.017 0.002 TRP H 113 HIS 0.007 0.002 HIS H 108 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 5740) covalent geometry : angle 0.62566 ( 7813) SS BOND : bond 0.00043 ( 1) SS BOND : angle 0.79454 ( 2) hydrogen bonds : bond 0.04264 ( 211) hydrogen bonds : angle 5.25992 ( 582) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: L 23 LEU cc_start: 0.8558 (mp) cc_final: 0.8283 (mp) REVERT: L 72 ILE cc_start: 0.9163 (mt) cc_final: 0.8783 (pt) REVERT: H 25 CYS cc_start: 0.8073 (p) cc_final: 0.7676 (t) REVERT: b 2 LYS cc_start: 0.8338 (tttt) cc_final: 0.7602 (mmtt) REVERT: b 24 ARG cc_start: 0.8891 (mtp180) cc_final: 0.6406 (tpt170) REVERT: b 60 LYS cc_start: 0.8967 (pttm) cc_final: 0.8525 (ptpp) REVERT: b 123 ASP cc_start: 0.9160 (t70) cc_final: 0.8751 (t0) REVERT: b 127 GLN cc_start: 0.9058 (mp10) cc_final: 0.8852 (mm110) REVERT: B 47 ARG cc_start: 0.8464 (ptp-170) cc_final: 0.8095 (ptp-110) REVERT: C 16 LYS cc_start: 0.9213 (mttt) cc_final: 0.8889 (mttt) REVERT: C 121 LEU cc_start: 0.8687 (mm) cc_final: 0.8414 (mt) outliers start: 16 outliers final: 8 residues processed: 136 average time/residue: 0.1068 time to fit residues: 17.8038 Evaluate side-chains 110 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 75 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain C residue 51 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- 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: 50.6489 > 50: distance: 17 - 42: 12.536 distance: 22 - 50: 17.479 distance: 27 - 28: 6.418 distance: 27 - 30: 10.356 distance: 28 - 29: 6.635 distance: 28 - 34: 9.369 distance: 29 - 58: 11.454 distance: 30 - 31: 14.225 distance: 31 - 32: 5.424 distance: 31 - 33: 10.597 distance: 34 - 35: 5.712 distance: 35 - 36: 6.992 distance: 35 - 38: 5.017 distance: 36 - 37: 17.934 distance: 37 - 63: 19.012 distance: 38 - 39: 9.529 distance: 39 - 40: 12.419 distance: 42 - 43: 13.171 distance: 43 - 44: 4.937 distance: 43 - 46: 8.440 distance: 44 - 45: 5.819 distance: 44 - 50: 10.700 distance: 46 - 47: 11.622 distance: 46 - 48: 11.520 distance: 47 - 49: 7.307 distance: 50 - 51: 8.459 distance: 51 - 52: 19.760 distance: 51 - 54: 14.883 distance: 52 - 53: 14.015 distance: 52 - 58: 4.564 distance: 54 - 55: 17.330 distance: 55 - 56: 23.602 distance: 55 - 57: 12.006 distance: 58 - 59: 7.728 distance: 59 - 60: 7.294 distance: 59 - 62: 26.341 distance: 60 - 61: 13.447 distance: 60 - 63: 3.286 distance: 63 - 64: 8.536 distance: 64 - 65: 9.991 distance: 64 - 67: 15.941 distance: 65 - 66: 16.618 distance: 65 - 71: 15.464 distance: 67 - 68: 8.303 distance: 67 - 69: 16.660 distance: 68 - 70: 10.403 distance: 71 - 72: 10.255 distance: 72 - 73: 10.089 distance: 72 - 75: 8.277 distance: 73 - 74: 15.688 distance: 73 - 79: 12.072 distance: 75 - 76: 9.972 distance: 76 - 77: 15.584 distance: 76 - 78: 10.432 distance: 79 - 80: 10.150 distance: 80 - 81: 9.230 distance: 80 - 83: 5.872 distance: 81 - 82: 5.808 distance: 81 - 88: 8.171 distance: 83 - 84: 6.695 distance: 84 - 85: 20.185 distance: 85 - 86: 8.850 distance: 85 - 87: 7.170 distance: 88 - 89: 13.501 distance: 89 - 90: 27.343 distance: 89 - 92: 20.317 distance: 90 - 91: 22.754 distance: 90 - 96: 6.236 distance: 92 - 93: 15.272 distance: 93 - 94: 34.242 distance: 93 - 95: 22.186 distance: 96 - 97: 14.795 distance: 97 - 98: 17.942 distance: 97 - 100: 39.175 distance: 98 - 99: 6.786 distance: 98 - 104: 7.720 distance: 100 - 101: 26.575 distance: 101 - 102: 23.401 distance: 101 - 103: 5.683