Starting phenix.real_space_refine on Wed Jun 11 21:11:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pc6_17595/06_2025/8pc6_17595.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pc6_17595/06_2025/8pc6_17595.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pc6_17595/06_2025/8pc6_17595.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pc6_17595/06_2025/8pc6_17595.map" model { file = "/net/cci-nas-00/data/ceres_data/8pc6_17595/06_2025/8pc6_17595.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pc6_17595/06_2025/8pc6_17595.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 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 293 5.49 5 S 15 5.16 5 C 7600 2.51 5 N 2518 2.21 5 O 3067 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 13493 Number of models: 1 Model: "" Number of chains: 12 Chain: "I" Number of atoms: 2971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2971 Inner-chain residues flagged as termini: ['pdbres=" DT I -72 "'] Classifications: {'DNA': 147} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 146} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 828 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Planarities with less than four sites: {'ML3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 656 Classifications: {'peptide': 82} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 692 Classifications: {'peptide': 86} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "G" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "K" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 708 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 11, 'TRANS': 74} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Chain: "J" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3014 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen planarities: 17 Chain: "L" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 710 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 11, 'TRANS': 74} Chain breaks: 1 Time building chain proxies: 9.86, per 1000 atoms: 0.73 Number of scatterers: 13493 At special positions: 0 Unit cell: (104.2, 140.045, 120.872, 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 15 16.00 P 293 15.00 O 3067 8.00 N 2518 7.00 C 7600 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: 3.43 Conformation dependent library (CDL) restraints added in 1.1 seconds 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1756 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 12 sheets defined 59.5% alpha, 6.2% beta 129 base pairs and 267 stacking pairs defined. Time for finding SS restraints: 6.27 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.602A pdb=" N ALA A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.583A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.882A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.566A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.826A pdb=" N ARG C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.556A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.501A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 121 removed outlier: 3.899A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.251A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.666A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.546A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.377A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 4.234A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 83 Processing helix chain 'L' and resid 76 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.649A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.464A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.155A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.424A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.223A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 49 through 53 removed outlier: 3.950A pdb=" N GLU K 49 " --> pdb=" O PHE K 44 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA K 51 " --> pdb=" O ILE K 42 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE K 42 " --> pdb=" O ALA K 51 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 49 through 53 removed outlier: 3.967A pdb=" N GLU L 49 " --> pdb=" O PHE L 44 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA L 51 " --> pdb=" O ILE L 42 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE L 42 " --> pdb=" O ALA L 51 " (cutoff:3.500A) 424 hydrogen bonds defined for protein. 1245 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 329 hydrogen bonds 654 hydrogen bond angles 0 basepair planarities 129 basepair parallelities 267 stacking parallelities Total time for adding SS restraints: 4.92 Time building geometry restraints manager: 4.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2773 1.33 - 1.45: 4380 1.45 - 1.57: 6591 1.57 - 1.69: 584 1.69 - 1.81: 30 Bond restraints: 14358 Sorted by residual: bond pdb=" SG ML3 A 36 " pdb=" CD ML3 A 36 " ideal model delta sigma weight residual 1.815 1.757 0.058 2.00e-02 2.50e+03 8.35e+00 bond pdb=" CB ML3 A 36 " pdb=" SG ML3 A 36 " ideal model delta sigma weight residual 1.817 1.766 0.051 2.00e-02 2.50e+03 6.52e+00 bond pdb=" N LEU L 53 " pdb=" CA LEU L 53 " ideal model delta sigma weight residual 1.454 1.483 -0.029 1.29e-02 6.01e+03 4.99e+00 bond pdb=" C3' DG J 64 " pdb=" O3' DG J 64 " ideal model delta sigma weight residual 1.422 1.474 -0.052 3.00e-02 1.11e+03 2.98e+00 bond pdb=" C3' DT J -72 " pdb=" O3' DT J -72 " ideal model delta sigma weight residual 1.422 1.469 -0.047 3.00e-02 1.11e+03 2.44e+00 ... (remaining 14353 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 20408 2.54 - 5.09: 194 5.09 - 7.63: 15 7.63 - 10.18: 4 10.18 - 12.72: 1 Bond angle restraints: 20622 Sorted by residual: angle pdb=" CB MET L 1 " pdb=" CG MET L 1 " pdb=" SD MET L 1 " ideal model delta sigma weight residual 112.70 125.42 -12.72 3.00e+00 1.11e-01 1.80e+01 angle pdb=" C3' DC I 49 " pdb=" O3' DC I 49 " pdb=" P DA I 50 " ideal model delta sigma weight residual 120.20 125.88 -5.68 1.50e+00 4.44e-01 1.43e+01 angle pdb=" N LEU L 53 " pdb=" CA LEU L 53 " pdb=" CB LEU L 53 " ideal model delta sigma weight residual 111.55 105.15 6.40 1.74e+00 3.30e-01 1.35e+01 angle pdb=" CA TYR L 61 " pdb=" CB TYR L 61 " pdb=" CG TYR L 61 " ideal model delta sigma weight residual 113.90 120.41 -6.51 1.80e+00 3.09e-01 1.31e+01 angle pdb=" N MET L 1 " pdb=" CA MET L 1 " pdb=" C MET L 1 " ideal model delta sigma weight residual 111.00 101.39 9.61 2.80e+00 1.28e-01 1.18e+01 ... (remaining 20617 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 6328 35.96 - 71.91: 1552 71.91 - 107.86: 27 107.86 - 143.82: 3 143.82 - 179.77: 3 Dihedral angle restraints: 7913 sinusoidal: 5194 harmonic: 2719 Sorted by residual: dihedral pdb=" C4' DT J 69 " pdb=" C3' DT J 69 " pdb=" O3' DT J 69 " pdb=" P DC J 70 " ideal model delta sinusoidal sigma weight residual 220.00 40.23 179.77 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC J 68 " pdb=" C3' DC J 68 " pdb=" O3' DC J 68 " pdb=" P DT J 69 " ideal model delta sinusoidal sigma weight residual -140.00 25.50 -165.50 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DA J -73 " pdb=" C3' DA J -73 " pdb=" O3' DA J -73 " pdb=" P DT J -72 " ideal model delta sinusoidal sigma weight residual -140.00 18.32 -158.32 1 3.50e+01 8.16e-04 1.51e+01 ... (remaining 7910 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2023 0.064 - 0.127: 278 0.127 - 0.191: 14 0.191 - 0.254: 5 0.254 - 0.318: 2 Chirality restraints: 2322 Sorted by residual: chirality pdb=" CA LEU L 53 " pdb=" N LEU L 53 " pdb=" C LEU L 53 " pdb=" CB LEU L 53 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CB ILE L 58 " pdb=" CA ILE L 58 " pdb=" CG1 ILE L 58 " pdb=" CG2 ILE L 58 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" C1' DT J -72 " pdb=" O4' DT J -72 " pdb=" C2' DT J -72 " pdb=" N1 DT J -72 " both_signs ideal model delta sigma weight residual False 2.47 2.27 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 2319 not shown) Planarity restraints: 1605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS F 59 " -0.019 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C LYS F 59 " 0.064 2.00e-02 2.50e+03 pdb=" O LYS F 59 " -0.024 2.00e-02 2.50e+03 pdb=" N VAL F 60 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU F 62 " 0.017 2.00e-02 2.50e+03 3.37e-02 1.14e+01 pdb=" C LEU F 62 " -0.058 2.00e-02 2.50e+03 pdb=" O LEU F 62 " 0.022 2.00e-02 2.50e+03 pdb=" N GLU F 63 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 108 " -0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C VAL D 108 " 0.055 2.00e-02 2.50e+03 pdb=" O VAL D 108 " -0.021 2.00e-02 2.50e+03 pdb=" N SER D 109 " -0.019 2.00e-02 2.50e+03 ... (remaining 1602 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 454 2.69 - 3.25: 11465 3.25 - 3.80: 25026 3.80 - 4.35: 31928 4.35 - 4.90: 46216 Nonbonded interactions: 115089 Sorted by model distance: nonbonded pdb=" O TYR L 61 " pdb=" NZ LYS L 65 " model vdw 2.142 3.120 nonbonded pdb=" OG SER G 18 " pdb=" O PHE G 25 " model vdw 2.206 3.040 nonbonded pdb=" N THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.215 3.120 nonbonded pdb=" NH1 ARG A 129 " pdb=" OD1 ASP E 106 " model vdw 2.286 3.120 nonbonded pdb=" N4 DC I 51 " pdb=" O6 DG J -51 " model vdw 2.310 3.120 ... (remaining 115084 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 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and (resid 20 through 100 or (resid 101 and (name N or name CA or nam \ e C )))) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'K' selection = (chain 'L' and (resid 1 through 28 or (resid 29 and (name N or name CA or name C \ or name CB or name CG or name CD )) or resid 35 through 90 or (resid 91 and (na \ me N or name CA or name C or name CB or name CG or name CD or name CE or name NZ \ )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.890 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: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 38.230 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.060 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 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 : 0.004 0.058 14358 Z= 0.173 Angle : 0.682 12.723 20622 Z= 0.402 Chirality : 0.044 0.318 2322 Planarity : 0.007 0.074 1605 Dihedral : 28.540 179.771 6157 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.13 % Allowed : 2.15 % Favored : 97.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.27), residues: 913 helix: 1.72 (0.22), residues: 556 sheet: -3.79 (0.60), residues: 23 loop : -1.15 (0.30), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 21 HIS 0.004 0.001 HIS K 20 PHE 0.041 0.002 PHE C 25 TYR 0.030 0.001 TYR L 61 ARG 0.018 0.001 ARG E 42 Details of bonding type rmsd hydrogen bonds : bond 0.19305 ( 753) hydrogen bonds : angle 6.21305 ( 1899) covalent geometry : bond 0.00373 (14358) covalent geometry : angle 0.68243 (20622) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 181 time to evaluate : 0.921 Fit side-chains TARDY: cannot create tardy model for: "LYS G 118 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 182 average time/residue: 0.3868 time to fit residues: 90.6549 Evaluate side-chains 111 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 53 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 47 optimal weight: 0.0570 chunk 91 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS E 93 GLN K 20 HIS K 72 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.082687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.054285 restraints weight = 42148.299| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.90 r_work: 0.2793 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14358 Z= 0.198 Angle : 0.581 8.442 20622 Z= 0.342 Chirality : 0.038 0.184 2322 Planarity : 0.005 0.048 1605 Dihedral : 31.110 163.485 4252 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.76 % Allowed : 7.10 % Favored : 92.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.28), residues: 913 helix: 2.29 (0.22), residues: 567 sheet: -3.55 (0.64), residues: 23 loop : -1.00 (0.31), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L 21 HIS 0.004 0.001 HIS D 46 PHE 0.021 0.002 PHE C 25 TYR 0.010 0.001 TYR G 50 ARG 0.011 0.001 ARG K 74 Details of bonding type rmsd hydrogen bonds : bond 0.04996 ( 753) hydrogen bonds : angle 3.22171 ( 1899) covalent geometry : bond 0.00451 (14358) covalent geometry : angle 0.58145 (20622) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 113 time to evaluate : 1.022 Fit side-chains TARDY: cannot create tardy model for: "LYS G 118 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 91 GLU cc_start: 0.8461 (tm-30) cc_final: 0.8064 (tm-30) REVERT: K 45 PHE cc_start: 0.6405 (m-10) cc_final: 0.6099 (m-10) REVERT: L 53 LEU cc_start: 0.5032 (OUTLIER) cc_final: 0.4541 (mp) outliers start: 6 outliers final: 3 residues processed: 118 average time/residue: 0.3079 time to fit residues: 49.7821 Evaluate side-chains 105 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 101 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 68 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 91 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 31 optimal weight: 0.0470 chunk 78 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 overall best weight: 0.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.082170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.054096 restraints weight = 42571.020| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.89 r_work: 0.2789 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14358 Z= 0.171 Angle : 0.537 7.007 20622 Z= 0.317 Chirality : 0.035 0.169 2322 Planarity : 0.004 0.039 1605 Dihedral : 30.532 164.823 4252 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.27 % Allowed : 8.24 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.28), residues: 913 helix: 2.55 (0.22), residues: 573 sheet: -3.18 (0.69), residues: 29 loop : -0.95 (0.31), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP L 82 HIS 0.003 0.001 HIS E 113 PHE 0.017 0.001 PHE C 25 TYR 0.015 0.001 TYR L 61 ARG 0.004 0.000 ARG K 74 Details of bonding type rmsd hydrogen bonds : bond 0.04484 ( 753) hydrogen bonds : angle 2.96798 ( 1899) covalent geometry : bond 0.00382 (14358) covalent geometry : angle 0.53664 (20622) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 1.006 Fit side-chains TARDY: cannot create tardy model for: "LYS G 118 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: C 56 GLU cc_start: 0.9093 (OUTLIER) cc_final: 0.8814 (tt0) REVERT: K 15 MET cc_start: 0.7032 (ppp) cc_final: 0.6804 (ppp) REVERT: K 45 PHE cc_start: 0.6673 (m-10) cc_final: 0.5839 (m-10) REVERT: L 53 LEU cc_start: 0.5513 (OUTLIER) cc_final: 0.4954 (mp) outliers start: 10 outliers final: 3 residues processed: 117 average time/residue: 0.3137 time to fit residues: 50.0413 Evaluate side-chains 105 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 100 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 68 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 109 optimal weight: 0.0020 chunk 23 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 60 optimal weight: 0.0070 chunk 86 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 overall best weight: 0.4606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 46 HIS L 72 ASN L 86 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.083507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.055669 restraints weight = 42170.612| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.88 r_work: 0.2837 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14358 Z= 0.140 Angle : 0.504 5.923 20622 Z= 0.299 Chirality : 0.034 0.145 2322 Planarity : 0.004 0.036 1605 Dihedral : 30.297 167.447 4252 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.89 % Allowed : 9.25 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.28), residues: 913 helix: 2.82 (0.22), residues: 573 sheet: -2.78 (0.64), residues: 37 loop : -0.76 (0.32), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP K 21 HIS 0.003 0.001 HIS E 113 PHE 0.012 0.001 PHE L 5 TYR 0.007 0.001 TYR B 51 ARG 0.005 0.000 ARG K 74 Details of bonding type rmsd hydrogen bonds : bond 0.03846 ( 753) hydrogen bonds : angle 2.78304 ( 1899) covalent geometry : bond 0.00306 (14358) covalent geometry : angle 0.50392 (20622) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 108 time to evaluate : 1.113 Fit side-chains TARDY: cannot create tardy model for: "LYS G 118 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8789 (mptp) REVERT: C 56 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8544 (tt0) REVERT: K 15 MET cc_start: 0.6904 (ppp) cc_final: 0.6512 (ppp) REVERT: K 45 PHE cc_start: 0.6132 (m-10) cc_final: 0.5590 (m-10) REVERT: L 53 LEU cc_start: 0.5318 (OUTLIER) cc_final: 0.4700 (mp) outliers start: 7 outliers final: 2 residues processed: 114 average time/residue: 0.3278 time to fit residues: 51.0733 Evaluate side-chains 100 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 95 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 68 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 95 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 chunk 86 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 1 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3641 r_free = 0.3641 target = 0.081210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.052980 restraints weight = 41852.552| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 1.86 r_work: 0.2762 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14358 Z= 0.184 Angle : 0.532 9.132 20622 Z= 0.312 Chirality : 0.035 0.164 2322 Planarity : 0.004 0.037 1605 Dihedral : 30.355 177.345 4252 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.01 % Allowed : 9.76 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.28), residues: 913 helix: 2.78 (0.22), residues: 575 sheet: -2.79 (0.66), residues: 37 loop : -0.67 (0.33), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 21 HIS 0.004 0.001 HIS B 75 PHE 0.018 0.001 PHE C 25 TYR 0.010 0.001 TYR B 51 ARG 0.004 0.000 ARG L 3 Details of bonding type rmsd hydrogen bonds : bond 0.04562 ( 753) hydrogen bonds : angle 2.88181 ( 1899) covalent geometry : bond 0.00417 (14358) covalent geometry : angle 0.53185 (20622) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 1.030 Fit side-chains TARDY: cannot create tardy model for: "LYS G 118 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: C 56 GLU cc_start: 0.9093 (OUTLIER) cc_final: 0.8796 (tt0) REVERT: C 91 GLU cc_start: 0.8843 (tm-30) cc_final: 0.8524 (tm-30) REVERT: K 15 MET cc_start: 0.7231 (ppp) cc_final: 0.6808 (ppp) REVERT: K 49 GLU cc_start: 0.6927 (mm-30) cc_final: 0.6682 (mm-30) REVERT: L 1 MET cc_start: 0.5807 (tpp) cc_final: 0.5239 (tpp) REVERT: L 53 LEU cc_start: 0.5590 (OUTLIER) cc_final: 0.5033 (mp) outliers start: 8 outliers final: 3 residues processed: 110 average time/residue: 0.3140 time to fit residues: 47.3484 Evaluate side-chains 97 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 92 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 68 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.2258 > 50: distance: 106 - 111: 35.393 distance: 111 - 112: 40.692 distance: 113 - 118: 56.567 distance: 115 - 116: 40.503 distance: 119 - 120: 41.076 distance: 119 - 122: 55.232 distance: 120 - 121: 9.532 distance: 120 - 126: 30.781 distance: 122 - 123: 40.045 distance: 122 - 124: 69.514 distance: 123 - 125: 68.751 distance: 127 - 130: 44.858 distance: 128 - 131: 39.497 distance: 131 - 132: 41.096 distance: 132 - 133: 39.136 distance: 132 - 135: 40.666 distance: 133 - 134: 39.515 distance: 135 - 136: 40.120 distance: 136 - 137: 10.239 distance: 137 - 138: 38.313 distance: 137 - 139: 41.604 distance: 142 - 144: 39.500 distance: 144 - 145: 39.341 distance: 145 - 146: 12.741 distance: 146 - 147: 42.106 distance: 146 - 148: 27.784 distance: 149 - 150: 14.258 distance: 150 - 151: 14.802 distance: 150 - 155: 47.650 distance: 152 - 153: 31.657 distance: 152 - 154: 40.222 distance: 155 - 156: 22.732 distance: 156 - 157: 18.019 distance: 156 - 159: 18.124 distance: 157 - 158: 11.982 distance: 157 - 163: 5.838 distance: 159 - 160: 41.934 distance: 160 - 162: 56.397 distance: 163 - 164: 5.237 distance: 163 - 169: 33.180 distance: 164 - 165: 40.117 distance: 164 - 167: 56.154 distance: 165 - 166: 5.771 distance: 165 - 170: 40.262 distance: 168 - 169: 40.190 distance: 170 - 171: 20.865 distance: 171 - 172: 28.219 distance: 171 - 174: 36.883 distance: 172 - 173: 5.610 distance: 172 - 178: 28.257 distance: 175 - 176: 18.155