Starting phenix.real_space_refine on Fri Aug 22 16:53:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sau_24957/08_2025/7sau_24957.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sau_24957/08_2025/7sau_24957.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sau_24957/08_2025/7sau_24957.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sau_24957/08_2025/7sau_24957.map" model { file = "/net/cci-nas-00/data/ceres_data/7sau_24957/08_2025/7sau_24957.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sau_24957/08_2025/7sau_24957.cif" } resolution = 3.0 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= 0.005 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 24 5.16 5 C 4140 2.51 5 N 1018 2.21 5 O 1135 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s 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: 6317 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1749 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 5, 'TRANS': 213} Chain: "B" Number of atoms: 1731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1731 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 5, 'TRANS': 210} Chain: "C" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 564 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 67} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 567 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "E" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 572 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 68} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 567 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "G" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 567 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Time building chain proxies: 1.86, per 1000 atoms: 0.29 Number of scatterers: 6317 At special positions: 0 Unit cell: (70.72, 69.056, 134.784, 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 24 16.00 O 1135 8.00 N 1018 7.00 C 4140 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.54 Conformation dependent library (CDL) restraints added in 419.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1484 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 1 sheets defined 76.4% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 7 through 23 Processing helix chain 'A' and resid 24 through 26 No H-bonds generated for 'chain 'A' and resid 24 through 26' Processing helix chain 'A' and resid 29 through 68 removed outlier: 3.795A pdb=" N PHE A 56 " --> pdb=" O LYS A 52 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 104 Processing helix chain 'A' and resid 122 through 127 Processing helix chain 'A' and resid 134 through 150 Processing helix chain 'A' and resid 151 through 153 No H-bonds generated for 'chain 'A' and resid 151 through 153' Processing helix chain 'A' and resid 156 through 167 Processing helix chain 'A' and resid 180 through 187 Processing helix chain 'A' and resid 190 through 219 Proline residue: A 196 - end of helix removed outlier: 3.697A pdb=" N ASN A 219 " --> pdb=" O HIS A 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 28 removed outlier: 4.738A pdb=" N LEU B 18 " --> pdb=" O ASN B 14 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL B 19 " --> pdb=" O MET B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 66 removed outlier: 3.781A pdb=" N PHE B 56 " --> pdb=" O LYS B 52 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE B 57 " --> pdb=" O LYS B 53 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 103 removed outlier: 3.567A pdb=" N ALA B 72 " --> pdb=" O ASN B 68 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N VAL B 74 " --> pdb=" O GLU B 70 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N TRP B 75 " --> pdb=" O LYS B 71 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL B 82 " --> pdb=" O LYS B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 129 Processing helix chain 'B' and resid 130 through 132 No H-bonds generated for 'chain 'B' and resid 130 through 132' Processing helix chain 'B' and resid 133 through 152 removed outlier: 4.309A pdb=" N GLU B 137 " --> pdb=" O GLY B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 167 Processing helix chain 'B' and resid 182 through 187 removed outlier: 3.537A pdb=" N PHE B 186 " --> pdb=" O GLU B 182 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU B 187 " --> pdb=" O ASN B 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 182 through 187' Processing helix chain 'B' and resid 190 through 218 Proline residue: B 196 - end of helix removed outlier: 3.689A pdb=" N HIS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 36 Processing helix chain 'C' and resid 39 through 59 Processing helix chain 'C' and resid 68 through 72 Processing helix chain 'D' and resid 9 through 36 Processing helix chain 'D' and resid 39 through 58 removed outlier: 3.623A pdb=" N ILE D 45 " --> pdb=" O ASP D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 61 No H-bonds generated for 'chain 'D' and resid 59 through 61' Processing helix chain 'D' and resid 68 through 72 Processing helix chain 'E' and resid 8 through 36 removed outlier: 3.614A pdb=" N LYS E 12 " --> pdb=" O GLY E 8 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE E 14 " --> pdb=" O LYS E 10 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS E 17 " --> pdb=" O ASN E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 58 Processing helix chain 'E' and resid 68 through 72 Processing helix chain 'F' and resid 9 through 36 removed outlier: 3.517A pdb=" N PHE F 14 " --> pdb=" O LYS F 10 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR F 19 " --> pdb=" O LEU F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 59 removed outlier: 3.532A pdb=" N MET F 43 " --> pdb=" O GLY F 39 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA F 59 " --> pdb=" O PHE F 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 36 removed outlier: 3.503A pdb=" N PHE G 14 " --> pdb=" O LYS G 10 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR G 19 " --> pdb=" O LEU G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 59 Processing sheet with id=AA1, first strand: chain 'A' and resid 172 through 174 removed outlier: 3.727A pdb=" N VAL A 177 " --> pdb=" O VAL A 174 " (cutoff:3.500A) 448 hydrogen bonds defined for protein. 1323 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: 0.93 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1979 1.34 - 1.46: 920 1.46 - 1.57: 3508 1.57 - 1.69: 0 1.69 - 1.80: 48 Bond restraints: 6455 Sorted by residual: bond pdb=" CB PRO C 74 " pdb=" CG PRO C 74 " ideal model delta sigma weight residual 1.492 1.569 -0.077 5.00e-02 4.00e+02 2.35e+00 bond pdb=" CG1 ILE B 28 " pdb=" CD1 ILE B 28 " ideal model delta sigma weight residual 1.513 1.455 0.058 3.90e-02 6.57e+02 2.23e+00 bond pdb=" CB VAL A 82 " pdb=" CG1 VAL A 82 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.14e+00 bond pdb=" CB MET A 16 " pdb=" CG MET A 16 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.81e+00 bond pdb=" CB ARG A 139 " pdb=" CG ARG A 139 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.61e+00 ... (remaining 6450 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 8448 1.47 - 2.95: 200 2.95 - 4.42: 57 4.42 - 5.90: 7 5.90 - 7.37: 5 Bond angle restraints: 8717 Sorted by residual: angle pdb=" CA ARG B 120 " pdb=" C ARG B 120 " pdb=" N GLU B 121 " ideal model delta sigma weight residual 116.84 122.70 -5.86 1.71e+00 3.42e-01 1.17e+01 angle pdb=" C MET B 16 " pdb=" N TYR B 17 " pdb=" CA TYR B 17 " ideal model delta sigma weight residual 120.31 115.17 5.14 1.52e+00 4.33e-01 1.14e+01 angle pdb=" N LEU A 128 " pdb=" CA LEU A 128 " pdb=" C LEU A 128 " ideal model delta sigma weight residual 110.80 117.77 -6.97 2.13e+00 2.20e-01 1.07e+01 angle pdb=" CA ARG B 120 " pdb=" C ARG B 120 " pdb=" O ARG B 120 " ideal model delta sigma weight residual 120.51 116.47 4.04 1.43e+00 4.89e-01 7.97e+00 angle pdb=" CB ARG B 76 " pdb=" CG ARG B 76 " pdb=" CD ARG B 76 " ideal model delta sigma weight residual 111.30 117.73 -6.43 2.30e+00 1.89e-01 7.82e+00 ... (remaining 8712 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.04: 3427 17.04 - 34.07: 343 34.07 - 51.11: 48 51.11 - 68.15: 14 68.15 - 85.19: 5 Dihedral angle restraints: 3837 sinusoidal: 1542 harmonic: 2295 Sorted by residual: dihedral pdb=" CA GLU A 131 " pdb=" C GLU A 131 " pdb=" N GLY A 132 " pdb=" CA GLY A 132 " ideal model delta harmonic sigma weight residual -180.00 -159.44 -20.56 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA TRP D 37 " pdb=" C TRP D 37 " pdb=" N THR D 38 " pdb=" CA THR D 38 " ideal model delta harmonic sigma weight residual 180.00 -161.42 -18.58 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA TRP F 37 " pdb=" C TRP F 37 " pdb=" N THR F 38 " pdb=" CA THR F 38 " ideal model delta harmonic sigma weight residual -180.00 -161.52 -18.48 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 3834 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 539 0.029 - 0.058: 304 0.058 - 0.086: 89 0.086 - 0.115: 37 0.115 - 0.144: 5 Chirality restraints: 974 Sorted by residual: chirality pdb=" CA ASP A 211 " pdb=" N ASP A 211 " pdb=" C ASP A 211 " pdb=" CB ASP A 211 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA GLN B 151 " pdb=" N GLN B 151 " pdb=" C GLN B 151 " pdb=" CB GLN B 151 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.75e-01 chirality pdb=" CA PRO A 196 " pdb=" N PRO A 196 " pdb=" C PRO A 196 " pdb=" CB PRO A 196 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.51e-01 ... (remaining 971 not shown) Planarity restraints: 1095 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR G 73 " 0.073 5.00e-02 4.00e+02 1.10e-01 1.93e+01 pdb=" N PRO G 74 " -0.190 5.00e-02 4.00e+02 pdb=" CA PRO G 74 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO G 74 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 73 " 0.055 5.00e-02 4.00e+02 8.19e-02 1.07e+01 pdb=" N PRO C 74 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO C 74 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO C 74 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 73 " -0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO E 74 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO E 74 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 74 " -0.025 5.00e-02 4.00e+02 ... (remaining 1092 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 66 2.68 - 3.23: 6309 3.23 - 3.79: 9837 3.79 - 4.34: 13280 4.34 - 4.90: 21807 Nonbonded interactions: 51299 Sorted by model distance: nonbonded pdb=" OH TYR B 58 " pdb=" OE2 GLU B 209 " model vdw 2.122 3.040 nonbonded pdb=" OD2 ASP A 62 " pdb=" OH TYR A 80 " model vdw 2.232 3.040 nonbonded pdb=" OH TYR A 58 " pdb=" OE2 GLU A 209 " model vdw 2.238 3.040 nonbonded pdb=" O ASN B 119 " pdb=" ND2 ASN B 119 " model vdw 2.314 3.120 nonbonded pdb=" OD1 ASN B 125 " pdb=" N TYR B 126 " model vdw 2.359 3.120 ... (remaining 51294 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 5 through 220) selection = chain 'B' } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 6 through 75 or (resid 76 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'E' and resid 6 through 76) selection = (chain 'F' and (resid 6 through 75 or (resid 76 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'G' and (resid 6 through 75 or (resid 76 and (name N or name CA or name C \ or name O or name CB )))) } 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: 1.170 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.000 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 6455 Z= 0.195 Angle : 0.606 7.370 8717 Z= 0.331 Chirality : 0.040 0.144 974 Planarity : 0.005 0.110 1095 Dihedral : 13.767 85.186 2353 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.15 % Allowed : 0.00 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.30), residues: 777 helix: 0.82 (0.21), residues: 573 sheet: None (None), residues: 0 loop : -0.46 (0.48), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 76 TYR 0.031 0.002 TYR B 17 PHE 0.012 0.001 PHE G 55 TRP 0.007 0.001 TRP A 75 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00488 ( 6455) covalent geometry : angle 0.60648 ( 8717) hydrogen bonds : bond 0.17038 ( 448) hydrogen bonds : angle 6.07327 ( 1323) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 156 time to evaluate : 0.265 Fit side-chains REVERT: A 30 LYS cc_start: 0.7710 (tmmt) cc_final: 0.7429 (ttmm) REVERT: A 38 LYS cc_start: 0.7866 (mmmt) cc_final: 0.7155 (mmtp) REVERT: A 59 GLN cc_start: 0.7322 (mt0) cc_final: 0.6849 (mp10) REVERT: A 84 LYS cc_start: 0.7920 (tttp) cc_final: 0.7515 (ttmp) REVERT: A 118 ASP cc_start: 0.8119 (p0) cc_final: 0.7883 (p0) REVERT: B 34 GLU cc_start: 0.7029 (mt-10) cc_final: 0.6806 (mm-30) REVERT: B 80 TYR cc_start: 0.6974 (m-80) cc_final: 0.6663 (m-10) REVERT: B 85 GLN cc_start: 0.7652 (mt0) cc_final: 0.7330 (mt0) REVERT: B 91 ASN cc_start: 0.7662 (m-40) cc_final: 0.7425 (m-40) REVERT: B 113 ARG cc_start: 0.7124 (mtt180) cc_final: 0.6588 (mtt90) REVERT: B 122 LYS cc_start: 0.7702 (mttp) cc_final: 0.7426 (mtmt) REVERT: B 126 TYR cc_start: 0.8093 (t80) cc_final: 0.7632 (t80) REVERT: B 143 GLU cc_start: 0.6765 (mt-10) cc_final: 0.6409 (mt-10) REVERT: B 149 MET cc_start: 0.7400 (mmp) cc_final: 0.7137 (mpm) REVERT: C 33 LYS cc_start: 0.8531 (tptm) cc_final: 0.8317 (tptp) REVERT: D 38 THR cc_start: 0.8002 (p) cc_final: 0.7799 (m) REVERT: D 43 MET cc_start: 0.8181 (mtp) cc_final: 0.7950 (mtp) REVERT: E 33 LYS cc_start: 0.8641 (tptt) cc_final: 0.8297 (tppt) REVERT: E 41 ASP cc_start: 0.7976 (m-30) cc_final: 0.7751 (m-30) REVERT: F 13 ASN cc_start: 0.7162 (t0) cc_final: 0.6864 (m110) REVERT: F 61 GLU cc_start: 0.7110 (pt0) cc_final: 0.6890 (pt0) REVERT: G 7 ASN cc_start: 0.6154 (m110) cc_final: 0.5763 (m-40) REVERT: G 62 LYS cc_start: 0.5998 (mppt) cc_final: 0.5785 (mttp) REVERT: G 67 TYR cc_start: 0.7524 (m-80) cc_final: 0.7272 (m-80) outliers start: 1 outliers final: 0 residues processed: 156 average time/residue: 0.6526 time to fit residues: 106.0293 Evaluate side-chains 115 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN B 40 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.138552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.097921 restraints weight = 7421.026| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.78 r_work: 0.2860 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 6455 Z= 0.152 Angle : 0.555 7.582 8717 Z= 0.293 Chirality : 0.039 0.141 974 Planarity : 0.005 0.077 1095 Dihedral : 4.234 20.071 833 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.97 % Allowed : 9.85 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.30), residues: 777 helix: 1.48 (0.21), residues: 582 sheet: None (None), residues: 0 loop : -0.49 (0.48), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 76 TYR 0.015 0.001 TYR A 80 PHE 0.015 0.001 PHE G 55 TRP 0.006 0.001 TRP E 69 HIS 0.002 0.001 HIS E 36 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 6455) covalent geometry : angle 0.55491 ( 8717) hydrogen bonds : bond 0.05025 ( 448) hydrogen bonds : angle 4.06822 ( 1323) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.253 Fit side-chains REVERT: A 30 LYS cc_start: 0.7449 (tmmt) cc_final: 0.6976 (ttmm) REVERT: A 34 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7625 (mm-30) REVERT: A 38 LYS cc_start: 0.8155 (mmmt) cc_final: 0.7229 (mmtp) REVERT: A 59 GLN cc_start: 0.7651 (mt0) cc_final: 0.6983 (mp10) REVERT: A 84 LYS cc_start: 0.8049 (tttp) cc_final: 0.7715 (ttmp) REVERT: A 214 SER cc_start: 0.8150 (m) cc_final: 0.7732 (p) REVERT: B 34 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7240 (mm-30) REVERT: B 80 TYR cc_start: 0.7058 (m-80) cc_final: 0.6706 (m-10) REVERT: B 91 ASN cc_start: 0.7702 (m-40) cc_final: 0.7481 (m-40) REVERT: B 113 ARG cc_start: 0.7074 (mtt180) cc_final: 0.6449 (mtt90) REVERT: B 126 TYR cc_start: 0.8015 (t80) cc_final: 0.7436 (t80) REVERT: B 131 GLU cc_start: 0.6990 (mp0) cc_final: 0.6734 (mp0) REVERT: B 143 GLU cc_start: 0.7033 (mt-10) cc_final: 0.6657 (mt-10) REVERT: B 149 MET cc_start: 0.7455 (mmp) cc_final: 0.7051 (mpm) REVERT: B 163 LEU cc_start: 0.7083 (mt) cc_final: 0.6785 (mp) REVERT: B 182 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7962 (pm20) REVERT: C 33 LYS cc_start: 0.8641 (tptm) cc_final: 0.8387 (tptp) REVERT: E 10 LYS cc_start: 0.7506 (mtmt) cc_final: 0.7047 (mttm) REVERT: E 25 ILE cc_start: 0.8691 (mm) cc_final: 0.8417 (mt) REVERT: E 33 LYS cc_start: 0.8750 (tptt) cc_final: 0.8473 (tppt) REVERT: F 61 GLU cc_start: 0.7490 (pt0) cc_final: 0.7190 (pt0) REVERT: G 7 ASN cc_start: 0.6174 (m110) cc_final: 0.5724 (m-40) REVERT: G 62 LYS cc_start: 0.6500 (mppt) cc_final: 0.6099 (mttp) outliers start: 13 outliers final: 5 residues processed: 130 average time/residue: 0.6537 time to fit residues: 88.4885 Evaluate side-chains 114 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 108 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 136 ARG Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain F residue 15 LEU 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: 69.2208 > 50: distance: 71 - 102: 6.954 distance: 78 - 110: 34.187 distance: 97 - 102: 3.286 distance: 102 - 103: 31.298 distance: 103 - 104: 21.852 distance: 103 - 106: 69.221 distance: 104 - 105: 17.905 distance: 104 - 110: 19.440 distance: 106 - 107: 5.615 distance: 107 - 108: 55.291 distance: 107 - 109: 7.129 distance: 110 - 111: 10.135 distance: 111 - 112: 29.416 distance: 111 - 114: 12.480 distance: 112 - 113: 12.574 distance: 112 - 120: 11.277 distance: 115 - 116: 4.956 distance: 116 - 118: 24.155 distance: 117 - 119: 21.808 distance: 118 - 119: 9.483 distance: 120 - 121: 18.309 distance: 122 - 134: 30.975 distance: 127 - 129: 20.592 distance: 127 - 130: 38.944 distance: 128 - 129: 18.899 distance: 129 - 131: 42.006 distance: 132 - 133: 8.572 distance: 134 - 135: 36.195 distance: 135 - 136: 28.843 distance: 135 - 138: 11.456 distance: 136 - 137: 24.918 distance: 136 - 141: 27.149 distance: 138 - 139: 27.759 distance: 138 - 140: 41.138 distance: 141 - 142: 15.377 distance: 142 - 143: 33.853 distance: 143 - 144: 6.861 distance: 143 - 145: 33.633 distance: 145 - 146: 42.686 distance: 146 - 147: 5.797 distance: 146 - 149: 6.132 distance: 147 - 148: 15.825 distance: 147 - 150: 26.030 distance: 148 - 174: 26.003 distance: 150 - 151: 5.133 distance: 151 - 152: 20.139 distance: 151 - 154: 21.424 distance: 152 - 153: 6.004 distance: 153 - 182: 27.364 distance: 154 - 155: 14.847 distance: 155 - 157: 41.838 distance: 158 - 159: 16.307 distance: 159 - 160: 26.113 distance: 159 - 162: 8.852 distance: 160 - 161: 26.526 distance: 160 - 166: 20.792 distance: 161 - 190: 30.386 distance: 162 - 163: 17.527 distance: 163 - 164: 19.185 distance: 163 - 165: 38.918 distance: 166 - 167: 11.985 distance: 167 - 168: 20.763 distance: 167 - 170: 10.763 distance: 168 - 169: 12.130 distance: 168 - 174: 6.543 distance: 169 - 196: 18.359 distance: 170 - 171: 14.339 distance: 171 - 172: 22.167 distance: 172 - 173: 53.739 distance: 174 - 175: 9.980 distance: 175 - 176: 10.161 distance: 175 - 178: 4.497 distance: 176 - 177: 4.573 distance: 176 - 182: 19.315 distance: 177 - 199: 22.742 distance: 178 - 179: 21.822 distance: 179 - 180: 27.442 distance: 179 - 181: 21.724