Starting phenix.real_space_refine on Sat Aug 23 11:34:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6t93_10408/08_2025/6t93_10408.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t93_10408/08_2025/6t93_10408.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6t93_10408/08_2025/6t93_10408.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t93_10408/08_2025/6t93_10408.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6t93_10408/08_2025/6t93_10408.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t93_10408/08_2025/6t93_10408.map" } resolution = 3.49 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= 0.003 sd= 0.051 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 300 5.49 5 S 14 5.16 5 C 6730 2.51 5 N 2287 2.21 5 O 2868 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 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: 12199 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 3072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 3072 Classifications: {'DNA': 151} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 150} Chain: "J" Number of atoms: 3113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 3113 Classifications: {'DNA': 151} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 150} Time building chain proxies: 2.66, per 1000 atoms: 0.22 Number of scatterers: 12199 At special positions: 0 Unit cell: (73.96, 121.26, 117.82, 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 14 16.00 P 300 15.00 O 2868 8.00 N 2287 7.00 C 6730 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: 0.95 Conformation dependent library (CDL) restraints added in 266.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1412 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 10 sheets defined 70.7% alpha, 2.9% beta 151 base pairs and 279 stacking pairs defined. Time for finding SS restraints: 2.22 Creating SS restraints... Processing helix chain 'A' and resid 45 through 58 Processing helix chain 'A' and resid 64 through 77 Processing helix chain 'A' and resid 86 through 115 Processing helix chain 'A' and resid 121 through 132 removed outlier: 3.502A pdb=" N ILE A 125 " --> pdb=" O MET A 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 30 Processing helix chain 'B' and resid 31 through 42 Processing helix chain 'B' and resid 50 through 77 Processing helix chain 'B' and resid 83 through 93 Processing helix chain 'C' and resid 17 through 23 removed outlier: 3.717A pdb=" N ARG C 21 " --> pdb=" O THR C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 37 Processing helix chain 'C' and resid 47 through 74 Processing helix chain 'C' and resid 80 through 90 Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'D' and resid 38 through 50 Processing helix chain 'D' and resid 56 through 85 Processing helix chain 'D' and resid 91 through 103 Processing helix chain 'D' and resid 104 through 125 Processing helix chain 'E' and resid 45 through 58 removed outlier: 3.530A pdb=" N ARG E 50 " --> pdb=" O THR E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 77 removed outlier: 3.699A pdb=" N PHE E 68 " --> pdb=" O ARG E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 115 Processing helix chain 'E' and resid 121 through 132 Processing helix chain 'F' and resid 31 through 42 Processing helix chain 'F' and resid 50 through 77 removed outlier: 3.598A pdb=" N GLU F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 removed outlier: 3.519A pdb=" N ARG F 93 " --> pdb=" O TYR F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 22 removed outlier: 3.571A pdb=" N ARG G 21 " --> pdb=" O THR G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 37 Processing helix chain 'G' and resid 47 through 73 Processing helix chain 'G' and resid 80 through 91 Processing helix chain 'G' and resid 93 through 98 Processing helix chain 'G' and resid 113 through 117 Processing helix chain 'H' and resid 38 through 48 Processing helix chain 'H' and resid 56 through 85 Processing helix chain 'H' and resid 91 through 103 Processing helix chain 'H' and resid 104 through 125 removed outlier: 3.535A pdb=" N HIS H 110 " --> pdb=" O GLU H 106 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.007A pdb=" N ARG A 84 " --> pdb=" O VAL B 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120 Processing sheet with id=AA3, first strand: chain 'B' and resid 98 through 99 Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.190A pdb=" N ARG C 43 " --> pdb=" O ILE D 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 103 Processing sheet with id=AA7, first strand: chain 'E' and resid 84 through 85 removed outlier: 6.887A pdb=" N ARG E 84 " --> pdb=" O VAL F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 119 through 120 Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.000A pdb=" N ARG G 43 " --> pdb=" O ILE H 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79 398 hydrogen bonds defined for protein. 1176 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 380 hydrogen bonds 760 hydrogen bond angles 0 basepair planarities 151 basepair parallelities 279 stacking parallelities Total time for adding SS restraints: 2.32 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1888 1.32 - 1.44: 4716 1.44 - 1.57: 5804 1.57 - 1.69: 600 1.69 - 1.81: 24 Bond restraints: 13032 Sorted by residual: bond pdb=" CD ARG E 129 " pdb=" NE ARG E 129 " ideal model delta sigma weight residual 1.458 1.395 0.063 1.40e-02 5.10e+03 2.05e+01 bond pdb=" CD ARG D 100 " pdb=" NE ARG D 100 " ideal model delta sigma weight residual 1.458 1.395 0.063 1.40e-02 5.10e+03 2.03e+01 bond pdb=" CD ARG B 93 " pdb=" NE ARG B 93 " ideal model delta sigma weight residual 1.458 1.395 0.063 1.40e-02 5.10e+03 2.00e+01 bond pdb=" CD ARG A 129 " pdb=" NE ARG A 129 " ideal model delta sigma weight residual 1.458 1.396 0.062 1.40e-02 5.10e+03 1.96e+01 bond pdb=" CD ARG F 93 " pdb=" NE ARG F 93 " ideal model delta sigma weight residual 1.458 1.398 0.060 1.40e-02 5.10e+03 1.86e+01 ... (remaining 13027 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 17023 1.88 - 3.76: 1660 3.76 - 5.64: 173 5.64 - 7.51: 32 7.51 - 9.39: 5 Bond angle restraints: 18893 Sorted by residual: angle pdb=" C HIS D 50 " pdb=" N PRO D 51 " pdb=" CA PRO D 51 " ideal model delta sigma weight residual 119.56 127.54 -7.98 1.02e+00 9.61e-01 6.12e+01 angle pdb=" C HIS H 50 " pdb=" N PRO H 51 " pdb=" CA PRO H 51 " ideal model delta sigma weight residual 119.56 127.23 -7.67 1.02e+00 9.61e-01 5.66e+01 angle pdb=" C LEU D 103 " pdb=" N PRO D 104 " pdb=" CA PRO D 104 " ideal model delta sigma weight residual 119.78 126.98 -7.20 1.03e+00 9.43e-01 4.88e+01 angle pdb=" C PHE C 26 " pdb=" N PRO C 27 " pdb=" CA PRO C 27 " ideal model delta sigma weight residual 119.76 126.26 -6.50 1.00e+00 1.00e+00 4.22e+01 angle pdb=" C ILE G 80 " pdb=" N PRO G 81 " pdb=" CA PRO G 81 " ideal model delta sigma weight residual 119.32 126.49 -7.17 1.14e+00 7.69e-01 3.95e+01 ... (remaining 18888 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.25: 5714 34.25 - 68.50: 1356 68.50 - 102.75: 12 102.75 - 137.00: 0 137.00 - 171.25: 4 Dihedral angle restraints: 7086 sinusoidal: 4894 harmonic: 2192 Sorted by residual: dihedral pdb=" C4' DT J 89 " pdb=" C3' DT J 89 " pdb=" O3' DT J 89 " pdb=" P DA J 90 " ideal model delta sinusoidal sigma weight residual 220.00 48.75 171.25 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DT J 15 " pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DC J 16 " ideal model delta sinusoidal sigma weight residual 220.00 56.09 163.91 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DG I 3 " pdb=" C3' DG I 3 " pdb=" O3' DG I 3 " pdb=" P DG I 4 " ideal model delta sinusoidal sigma weight residual 220.00 63.58 156.42 1 3.50e+01 8.16e-04 1.50e+01 ... (remaining 7083 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1519 0.063 - 0.127: 549 0.127 - 0.190: 70 0.190 - 0.253: 6 0.253 - 0.317: 2 Chirality restraints: 2146 Sorted by residual: chirality pdb=" CA LYS F 32 " pdb=" N LYS F 32 " pdb=" C LYS F 32 " pdb=" CB LYS F 32 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CA LEU A 66 " pdb=" N LEU A 66 " pdb=" C LEU A 66 " pdb=" CB LEU A 66 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA LYS B 32 " pdb=" N LYS B 32 " pdb=" C LYS B 32 " pdb=" CB LYS B 32 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 2143 not shown) Planarity restraints: 1346 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS G 37 " -0.020 2.00e-02 2.50e+03 3.98e-02 1.59e+01 pdb=" C LYS G 37 " 0.069 2.00e-02 2.50e+03 pdb=" O LYS G 37 " -0.026 2.00e-02 2.50e+03 pdb=" N GLY G 38 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 52 " 0.055 2.00e-02 2.50e+03 2.79e-02 1.55e+01 pdb=" CG TYR F 52 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR F 52 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR F 52 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR F 52 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR F 52 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR F 52 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR F 52 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 103 " -0.019 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C GLY B 103 " 0.067 2.00e-02 2.50e+03 pdb=" O GLY B 103 " -0.024 2.00e-02 2.50e+03 pdb=" OXT GLY B 103 " -0.024 2.00e-02 2.50e+03 ... (remaining 1343 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.93: 4776 2.93 - 3.42: 10638 3.42 - 3.91: 24618 3.91 - 4.41: 29004 4.41 - 4.90: 36678 Nonbonded interactions: 105714 Sorted by model distance: nonbonded pdb=" NZ LYS F 60 " pdb=" OE2 GLU F 64 " model vdw 2.435 3.120 nonbonded pdb=" O ARG A 43 " pdb=" OG1 THR A 46 " model vdw 2.481 3.040 nonbonded pdb=" N GLY C 38 " pdb=" N ASN C 39 " model vdw 2.491 2.560 nonbonded pdb=" N GLY G 38 " pdb=" N ASN G 39 " model vdw 2.493 2.560 nonbonded pdb=" N ASP D 52 " pdb=" OD1 ASP D 52 " model vdw 2.497 3.120 ... (remaining 105709 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 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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=0.99 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: 1.060 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: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.830 Find NCS groups from input model: 0.070 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 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 : 0.014 0.118 13032 Z= 0.728 Angle : 1.153 9.394 18893 Z= 0.772 Chirality : 0.062 0.317 2146 Planarity : 0.010 0.069 1346 Dihedral : 27.104 171.253 5674 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 0.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % 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: 0.78 (0.26), residues: 742 helix: 0.67 (0.19), residues: 528 sheet: None (None), residues: 0 loop : 0.50 (0.36), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG B 37 TYR 0.055 0.011 TYR F 52 PHE 0.032 0.007 PHE D 71 HIS 0.013 0.003 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.01445 (13032) covalent geometry : angle 1.15255 (18893) hydrogen bonds : bond 0.16604 ( 778) hydrogen bonds : angle 5.31406 ( 1936) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ILE cc_start: 0.9462 (mt) cc_final: 0.9125 (mm) REVERT: A 77 GLN cc_start: 0.8200 (pt0) cc_final: 0.7993 (pp30) REVERT: A 82 ASP cc_start: 0.8647 (m-30) cc_final: 0.8388 (m-30) REVERT: A 114 HIS cc_start: 0.8772 (t70) cc_final: 0.8462 (t-90) REVERT: B 24 ARG cc_start: 0.8295 (mtm110) cc_final: 0.8031 (ppt170) REVERT: B 97 THR cc_start: 0.8583 (m) cc_final: 0.8379 (p) REVERT: C 74 ASN cc_start: 0.8984 (m-40) cc_final: 0.8406 (t0) REVERT: C 102 THR cc_start: 0.8968 (m) cc_final: 0.8690 (p) REVERT: D 35 LYS cc_start: 0.8194 (mmtt) cc_final: 0.7583 (mmtm) REVERT: D 52 ASP cc_start: 0.8489 (p0) cc_final: 0.8131 (p0) REVERT: D 60 MET cc_start: 0.9081 (tpp) cc_final: 0.8870 (tpp) REVERT: D 72 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7935 (tp30) REVERT: D 80 ARG cc_start: 0.8635 (mtm-85) cc_final: 0.8274 (mtm-85) REVERT: E 104 LEU cc_start: 0.9483 (tp) cc_final: 0.9220 (tp) REVERT: E 121 MET cc_start: 0.8348 (mmm) cc_final: 0.8148 (mmm) REVERT: G 37 LYS cc_start: 0.7759 (mttm) cc_final: 0.7536 (mttp) REVERT: G 105 GLN cc_start: 0.8637 (mp10) cc_final: 0.8409 (mp10) REVERT: G 119 LYS cc_start: 0.8693 (pttt) cc_final: 0.8380 (tppt) REVERT: H 80 ARG cc_start: 0.8980 (mtm-85) cc_final: 0.8188 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 308 average time/residue: 0.1225 time to fit residues: 52.1307 Evaluate side-chains 227 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN D 110 HIS E 40 HIS E 77 GLN G 69 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.071770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.054061 restraints weight = 44233.027| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.41 r_work: 0.2814 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13032 Z= 0.191 Angle : 0.640 6.490 18893 Z= 0.377 Chirality : 0.037 0.149 2146 Planarity : 0.005 0.034 1346 Dihedral : 30.377 177.257 4172 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.70 % Allowed : 13.97 % Favored : 83.33 % 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: 2.96 (0.29), residues: 742 helix: 2.56 (0.21), residues: 540 sheet: None (None), residues: 0 loop : 0.31 (0.37), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 36 TYR 0.015 0.002 TYR H 41 PHE 0.012 0.002 PHE E 68 HIS 0.008 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00422 (13032) covalent geometry : angle 0.63997 (18893) hydrogen bonds : bond 0.05420 ( 778) hydrogen bonds : angle 3.13286 ( 1936) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 292 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8572 (tt0) cc_final: 0.7890 (mt-10) REVERT: A 77 GLN cc_start: 0.8239 (pt0) cc_final: 0.7916 (pp30) REVERT: A 114 HIS cc_start: 0.8952 (t70) cc_final: 0.8708 (t-90) REVERT: B 74 THR cc_start: 0.9308 (OUTLIER) cc_final: 0.8981 (p) REVERT: B 97 THR cc_start: 0.9133 (m) cc_final: 0.8751 (p) REVERT: B 99 TYR cc_start: 0.9046 (m-10) cc_final: 0.8535 (m-80) REVERT: C 57 GLU cc_start: 0.9071 (tt0) cc_final: 0.8830 (tt0) REVERT: C 74 ASN cc_start: 0.8875 (m-40) cc_final: 0.8451 (t0) REVERT: C 93 GLU cc_start: 0.9448 (mp0) cc_final: 0.9218 (mp0) REVERT: C 102 THR cc_start: 0.9140 (m) cc_final: 0.8775 (p) REVERT: C 103 ILE cc_start: 0.9347 (mm) cc_final: 0.9097 (mm) REVERT: D 52 ASP cc_start: 0.8914 (p0) cc_final: 0.8670 (p0) REVERT: D 69 ASP cc_start: 0.9000 (t0) cc_final: 0.8772 (t0) REVERT: D 89 THR cc_start: 0.9207 (p) cc_final: 0.8848 (p) REVERT: D 94 GLU cc_start: 0.8955 (mp0) cc_final: 0.8205 (mp0) REVERT: D 120 THR cc_start: 0.9052 (p) cc_final: 0.8850 (t) REVERT: D 121 LYS cc_start: 0.9624 (ttmt) cc_final: 0.9250 (ttpp) REVERT: E 42 TYR cc_start: 0.8346 (m-10) cc_final: 0.8070 (m-10) REVERT: F 60 LYS cc_start: 0.8819 (tttm) cc_final: 0.8469 (tttt) REVERT: F 64 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8765 (mp0) REVERT: G 40 TYR cc_start: 0.8858 (m-80) cc_final: 0.8547 (m-80) REVERT: G 51 TYR cc_start: 0.9166 (t80) cc_final: 0.8864 (t80) REVERT: G 57 GLU cc_start: 0.8982 (tt0) cc_final: 0.8683 (tt0) REVERT: G 119 LYS cc_start: 0.8938 (pttt) cc_final: 0.8626 (tppt) REVERT: H 43 TYR cc_start: 0.8703 (t80) cc_final: 0.8377 (t80) REVERT: H 77 GLU cc_start: 0.8948 (mm-30) cc_final: 0.8601 (mm-30) REVERT: H 96 GLN cc_start: 0.8627 (tt0) cc_final: 0.8343 (tt0) REVERT: H 102 LEU cc_start: 0.9126 (mt) cc_final: 0.8841 (mt) outliers start: 17 outliers final: 11 residues processed: 300 average time/residue: 0.1201 time to fit residues: 49.3760 Evaluate side-chains 262 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 250 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 10 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 20 optimal weight: 0.0370 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 HIS ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 HIS ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.070234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.052135 restraints weight = 44758.229| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.45 r_work: 0.2765 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13032 Z= 0.195 Angle : 0.599 8.475 18893 Z= 0.353 Chirality : 0.034 0.149 2146 Planarity : 0.004 0.044 1346 Dihedral : 30.228 173.901 4172 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 3.17 % Allowed : 17.14 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.41 (0.29), residues: 742 helix: 2.94 (0.21), residues: 538 sheet: None (None), residues: 0 loop : 0.38 (0.38), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 80 TYR 0.015 0.002 TYR D 122 PHE 0.009 0.001 PHE A 68 HIS 0.004 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00436 (13032) covalent geometry : angle 0.59943 (18893) hydrogen bonds : bond 0.04891 ( 778) hydrogen bonds : angle 3.00719 ( 1936) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 264 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8668 (tt0) cc_final: 0.8374 (tt0) REVERT: A 77 GLN cc_start: 0.8566 (pt0) cc_final: 0.8328 (pp30) REVERT: A 114 HIS cc_start: 0.9149 (t-90) cc_final: 0.8768 (t-90) REVERT: B 24 ARG cc_start: 0.8476 (mtm110) cc_final: 0.8225 (mmt180) REVERT: B 74 THR cc_start: 0.9370 (OUTLIER) cc_final: 0.8990 (p) REVERT: B 80 LYS cc_start: 0.8673 (mttp) cc_final: 0.8441 (mtmm) REVERT: C 57 GLU cc_start: 0.9138 (tt0) cc_final: 0.8869 (tt0) REVERT: C 93 GLU cc_start: 0.9513 (mp0) cc_final: 0.9241 (mp0) REVERT: C 102 THR cc_start: 0.9193 (m) cc_final: 0.8852 (p) REVERT: C 113 GLN cc_start: 0.8331 (mp10) cc_final: 0.8121 (mp10) REVERT: D 52 ASP cc_start: 0.8948 (p0) cc_final: 0.8656 (p0) REVERT: D 69 ASP cc_start: 0.9011 (t0) cc_final: 0.8794 (t0) REVERT: D 94 GLU cc_start: 0.8982 (mp0) cc_final: 0.8189 (mp0) REVERT: E 42 TYR cc_start: 0.8873 (m-10) cc_final: 0.8452 (m-10) REVERT: E 82 ASP cc_start: 0.9186 (t0) cc_final: 0.8904 (t0) REVERT: E 123 LYS cc_start: 0.9271 (pttt) cc_final: 0.9068 (pttm) REVERT: F 60 LYS cc_start: 0.8919 (tttm) cc_final: 0.8438 (tttt) REVERT: F 64 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8737 (mp0) REVERT: F 85 MET cc_start: 0.8824 (mmm) cc_final: 0.8114 (mmm) REVERT: G 51 TYR cc_start: 0.9185 (t80) cc_final: 0.8872 (t80) REVERT: G 119 LYS cc_start: 0.9058 (pttt) cc_final: 0.8784 (tppt) REVERT: H 69 ASP cc_start: 0.8564 (t0) cc_final: 0.8330 (t0) REVERT: H 96 GLN cc_start: 0.8771 (tt0) cc_final: 0.8417 (tt0) outliers start: 20 outliers final: 13 residues processed: 272 average time/residue: 0.1295 time to fit residues: 47.9663 Evaluate side-chains 249 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 235 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 95 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 46 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 98 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 63 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN D 85 ASN H 110 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.070628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.052562 restraints weight = 44631.204| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.41 r_work: 0.2777 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13032 Z= 0.166 Angle : 0.589 7.531 18893 Z= 0.346 Chirality : 0.034 0.141 2146 Planarity : 0.004 0.038 1346 Dihedral : 29.944 173.794 4172 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 3.33 % Allowed : 19.52 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.46 (0.29), residues: 742 helix: 2.98 (0.22), residues: 538 sheet: None (None), residues: 0 loop : 0.38 (0.38), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 100 TYR 0.012 0.001 TYR C 58 PHE 0.009 0.001 PHE A 68 HIS 0.002 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00367 (13032) covalent geometry : angle 0.58881 (18893) hydrogen bonds : bond 0.04365 ( 778) hydrogen bonds : angle 2.84281 ( 1936) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 250 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLN cc_start: 0.9352 (tt0) cc_final: 0.8987 (tm-30) REVERT: A 74 GLU cc_start: 0.8860 (tt0) cc_final: 0.8455 (tt0) REVERT: A 77 GLN cc_start: 0.8759 (pt0) cc_final: 0.8376 (pp30) REVERT: A 80 LYS cc_start: 0.8813 (tppp) cc_final: 0.8286 (ttmm) REVERT: A 114 HIS cc_start: 0.9113 (t-90) cc_final: 0.8729 (t-90) REVERT: B 24 ARG cc_start: 0.8504 (mtm110) cc_final: 0.8246 (mmt180) REVERT: C 93 GLU cc_start: 0.9508 (mp0) cc_final: 0.9128 (mp0) REVERT: C 96 LYS cc_start: 0.9167 (ttpt) cc_final: 0.8947 (tmmt) REVERT: C 102 THR cc_start: 0.9163 (m) cc_final: 0.8889 (p) REVERT: C 113 GLN cc_start: 0.8462 (mp10) cc_final: 0.8260 (mp10) REVERT: D 52 ASP cc_start: 0.8968 (p0) cc_final: 0.8663 (p0) REVERT: D 69 ASP cc_start: 0.9109 (t0) cc_final: 0.8792 (t0) REVERT: D 94 GLU cc_start: 0.8991 (mp0) cc_final: 0.8228 (mp0) REVERT: E 42 TYR cc_start: 0.8940 (m-10) cc_final: 0.8487 (m-10) REVERT: E 82 ASP cc_start: 0.9195 (t0) cc_final: 0.8856 (t0) REVERT: E 116 LYS cc_start: 0.9370 (mtpp) cc_final: 0.9167 (ttmm) REVERT: E 126 GLN cc_start: 0.8929 (mt0) cc_final: 0.8632 (mt0) REVERT: F 28 GLN cc_start: 0.8880 (mp10) cc_final: 0.8550 (mp10) REVERT: F 54 GLU cc_start: 0.9185 (mm-30) cc_final: 0.8856 (tt0) REVERT: F 60 LYS cc_start: 0.8943 (tttm) cc_final: 0.8622 (ttmt) REVERT: F 85 MET cc_start: 0.8834 (mmm) cc_final: 0.7972 (mmm) REVERT: F 93 ARG cc_start: 0.9153 (ptm-80) cc_final: 0.8681 (ptm160) REVERT: G 51 TYR cc_start: 0.9117 (t80) cc_final: 0.8786 (t80) REVERT: G 65 GLU cc_start: 0.8743 (tm-30) cc_final: 0.8436 (tm-30) REVERT: G 92 GLU cc_start: 0.8717 (pm20) cc_final: 0.8496 (pm20) REVERT: G 105 GLN cc_start: 0.8849 (mp10) cc_final: 0.8462 (mp10) REVERT: G 119 LYS cc_start: 0.9101 (pttt) cc_final: 0.8865 (tppt) REVERT: H 69 ASP cc_start: 0.8519 (t0) cc_final: 0.8267 (t0) REVERT: H 96 GLN cc_start: 0.8783 (tt0) cc_final: 0.8534 (tt0) REVERT: H 106 GLU cc_start: 0.8905 (tp30) cc_final: 0.8530 (tp30) REVERT: H 114 GLU cc_start: 0.9234 (mm-30) cc_final: 0.8668 (mm-30) REVERT: H 117 LYS cc_start: 0.8948 (mtmm) cc_final: 0.8563 (mtmm) outliers start: 21 outliers final: 13 residues processed: 257 average time/residue: 0.1318 time to fit residues: 46.5429 Evaluate side-chains 236 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 223 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 95 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 89 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 34 optimal weight: 0.2980 chunk 11 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 23 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.072112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.053617 restraints weight = 44468.531| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.53 r_work: 0.2811 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13032 Z= 0.155 Angle : 0.578 9.601 18893 Z= 0.339 Chirality : 0.033 0.148 2146 Planarity : 0.004 0.036 1346 Dihedral : 29.723 174.053 4172 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.33 % Allowed : 20.32 % Favored : 76.35 % 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: 3.37 (0.30), residues: 742 helix: 2.90 (0.22), residues: 540 sheet: None (None), residues: 0 loop : 0.38 (0.38), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 100 TYR 0.017 0.001 TYR A 100 PHE 0.008 0.001 PHE E 68 HIS 0.003 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00339 (13032) covalent geometry : angle 0.57847 (18893) hydrogen bonds : bond 0.04079 ( 778) hydrogen bonds : angle 2.81891 ( 1936) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 246 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8820 (tt0) cc_final: 0.8347 (tt0) REVERT: A 77 GLN cc_start: 0.8705 (pt0) cc_final: 0.8393 (pp30) REVERT: A 114 HIS cc_start: 0.9038 (t-90) cc_final: 0.8819 (t-90) REVERT: C 65 GLU cc_start: 0.9255 (tt0) cc_final: 0.8835 (tp30) REVERT: C 93 GLU cc_start: 0.9508 (mp0) cc_final: 0.9058 (mp0) REVERT: C 96 LYS cc_start: 0.9183 (ttpt) cc_final: 0.8966 (tmmt) REVERT: C 102 THR cc_start: 0.9187 (m) cc_final: 0.8873 (p) REVERT: D 52 ASP cc_start: 0.8984 (p0) cc_final: 0.8691 (p0) REVERT: D 69 ASP cc_start: 0.9200 (t0) cc_final: 0.8866 (t0) REVERT: D 94 GLU cc_start: 0.8946 (mp0) cc_final: 0.8232 (mp0) REVERT: D 122 TYR cc_start: 0.9271 (t80) cc_final: 0.9069 (t80) REVERT: E 42 TYR cc_start: 0.8935 (m-10) cc_final: 0.8427 (m-10) REVERT: E 82 ASP cc_start: 0.9171 (t0) cc_final: 0.8825 (t0) REVERT: F 85 MET cc_start: 0.8860 (mmm) cc_final: 0.8156 (mmm) REVERT: G 40 TYR cc_start: 0.8852 (m-80) cc_final: 0.8637 (m-80) REVERT: G 51 TYR cc_start: 0.9112 (t80) cc_final: 0.8783 (t80) REVERT: G 65 GLU cc_start: 0.8787 (tm-30) cc_final: 0.8462 (tm-30) REVERT: G 69 ASN cc_start: 0.8269 (m110) cc_final: 0.8011 (m-40) REVERT: G 105 GLN cc_start: 0.8848 (mp10) cc_final: 0.8249 (mp10) REVERT: G 119 LYS cc_start: 0.9163 (pttt) cc_final: 0.8945 (tppt) REVERT: H 69 ASP cc_start: 0.8598 (t0) cc_final: 0.8251 (t0) REVERT: H 96 GLN cc_start: 0.8817 (tt0) cc_final: 0.8525 (tt0) REVERT: H 114 GLU cc_start: 0.9260 (mm-30) cc_final: 0.8766 (mm-30) REVERT: H 117 LYS cc_start: 0.8918 (mtmm) cc_final: 0.8381 (mttp) outliers start: 21 outliers final: 13 residues processed: 257 average time/residue: 0.1324 time to fit residues: 46.7447 Evaluate side-chains 237 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 224 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 95 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 50 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 101 optimal weight: 10.0000 chunk 53 optimal weight: 0.7980 chunk 64 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 29 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN F 76 HIS G 74 ASN H 85 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.068197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.050138 restraints weight = 44846.807| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.47 r_work: 0.2706 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.4809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 13032 Z= 0.252 Angle : 0.648 11.830 18893 Z= 0.374 Chirality : 0.037 0.170 2146 Planarity : 0.004 0.037 1346 Dihedral : 30.129 176.582 4172 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 5.08 % Allowed : 21.11 % Favored : 73.81 % 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: 3.10 (0.30), residues: 742 helix: 2.70 (0.22), residues: 544 sheet: None (None), residues: 0 loop : 0.21 (0.38), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 100 TYR 0.036 0.002 TYR D 84 PHE 0.013 0.002 PHE A 79 HIS 0.005 0.001 HIS G 83 Details of bonding type rmsd covalent geometry : bond 0.00570 (13032) covalent geometry : angle 0.64794 (18893) hydrogen bonds : bond 0.05402 ( 778) hydrogen bonds : angle 3.23649 ( 1936) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 239 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8484 (mt-10) REVERT: A 77 GLN cc_start: 0.8993 (pt0) cc_final: 0.8565 (pp30) REVERT: A 98 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8147 (mt-10) REVERT: A 114 HIS cc_start: 0.9305 (t-90) cc_final: 0.8933 (t-90) REVERT: C 74 ASN cc_start: 0.8917 (OUTLIER) cc_final: 0.8675 (t0) REVERT: C 93 GLU cc_start: 0.9564 (mp0) cc_final: 0.9112 (mp0) REVERT: C 96 LYS cc_start: 0.9230 (ttpt) cc_final: 0.8972 (tmmt) REVERT: C 102 THR cc_start: 0.9182 (m) cc_final: 0.8824 (p) REVERT: D 52 ASP cc_start: 0.9022 (p0) cc_final: 0.8719 (p0) REVERT: D 69 ASP cc_start: 0.9229 (t0) cc_final: 0.8863 (t0) REVERT: D 94 GLU cc_start: 0.9095 (mp0) cc_final: 0.8193 (mp0) REVERT: E 58 SER cc_start: 0.9174 (m) cc_final: 0.8960 (p) REVERT: E 60 GLU cc_start: 0.8520 (pm20) cc_final: 0.8316 (pm20) REVERT: E 82 ASP cc_start: 0.9256 (t0) cc_final: 0.9003 (t0) REVERT: E 86 GLN cc_start: 0.8480 (mt0) cc_final: 0.8159 (mt0) REVERT: F 28 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.8715 (mm-40) REVERT: F 85 MET cc_start: 0.8940 (mmm) cc_final: 0.8258 (mmm) REVERT: F 99 TYR cc_start: 0.9360 (m-10) cc_final: 0.9076 (m-10) REVERT: G 51 TYR cc_start: 0.9286 (t80) cc_final: 0.9018 (t80) REVERT: G 62 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8472 (mm-30) REVERT: G 65 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8460 (tm-30) REVERT: G 69 ASN cc_start: 0.8304 (m110) cc_final: 0.7944 (m-40) REVERT: G 76 LYS cc_start: 0.8737 (mmtt) cc_final: 0.8142 (mmmm) REVERT: G 91 ASP cc_start: 0.9021 (t70) cc_final: 0.8382 (t0) REVERT: G 101 VAL cc_start: 0.9450 (t) cc_final: 0.9157 (p) REVERT: G 105 GLN cc_start: 0.8853 (mp10) cc_final: 0.8279 (mp10) REVERT: H 69 ASP cc_start: 0.8750 (t0) cc_final: 0.8533 (t0) REVERT: H 94 GLU cc_start: 0.9173 (mp0) cc_final: 0.8831 (mp0) REVERT: H 96 GLN cc_start: 0.9031 (tt0) cc_final: 0.8780 (tt0) REVERT: H 106 GLU cc_start: 0.8658 (tp30) cc_final: 0.8430 (tp30) REVERT: H 110 HIS cc_start: 0.8386 (m90) cc_final: 0.8010 (m90) REVERT: H 114 GLU cc_start: 0.9256 (mm-30) cc_final: 0.8712 (mm-30) REVERT: H 117 LYS cc_start: 0.8969 (mtmm) cc_final: 0.8367 (mttp) outliers start: 32 outliers final: 21 residues processed: 254 average time/residue: 0.1369 time to fit residues: 47.4572 Evaluate side-chains 254 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 230 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 28 GLN Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 39 ASN Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain H residue 95 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 17 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 HIS ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.068675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.050125 restraints weight = 44997.206| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 2.48 r_work: 0.2714 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.4971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13032 Z= 0.214 Angle : 0.630 10.610 18893 Z= 0.364 Chirality : 0.035 0.158 2146 Planarity : 0.004 0.036 1346 Dihedral : 30.046 177.039 4172 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 4.60 % Allowed : 23.49 % Favored : 71.90 % 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: 3.08 (0.30), residues: 742 helix: 2.71 (0.22), residues: 544 sheet: None (None), residues: 0 loop : 0.13 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 100 TYR 0.016 0.002 TYR F 89 PHE 0.015 0.001 PHE A 79 HIS 0.004 0.001 HIS F 76 Details of bonding type rmsd covalent geometry : bond 0.00485 (13032) covalent geometry : angle 0.63025 (18893) hydrogen bonds : bond 0.04619 ( 778) hydrogen bonds : angle 3.06879 ( 1936) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 241 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8399 (tt0) REVERT: A 77 GLN cc_start: 0.8960 (pt0) cc_final: 0.8564 (pp30) REVERT: A 114 HIS cc_start: 0.9233 (t-90) cc_final: 0.8863 (t-90) REVERT: B 80 LYS cc_start: 0.9006 (mtmm) cc_final: 0.8628 (mtmm) REVERT: B 85 MET cc_start: 0.9221 (mmm) cc_final: 0.8981 (mmm) REVERT: B 99 TYR cc_start: 0.9204 (m-10) cc_final: 0.8966 (m-80) REVERT: C 74 ASN cc_start: 0.8849 (OUTLIER) cc_final: 0.8549 (t0) REVERT: C 93 GLU cc_start: 0.9538 (mp0) cc_final: 0.8791 (mp0) REVERT: C 96 LYS cc_start: 0.9232 (ttpt) cc_final: 0.9021 (tmmt) REVERT: C 102 THR cc_start: 0.9190 (m) cc_final: 0.8897 (p) REVERT: D 52 ASP cc_start: 0.9017 (p0) cc_final: 0.8717 (p0) REVERT: D 69 ASP cc_start: 0.9259 (t0) cc_final: 0.8914 (t0) REVERT: D 94 GLU cc_start: 0.9111 (mp0) cc_final: 0.8224 (mp0) REVERT: E 58 SER cc_start: 0.9200 (m) cc_final: 0.8944 (p) REVERT: E 60 GLU cc_start: 0.8520 (pm20) cc_final: 0.8280 (pm20) REVERT: E 82 ASP cc_start: 0.9291 (t0) cc_final: 0.8955 (t0) REVERT: E 86 GLN cc_start: 0.8433 (mt0) cc_final: 0.8021 (mt0) REVERT: F 28 GLN cc_start: 0.8927 (mp10) cc_final: 0.8667 (mm-40) REVERT: F 61 VAL cc_start: 0.9348 (OUTLIER) cc_final: 0.9108 (p) REVERT: F 64 GLU cc_start: 0.9036 (mt-10) cc_final: 0.8746 (mp0) REVERT: F 85 MET cc_start: 0.8967 (mmm) cc_final: 0.8333 (mmm) REVERT: F 99 TYR cc_start: 0.9363 (m-10) cc_final: 0.9142 (m-10) REVERT: G 51 TYR cc_start: 0.9226 (t80) cc_final: 0.8931 (t80) REVERT: G 62 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8479 (mm-30) REVERT: G 65 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8473 (tm-30) REVERT: G 69 ASN cc_start: 0.8218 (m110) cc_final: 0.7666 (m-40) REVERT: G 91 ASP cc_start: 0.9050 (t70) cc_final: 0.8754 (t0) REVERT: G 105 GLN cc_start: 0.8883 (mp10) cc_final: 0.8323 (mp10) REVERT: H 69 ASP cc_start: 0.8738 (t0) cc_final: 0.8523 (t0) REVERT: H 94 GLU cc_start: 0.9163 (mp0) cc_final: 0.8849 (mp0) REVERT: H 96 GLN cc_start: 0.9035 (tt0) cc_final: 0.8755 (tt0) REVERT: H 114 GLU cc_start: 0.9244 (mm-30) cc_final: 0.8564 (mm-30) REVERT: H 117 LYS cc_start: 0.9016 (mtmm) cc_final: 0.8403 (mttp) outliers start: 29 outliers final: 20 residues processed: 254 average time/residue: 0.1397 time to fit residues: 48.3845 Evaluate side-chains 253 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 230 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain G residue 39 ASN Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain H residue 95 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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: 53.6589 > 50: distance: 57 - 72: 3.028 distance: 59 - 79: 8.112 distance: 64 - 87: 19.097 distance: 68 - 95: 21.232 distance: 74 - 79: 11.384 distance: 79 - 80: 19.957 distance: 80 - 81: 32.335 distance: 80 - 83: 29.227 distance: 81 - 82: 25.046 distance: 81 - 87: 24.463 distance: 83 - 84: 8.368 distance: 84 - 85: 37.363 distance: 84 - 86: 33.547 distance: 87 - 88: 14.534 distance: 88 - 89: 25.851 distance: 88 - 91: 22.901 distance: 89 - 95: 22.679 distance: 91 - 92: 25.035 distance: 92 - 93: 14.404 distance: 92 - 94: 20.363 distance: 95 - 96: 18.966 distance: 96 - 97: 20.258 distance: 96 - 99: 17.081 distance: 97 - 98: 7.628 distance: 97 - 103: 18.180 distance: 99 - 100: 11.153 distance: 100 - 101: 30.224 distance: 100 - 102: 33.785 distance: 103 - 104: 11.359 distance: 103 - 109: 3.653 distance: 104 - 105: 15.459 distance: 104 - 107: 7.886 distance: 105 - 106: 35.563 distance: 105 - 110: 6.048 distance: 106 - 131: 9.049 distance: 107 - 108: 11.876 distance: 108 - 109: 15.745 distance: 110 - 111: 40.100 distance: 111 - 112: 22.536 distance: 112 - 113: 30.045 distance: 112 - 114: 19.958 distance: 113 - 136: 20.387 distance: 114 - 115: 8.388 distance: 115 - 116: 20.178 distance: 115 - 118: 24.189 distance: 116 - 117: 30.068 distance: 116 - 123: 15.184 distance: 118 - 119: 10.795 distance: 119 - 120: 9.664 distance: 120 - 121: 24.104 distance: 120 - 122: 9.317 distance: 123 - 124: 14.946 distance: 124 - 125: 16.627 distance: 124 - 127: 34.019 distance: 125 - 126: 17.025 distance: 125 - 131: 17.301 distance: 126 - 155: 18.291 distance: 127 - 128: 9.159 distance: 128 - 129: 43.752 distance: 128 - 130: 29.312 distance: 132 - 133: 18.220 distance: 133 - 134: 16.458 distance: 133 - 136: 15.930 distance: 134 - 160: 18.247 distance: 136 - 137: 13.863 distance: 137 - 138: 13.855 distance: 137 - 140: 7.385 distance: 138 - 139: 25.451 distance: 138 - 145: 8.682 distance: 139 - 167: 20.126 distance: 140 - 141: 18.195 distance: 141 - 142: 11.928 distance: 145 - 146: 6.913 distance: 146 - 147: 12.984 distance: 146 - 149: 3.644 distance: 147 - 148: 10.240 distance: 147 - 155: 17.873 distance: 148 - 173: 24.397 distance: 149 - 150: 5.103 distance: 150 - 151: 12.155 distance: 150 - 152: 8.862 distance: 151 - 153: 8.054 distance: 152 - 154: 8.721 distance: 153 - 154: 6.882