Starting phenix.real_space_refine on Thu Nov 14 21:32:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9imh_60689/11_2024/9imh_60689.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9imh_60689/11_2024/9imh_60689.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9imh_60689/11_2024/9imh_60689.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9imh_60689/11_2024/9imh_60689.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9imh_60689/11_2024/9imh_60689.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9imh_60689/11_2024/9imh_60689.cif" } resolution = 4.2 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 ------------------------------------------------------------------------------- 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= 0.855 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 4842 2.51 5 N 1272 2.21 5 O 1524 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 7674 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1290 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 9, 'TRANS': 151} Chain: "B" Number of atoms: 1268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1268 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 9, 'TRANS': 149} Chain: "C" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1290 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 9, 'TRANS': 151} Chain: "D" Number of atoms: 1268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1268 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 9, 'TRANS': 149} Chain: "E" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1290 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 9, 'TRANS': 151} Chain: "F" Number of atoms: 1268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1268 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 9, 'TRANS': 149} Time building chain proxies: 5.48, per 1000 atoms: 0.71 Number of scatterers: 7674 At special positions: 0 Unit cell: (111.8, 107.9, 61.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1524 8.00 N 1272 7.00 C 4842 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: 1.90 Conformation dependent library (CDL) restraints added in 1.1 seconds 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1800 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 14 sheets defined 23.1% alpha, 27.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 3 through 19 Processing helix chain 'A' and resid 85 through 103 Processing helix chain 'B' and resid 3 through 20 Processing helix chain 'B' and resid 85 through 103 Processing helix chain 'C' and resid 3 through 20 removed outlier: 3.564A pdb=" N ASP C 20 " --> pdb=" O SER C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 103 Processing helix chain 'D' and resid 3 through 20 Processing helix chain 'D' and resid 85 through 103 Processing helix chain 'E' and resid 3 through 20 Processing helix chain 'E' and resid 85 through 104 removed outlier: 3.623A pdb=" N GLN E 89 " --> pdb=" O ASP E 85 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY E 104 " --> pdb=" O VAL E 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 20 removed outlier: 3.503A pdb=" N ILE F 7 " --> pdb=" O HIS F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 103 Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 53 Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 53 removed outlier: 3.983A pdb=" N MET A 70 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR A 152 " --> pdb=" O MET A 70 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A 148 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLU A 145 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N VAL A 131 " --> pdb=" O GLU A 145 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ASN A 147 " --> pdb=" O THR A 129 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 51 through 53 removed outlier: 3.546A pdb=" N TRP B 69 " --> pdb=" O GLN B 61 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 51 through 53 removed outlier: 3.543A pdb=" N MET B 70 " --> pdb=" O TYR B 152 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR B 152 " --> pdb=" O MET B 70 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL B 148 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLU B 145 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL B 131 " --> pdb=" O GLU B 145 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ASN B 147 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG B 151 " --> pdb=" O ASP B 125 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP B 125 " --> pdb=" O ARG B 151 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 108 through 109 Processing sheet with id=AA6, first strand: chain 'C' and resid 51 through 53 Processing sheet with id=AA7, first strand: chain 'C' and resid 51 through 53 removed outlier: 3.658A pdb=" N MET C 70 " --> pdb=" O TYR C 152 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR C 152 " --> pdb=" O MET C 70 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU C 143 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N THR C 133 " --> pdb=" O LEU C 143 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLU C 145 " --> pdb=" O VAL C 131 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL C 131 " --> pdb=" O GLU C 145 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ASN C 147 " --> pdb=" O THR C 129 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 51 through 53 Processing sheet with id=AA9, first strand: chain 'D' and resid 51 through 53 removed outlier: 3.594A pdb=" N MET D 70 " --> pdb=" O TYR D 152 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR D 152 " --> pdb=" O MET D 70 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL D 148 " --> pdb=" O LEU D 74 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLU D 145 " --> pdb=" O VAL D 131 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N VAL D 131 " --> pdb=" O GLU D 145 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ASN D 147 " --> pdb=" O THR D 129 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 51 through 53 Processing sheet with id=AB2, first strand: chain 'E' and resid 51 through 53 removed outlier: 3.633A pdb=" N MET E 70 " --> pdb=" O TYR E 152 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL E 148 " --> pdb=" O LEU E 74 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ASN E 147 " --> pdb=" O THR E 129 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 107 through 108 removed outlier: 4.531A pdb=" N LEU E 107 " --> pdb=" O ALA E 123 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 51 through 53 removed outlier: 3.510A pdb=" N TRP F 69 " --> pdb=" O GLN F 61 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 51 through 53 removed outlier: 3.698A pdb=" N TYR F 152 " --> pdb=" O MET F 70 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL F 148 " --> pdb=" O LEU F 74 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL F 78 " --> pdb=" O ALA F 144 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA F 144 " --> pdb=" O VAL F 78 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLU F 145 " --> pdb=" O VAL F 131 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N VAL F 131 " --> pdb=" O GLU F 145 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASN F 147 " --> pdb=" O THR F 129 " (cutoff:3.500A) 290 hydrogen bonds defined for protein. 837 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.82 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1335 1.31 - 1.44: 2014 1.44 - 1.56: 4415 1.56 - 1.69: 0 1.69 - 1.81: 66 Bond restraints: 7830 Sorted by residual: bond pdb=" CA TYR A 50 " pdb=" C TYR A 50 " ideal model delta sigma weight residual 1.524 1.441 0.083 1.27e-02 6.20e+03 4.22e+01 bond pdb=" CA PHE A 48 " pdb=" CB PHE A 48 " ideal model delta sigma weight residual 1.530 1.439 0.091 1.58e-02 4.01e+03 3.33e+01 bond pdb=" CA PHE B 48 " pdb=" CB PHE B 48 " ideal model delta sigma weight residual 1.530 1.443 0.087 1.58e-02 4.01e+03 3.05e+01 bond pdb=" CA GLU D 47 " pdb=" C GLU D 47 " ideal model delta sigma weight residual 1.524 1.465 0.059 1.31e-02 5.83e+03 2.06e+01 bond pdb=" CA PRO E 49 " pdb=" CB PRO E 49 " ideal model delta sigma weight residual 1.533 1.469 0.064 1.42e-02 4.96e+03 2.04e+01 ... (remaining 7825 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.04: 10364 3.04 - 6.09: 214 6.09 - 9.13: 43 9.13 - 12.18: 4 12.18 - 15.22: 1 Bond angle restraints: 10626 Sorted by residual: angle pdb=" N PHE D 28 " pdb=" CA PHE D 28 " pdb=" C PHE D 28 " ideal model delta sigma weight residual 107.62 122.84 -15.22 1.97e+00 2.58e-01 5.97e+01 angle pdb=" C GLU D 82 " pdb=" CA GLU D 82 " pdb=" CB GLU D 82 " ideal model delta sigma weight residual 117.23 107.87 9.36 1.36e+00 5.41e-01 4.74e+01 angle pdb=" CA GLU D 82 " pdb=" C GLU D 82 " pdb=" N LYS D 83 " ideal model delta sigma weight residual 119.98 114.84 5.14 8.50e-01 1.38e+00 3.66e+01 angle pdb=" C PRO C 49 " pdb=" N TYR C 50 " pdb=" CA TYR C 50 " ideal model delta sigma weight residual 122.19 130.29 -8.10 1.41e+00 5.03e-01 3.30e+01 angle pdb=" CA PRO F 49 " pdb=" N PRO F 49 " pdb=" CD PRO F 49 " ideal model delta sigma weight residual 112.00 104.68 7.32 1.40e+00 5.10e-01 2.73e+01 ... (remaining 10621 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 4217 17.88 - 35.76: 424 35.76 - 53.64: 100 53.64 - 71.52: 14 71.52 - 89.41: 9 Dihedral angle restraints: 4764 sinusoidal: 1956 harmonic: 2808 Sorted by residual: dihedral pdb=" C PHE D 48 " pdb=" N PHE D 48 " pdb=" CA PHE D 48 " pdb=" CB PHE D 48 " ideal model delta harmonic sigma weight residual -122.60 -148.93 26.33 0 2.50e+00 1.60e-01 1.11e+02 dihedral pdb=" N PHE D 48 " pdb=" C PHE D 48 " pdb=" CA PHE D 48 " pdb=" CB PHE D 48 " ideal model delta harmonic sigma weight residual 122.80 147.16 -24.36 0 2.50e+00 1.60e-01 9.50e+01 dihedral pdb=" C PHE F 48 " pdb=" N PHE F 48 " pdb=" CA PHE F 48 " pdb=" CB PHE F 48 " ideal model delta harmonic sigma weight residual -122.60 -141.98 19.38 0 2.50e+00 1.60e-01 6.01e+01 ... (remaining 4761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.232: 1171 0.232 - 0.465: 4 0.465 - 0.697: 4 0.697 - 0.929: 2 0.929 - 1.161: 1 Chirality restraints: 1182 Sorted by residual: chirality pdb=" CA PHE D 48 " pdb=" N PHE D 48 " pdb=" C PHE D 48 " pdb=" CB PHE D 48 " both_signs ideal model delta sigma weight residual False 2.51 1.35 1.16 2.00e-01 2.50e+01 3.37e+01 chirality pdb=" CA PHE F 48 " pdb=" N PHE F 48 " pdb=" C PHE F 48 " pdb=" CB PHE F 48 " both_signs ideal model delta sigma weight residual False 2.51 1.70 0.81 2.00e-01 2.50e+01 1.64e+01 chirality pdb=" CA PHE B 48 " pdb=" N PHE B 48 " pdb=" C PHE B 48 " pdb=" CB PHE B 48 " both_signs ideal model delta sigma weight residual False 2.51 1.78 0.73 2.00e-01 2.50e+01 1.34e+01 ... (remaining 1179 not shown) Planarity restraints: 1392 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE F 48 " 0.106 5.00e-02 4.00e+02 1.57e-01 3.95e+01 pdb=" N PRO F 49 " -0.272 5.00e-02 4.00e+02 pdb=" CA PRO F 49 " 0.085 5.00e-02 4.00e+02 pdb=" CD PRO F 49 " 0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 48 " -0.101 5.00e-02 4.00e+02 1.54e-01 3.78e+01 pdb=" N PRO D 49 " 0.266 5.00e-02 4.00e+02 pdb=" CA PRO D 49 " -0.084 5.00e-02 4.00e+02 pdb=" CD PRO D 49 " -0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 48 " -0.096 5.00e-02 4.00e+02 1.47e-01 3.44e+01 pdb=" N PRO C 49 " 0.254 5.00e-02 4.00e+02 pdb=" CA PRO C 49 " -0.082 5.00e-02 4.00e+02 pdb=" CD PRO C 49 " -0.075 5.00e-02 4.00e+02 ... (remaining 1389 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 445 2.72 - 3.26: 7800 3.26 - 3.81: 11681 3.81 - 4.35: 13461 4.35 - 4.90: 22994 Nonbonded interactions: 56381 Sorted by model distance: nonbonded pdb=" OG1 THR D 84 " pdb=" N ASP D 85 " model vdw 2.171 3.120 nonbonded pdb=" O THR B 39 " pdb=" OH TYR B 50 " model vdw 2.197 3.040 nonbonded pdb=" O THR D 39 " pdb=" OH TYR D 50 " model vdw 2.212 3.040 nonbonded pdb=" O LYS E 83 " pdb=" OG1 THR E 84 " model vdw 2.235 3.040 nonbonded pdb=" O THR A 99 " pdb=" OG1 THR A 103 " model vdw 2.256 3.040 ... (remaining 56376 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 1 through 159) selection = chain 'B' selection = (chain 'C' and resid 1 through 159) selection = chain 'D' selection = (chain 'E' and resid 1 through 159) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.840 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.460 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 7830 Z= 0.346 Angle : 1.059 15.223 10626 Z= 0.596 Chirality : 0.078 1.161 1182 Planarity : 0.011 0.157 1392 Dihedral : 15.415 89.406 2964 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 19.62 Ramachandran Plot: Outliers : 3.48 % Allowed : 12.03 % Favored : 84.49 % Rotamer: Outliers : 0.70 % Allowed : 0.93 % Favored : 98.37 % Cbeta Deviations : 0.78 % 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: -2.10 (0.28), residues: 948 helix: 0.75 (0.38), residues: 198 sheet: -0.50 (0.29), residues: 333 loop : -3.35 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 69 HIS 0.004 0.001 HIS D 3 PHE 0.029 0.002 PHE D 28 TYR 0.038 0.002 TYR B 109 ARG 0.005 0.000 ARG D 151 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 319 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASN cc_start: 0.7087 (m-40) cc_final: 0.6794 (m-40) REVERT: A 80 ASP cc_start: 0.7572 (t0) cc_final: 0.6350 (t0) REVERT: B 70 MET cc_start: 0.7965 (tpp) cc_final: 0.7541 (mtt) REVERT: B 88 GLU cc_start: 0.7151 (tp30) cc_final: 0.6905 (tm-30) REVERT: B 113 LYS cc_start: 0.6787 (tppt) cc_final: 0.6368 (tmmt) REVERT: C 45 ILE cc_start: 0.9069 (mp) cc_final: 0.8605 (mt) REVERT: C 69 TRP cc_start: 0.8906 (m100) cc_final: 0.8128 (m100) REVERT: D 46 ARG cc_start: 0.7385 (mpt90) cc_final: 0.5666 (ttt180) REVERT: E 29 ASN cc_start: 0.6881 (m110) cc_final: 0.6430 (m110) REVERT: E 45 ILE cc_start: 0.8224 (mm) cc_final: 0.7902 (tp) REVERT: F 3 HIS cc_start: 0.6935 (m170) cc_final: 0.6722 (m170) REVERT: F 70 MET cc_start: 0.8554 (tpp) cc_final: 0.8209 (mmt) REVERT: F 81 LYS cc_start: 0.7218 (ttpp) cc_final: 0.7017 (ttpt) REVERT: F 108 GLU cc_start: 0.6039 (mm-30) cc_final: 0.5663 (tp30) outliers start: 6 outliers final: 4 residues processed: 323 average time/residue: 0.1994 time to fit residues: 85.6331 Evaluate side-chains 223 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 219 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 47 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 28 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN A 68 GLN B 34 ASN C 29 ASN C 38 GLN D 34 ASN D 87 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 7830 Z= 0.321 Angle : 0.921 18.775 10626 Z= 0.466 Chirality : 0.051 0.243 1182 Planarity : 0.012 0.175 1392 Dihedral : 7.114 43.990 1056 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 2.43 % Allowed : 12.13 % Favored : 85.44 % Rotamer: Outliers : 0.58 % Allowed : 5.94 % Favored : 93.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.11 % Twisted General : 0.11 % 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: -1.97 (0.27), residues: 948 helix: 0.93 (0.37), residues: 198 sheet: -0.25 (0.28), residues: 351 loop : -3.61 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 69 HIS 0.006 0.001 HIS D 3 PHE 0.018 0.003 PHE E 71 TYR 0.037 0.002 TYR B 109 ARG 0.005 0.000 ARG D 4 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 272 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASN cc_start: 0.6982 (m110) cc_final: 0.6645 (m-40) REVERT: A 85 ASP cc_start: 0.6014 (t0) cc_final: 0.5449 (t0) REVERT: B 26 GLU cc_start: 0.6480 (OUTLIER) cc_final: 0.5359 (pm20) REVERT: B 70 MET cc_start: 0.8073 (tpp) cc_final: 0.7824 (mtt) REVERT: B 88 GLU cc_start: 0.7727 (tp30) cc_final: 0.7175 (tm-30) REVERT: B 92 LYS cc_start: 0.7955 (mmmt) cc_final: 0.7647 (mmtp) REVERT: C 45 ILE cc_start: 0.9104 (mp) cc_final: 0.8772 (mt) REVERT: C 46 ARG cc_start: 0.7113 (ttt180) cc_final: 0.5123 (ttp80) REVERT: C 80 ASP cc_start: 0.7804 (t0) cc_final: 0.7341 (t0) REVERT: C 85 ASP cc_start: 0.5382 (t0) cc_final: 0.5178 (t0) REVERT: D 23 GLN cc_start: 0.7592 (pm20) cc_final: 0.7335 (pm20) REVERT: D 29 ASN cc_start: 0.7990 (p0) cc_final: 0.7773 (p0) REVERT: D 46 ARG cc_start: 0.7390 (mpt90) cc_final: 0.5618 (ttt180) REVERT: D 134 ASP cc_start: 0.8276 (p0) cc_final: 0.8014 (p0) REVERT: E 1 MET cc_start: 0.7267 (ttm) cc_final: 0.6390 (mtp) REVERT: E 29 ASN cc_start: 0.6735 (m110) cc_final: 0.6472 (m-40) REVERT: E 141 TYR cc_start: 0.7684 (m-10) cc_final: 0.7229 (m-80) REVERT: F 3 HIS cc_start: 0.7254 (m170) cc_final: 0.7033 (m170) REVERT: F 108 GLU cc_start: 0.6139 (mm-30) cc_final: 0.5707 (tp30) REVERT: F 134 ASP cc_start: 0.8515 (p0) cc_final: 0.8044 (p0) outliers start: 5 outliers final: 3 residues processed: 276 average time/residue: 0.1811 time to fit residues: 68.5303 Evaluate side-chains 210 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 206 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 0.4980 chunk 26 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 91 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 89 GLN C 29 ASN D 89 GLN E 68 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 7830 Z= 0.267 Angle : 0.882 19.203 10626 Z= 0.438 Chirality : 0.050 0.228 1182 Planarity : 0.012 0.178 1392 Dihedral : 6.886 44.619 1056 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 2.43 % Allowed : 12.66 % Favored : 84.92 % Rotamer: Outliers : 0.58 % Allowed : 5.01 % Favored : 94.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.11 % Twisted General : 0.11 % 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: -1.62 (0.27), residues: 948 helix: 1.06 (0.37), residues: 198 sheet: 0.47 (0.30), residues: 297 loop : -3.35 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 69 HIS 0.008 0.001 HIS B 3 PHE 0.015 0.002 PHE A 119 TYR 0.026 0.002 TYR B 109 ARG 0.009 0.000 ARG C 4 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 275 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 ILE cc_start: 0.8974 (mt) cc_final: 0.8733 (mt) REVERT: A 29 ASN cc_start: 0.6906 (m110) cc_final: 0.6432 (m110) REVERT: A 45 ILE cc_start: 0.8670 (mp) cc_final: 0.8159 (mt) REVERT: A 85 ASP cc_start: 0.6755 (t0) cc_final: 0.6258 (t0) REVERT: B 70 MET cc_start: 0.8081 (tpp) cc_final: 0.7764 (mtt) REVERT: B 88 GLU cc_start: 0.7769 (tp30) cc_final: 0.7270 (tm-30) REVERT: C 29 ASN cc_start: 0.7657 (OUTLIER) cc_final: 0.6888 (m110) REVERT: C 45 ILE cc_start: 0.9101 (mp) cc_final: 0.8720 (mt) REVERT: C 50 TYR cc_start: 0.8600 (t80) cc_final: 0.8289 (t80) REVERT: C 80 ASP cc_start: 0.7852 (t0) cc_final: 0.7400 (t0) REVERT: C 91 GLU cc_start: 0.7246 (tm-30) cc_final: 0.6690 (tm-30) REVERT: D 29 ASN cc_start: 0.7985 (p0) cc_final: 0.7352 (p0) REVERT: D 46 ARG cc_start: 0.7366 (mpt90) cc_final: 0.5357 (ttt180) REVERT: D 50 TYR cc_start: 0.8588 (t80) cc_final: 0.8365 (t80) REVERT: D 80 ASP cc_start: 0.6245 (t0) cc_final: 0.5981 (t0) REVERT: D 90 LEU cc_start: 0.9180 (tp) cc_final: 0.8964 (tt) REVERT: D 134 ASP cc_start: 0.8406 (p0) cc_final: 0.8173 (p0) REVERT: E 1 MET cc_start: 0.7205 (ttm) cc_final: 0.6849 (mtp) REVERT: E 141 TYR cc_start: 0.7848 (m-10) cc_final: 0.7413 (m-80) REVERT: F 4 ARG cc_start: 0.7692 (ptp90) cc_final: 0.7490 (ttp80) REVERT: F 26 GLU cc_start: 0.7089 (pt0) cc_final: 0.6300 (mm-30) REVERT: F 70 MET cc_start: 0.8884 (tpp) cc_final: 0.8495 (tpp) REVERT: F 88 GLU cc_start: 0.7508 (tm-30) cc_final: 0.7067 (tm-30) REVERT: F 108 GLU cc_start: 0.6164 (mm-30) cc_final: 0.5649 (tp30) outliers start: 5 outliers final: 1 residues processed: 279 average time/residue: 0.1905 time to fit residues: 71.4807 Evaluate side-chains 222 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 220 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 56 optimal weight: 0.5980 chunk 84 optimal weight: 0.0170 chunk 89 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 80 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 overall best weight: 1.0022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 38 GLN D 34 ASN D 68 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 7830 Z= 0.247 Angle : 0.860 19.750 10626 Z= 0.424 Chirality : 0.049 0.223 1182 Planarity : 0.012 0.181 1392 Dihedral : 6.685 43.746 1056 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 2.53 % Allowed : 11.92 % Favored : 85.55 % Rotamer: Outliers : 0.23 % Allowed : 3.73 % Favored : 96.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.11 % Twisted General : 0.11 % 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: -1.51 (0.28), residues: 948 helix: 1.17 (0.37), residues: 198 sheet: 0.55 (0.32), residues: 285 loop : -3.21 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 69 HIS 0.007 0.001 HIS B 3 PHE 0.018 0.002 PHE C 119 TYR 0.023 0.002 TYR B 109 ARG 0.007 0.000 ARG F 151 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 274 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASN cc_start: 0.6748 (m110) cc_final: 0.6299 (m110) REVERT: A 45 ILE cc_start: 0.8632 (mp) cc_final: 0.8178 (mt) REVERT: A 72 LEU cc_start: 0.8844 (tp) cc_final: 0.8586 (tt) REVERT: B 70 MET cc_start: 0.8034 (tpp) cc_final: 0.7695 (mtt) REVERT: B 88 GLU cc_start: 0.7566 (tp30) cc_final: 0.7228 (tp30) REVERT: B 89 GLN cc_start: 0.7727 (tt0) cc_final: 0.7235 (tt0) REVERT: C 29 ASN cc_start: 0.7328 (m110) cc_final: 0.7093 (m-40) REVERT: C 45 ILE cc_start: 0.9001 (mp) cc_final: 0.8619 (mt) REVERT: C 50 TYR cc_start: 0.8556 (t80) cc_final: 0.8182 (t80) REVERT: C 80 ASP cc_start: 0.7840 (t0) cc_final: 0.7405 (t0) REVERT: C 91 GLU cc_start: 0.7219 (tm-30) cc_final: 0.6653 (tm-30) REVERT: D 28 PHE cc_start: 0.8245 (p90) cc_final: 0.7823 (p90) REVERT: D 38 GLN cc_start: 0.7202 (mm-40) cc_final: 0.6991 (mm-40) REVERT: D 46 ARG cc_start: 0.7469 (mpt90) cc_final: 0.5228 (ttt180) REVERT: D 90 LEU cc_start: 0.8977 (tp) cc_final: 0.8675 (tt) REVERT: D 91 GLU cc_start: 0.6715 (pp20) cc_final: 0.6385 (pp20) REVERT: E 45 ILE cc_start: 0.8571 (mt) cc_final: 0.8347 (mt) REVERT: F 46 ARG cc_start: 0.7684 (ttt180) cc_final: 0.7470 (ttt180) REVERT: F 98 LYS cc_start: 0.8616 (tttt) cc_final: 0.7913 (ttmt) REVERT: F 108 GLU cc_start: 0.6145 (mm-30) cc_final: 0.5652 (tp30) outliers start: 2 outliers final: 1 residues processed: 275 average time/residue: 0.1820 time to fit residues: 68.5569 Evaluate side-chains 218 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 217 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 2.9990 chunk 51 optimal weight: 0.0670 chunk 1 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 62 optimal weight: 8.9990 chunk 0 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 22 optimal weight: 0.1980 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 153 GLN C 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 7830 Z= 0.252 Angle : 0.855 20.942 10626 Z= 0.420 Chirality : 0.049 0.262 1182 Planarity : 0.012 0.185 1392 Dihedral : 6.598 43.616 1056 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 2.32 % Allowed : 13.19 % Favored : 84.49 % Rotamer: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.11 % Twisted General : 0.11 % 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: -1.50 (0.28), residues: 948 helix: 1.13 (0.37), residues: 198 sheet: 0.07 (0.30), residues: 315 loop : -2.99 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 69 HIS 0.006 0.001 HIS D 3 PHE 0.015 0.002 PHE A 119 TYR 0.021 0.002 TYR B 109 ARG 0.005 0.000 ARG F 151 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASN cc_start: 0.6922 (m110) cc_final: 0.6491 (m110) REVERT: A 72 LEU cc_start: 0.8783 (tp) cc_final: 0.8475 (tt) REVERT: B 89 GLN cc_start: 0.7715 (tt0) cc_final: 0.7400 (tt0) REVERT: B 134 ASP cc_start: 0.8010 (p0) cc_final: 0.7450 (p0) REVERT: C 29 ASN cc_start: 0.7189 (m110) cc_final: 0.6930 (m-40) REVERT: C 45 ILE cc_start: 0.9031 (mp) cc_final: 0.8690 (mt) REVERT: C 50 TYR cc_start: 0.8391 (t80) cc_final: 0.8111 (t80) REVERT: C 80 ASP cc_start: 0.7666 (t0) cc_final: 0.7332 (t0) REVERT: D 28 PHE cc_start: 0.8278 (p90) cc_final: 0.7881 (p90) REVERT: D 38 GLN cc_start: 0.7298 (mm-40) cc_final: 0.6930 (mm-40) REVERT: D 46 ARG cc_start: 0.7512 (mpt90) cc_final: 0.5377 (ttt180) REVERT: D 82 GLU cc_start: 0.7703 (mp0) cc_final: 0.7410 (mp0) REVERT: D 90 LEU cc_start: 0.9012 (tp) cc_final: 0.8812 (tt) REVERT: E 1 MET cc_start: 0.6961 (mtp) cc_final: 0.6593 (mtp) REVERT: E 45 ILE cc_start: 0.8551 (mt) cc_final: 0.8252 (mt) REVERT: E 72 LEU cc_start: 0.8790 (tp) cc_final: 0.8549 (tt) REVERT: E 74 LEU cc_start: 0.8851 (mp) cc_final: 0.8289 (mt) outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.1769 time to fit residues: 62.4511 Evaluate side-chains 211 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 22 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 38 GLN C 147 ASN D 68 GLN E 23 GLN F 29 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 7830 Z= 0.288 Angle : 0.878 21.942 10626 Z= 0.433 Chirality : 0.049 0.204 1182 Planarity : 0.012 0.185 1392 Dihedral : 6.795 43.775 1056 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 2.22 % Allowed : 13.50 % Favored : 84.28 % Rotamer: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.11 % Twisted General : 0.11 % 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: -1.50 (0.29), residues: 948 helix: 1.21 (0.37), residues: 198 sheet: -0.04 (0.30), residues: 315 loop : -2.92 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 69 HIS 0.005 0.001 HIS E 3 PHE 0.015 0.002 PHE B 28 TYR 0.028 0.002 TYR F 109 ARG 0.007 0.000 ARG A 4 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASN cc_start: 0.7236 (m110) cc_final: 0.6780 (m-40) REVERT: A 72 LEU cc_start: 0.8820 (tp) cc_final: 0.8540 (tt) REVERT: B 29 ASN cc_start: 0.6790 (p0) cc_final: 0.6341 (p0) REVERT: B 89 GLN cc_start: 0.7812 (tt0) cc_final: 0.7404 (tt0) REVERT: B 91 GLU cc_start: 0.6999 (pp20) cc_final: 0.6722 (pp20) REVERT: C 45 ILE cc_start: 0.9133 (mp) cc_final: 0.8699 (mt) REVERT: C 50 TYR cc_start: 0.8474 (t80) cc_final: 0.8255 (t80) REVERT: C 80 ASP cc_start: 0.7662 (t0) cc_final: 0.7308 (t0) REVERT: C 141 TYR cc_start: 0.7754 (m-10) cc_final: 0.7501 (m-10) REVERT: D 46 ARG cc_start: 0.7609 (mpt90) cc_final: 0.5701 (ttt180) REVERT: D 82 GLU cc_start: 0.7777 (mp0) cc_final: 0.7452 (mp0) REVERT: D 90 LEU cc_start: 0.9008 (tp) cc_final: 0.8722 (tt) REVERT: E 45 ILE cc_start: 0.8552 (mt) cc_final: 0.8188 (mt) REVERT: F 26 GLU cc_start: 0.7368 (pt0) cc_final: 0.6219 (mm-30) REVERT: F 88 GLU cc_start: 0.7499 (tm-30) cc_final: 0.7026 (tm-30) outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 0.1713 time to fit residues: 62.6209 Evaluate side-chains 194 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 6.9990 chunk 10 optimal weight: 0.0570 chunk 51 optimal weight: 0.0470 chunk 65 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 75 optimal weight: 0.0020 chunk 89 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.3606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN D 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.4839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 7830 Z= 0.228 Angle : 0.848 22.236 10626 Z= 0.417 Chirality : 0.048 0.212 1182 Planarity : 0.012 0.186 1392 Dihedral : 6.549 44.831 1056 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 2.00 % Allowed : 12.55 % Favored : 85.44 % Rotamer: Outliers : 0.12 % Allowed : 1.86 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.11 % Twisted General : 0.11 % 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: -1.39 (0.28), residues: 948 helix: 1.18 (0.36), residues: 195 sheet: 0.21 (0.30), residues: 303 loop : -2.84 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 69 HIS 0.006 0.001 HIS D 3 PHE 0.014 0.002 PHE D 28 TYR 0.024 0.002 TYR F 109 ARG 0.003 0.000 ARG F 151 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 261 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASN cc_start: 0.7259 (m110) cc_final: 0.6817 (m-40) REVERT: A 89 GLN cc_start: 0.7358 (tt0) cc_final: 0.6852 (tt0) REVERT: B 40 TYR cc_start: 0.6727 (p90) cc_final: 0.6470 (p90) REVERT: B 89 GLN cc_start: 0.7702 (tt0) cc_final: 0.7398 (tt0) REVERT: B 92 LYS cc_start: 0.8163 (mmtm) cc_final: 0.7571 (mmtm) REVERT: C 45 ILE cc_start: 0.9214 (mp) cc_final: 0.8711 (mt) REVERT: C 50 TYR cc_start: 0.8223 (t80) cc_final: 0.7967 (t80) REVERT: C 141 TYR cc_start: 0.7638 (m-10) cc_final: 0.7359 (m-10) REVERT: D 46 ARG cc_start: 0.7507 (mpt90) cc_final: 0.5437 (ttt180) REVERT: D 70 MET cc_start: 0.8168 (mmt) cc_final: 0.7891 (mmt) REVERT: D 82 GLU cc_start: 0.7768 (mp0) cc_final: 0.7387 (mp0) REVERT: D 90 LEU cc_start: 0.8842 (tp) cc_final: 0.8558 (tt) REVERT: D 91 GLU cc_start: 0.6670 (pp20) cc_final: 0.6318 (pp20) REVERT: E 20 ASP cc_start: 0.7603 (p0) cc_final: 0.6807 (p0) REVERT: F 108 GLU cc_start: 0.5997 (mm-30) cc_final: 0.5473 (tp30) outliers start: 1 outliers final: 0 residues processed: 262 average time/residue: 0.1693 time to fit residues: 62.2193 Evaluate side-chains 203 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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-5513/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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-5513/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-5513/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-5513/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-5513/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-5513/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-5513/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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-5513/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-5513/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-5513/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-5513/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: 56.9025 > 50: distance: 4 - 9: 28.599 distance: 9 - 10: 36.679 distance: 10 - 11: 28.981 distance: 11 - 12: 22.510 distance: 11 - 13: 38.238 distance: 13 - 14: 38.328 distance: 13 - 80: 27.732 distance: 14 - 15: 7.174 distance: 14 - 17: 39.932 distance: 15 - 16: 34.606 distance: 15 - 22: 30.927 distance: 16 - 77: 34.183 distance: 17 - 18: 35.289 distance: 18 - 19: 6.954 distance: 19 - 20: 9.635 distance: 19 - 21: 18.182 distance: 22 - 23: 12.721 distance: 23 - 24: 12.148 distance: 23 - 26: 23.253 distance: 24 - 25: 30.396 distance: 24 - 34: 38.211 distance: 26 - 27: 7.350 distance: 27 - 28: 6.413 distance: 27 - 29: 6.160 distance: 28 - 30: 18.421 distance: 29 - 31: 8.184 distance: 30 - 32: 9.999 distance: 31 - 32: 10.362 distance: 32 - 33: 6.225 distance: 34 - 35: 42.290 distance: 35 - 36: 24.017 distance: 35 - 38: 22.849 distance: 36 - 37: 46.738 distance: 36 - 42: 25.295 distance: 38 - 39: 38.634 distance: 39 - 40: 53.426 distance: 39 - 41: 40.700 distance: 42 - 43: 21.656 distance: 42 - 48: 40.944 distance: 43 - 44: 13.162 distance: 43 - 46: 35.742 distance: 44 - 45: 20.459 distance: 44 - 49: 39.564 distance: 46 - 47: 31.863 distance: 47 - 48: 27.899 distance: 49 - 50: 31.879 distance: 50 - 51: 16.659 distance: 50 - 53: 17.628 distance: 51 - 52: 23.924 distance: 51 - 55: 27.620 distance: 53 - 54: 33.773 distance: 55 - 56: 19.620 distance: 56 - 57: 21.669 distance: 57 - 58: 20.837 distance: 57 - 59: 26.141 distance: 59 - 60: 11.396 distance: 60 - 61: 19.412 distance: 60 - 63: 24.220 distance: 61 - 62: 15.386 distance: 61 - 68: 23.710 distance: 63 - 64: 39.534 distance: 64 - 65: 10.504 distance: 65 - 66: 16.165 distance: 65 - 67: 22.486 distance: 68 - 69: 24.016 distance: 69 - 70: 25.751 distance: 69 - 72: 25.023 distance: 70 - 71: 56.853 distance: 70 - 77: 55.312 distance: 72 - 73: 33.589 distance: 73 - 74: 17.964 distance: 74 - 75: 11.514 distance: 74 - 76: 11.139 distance: 77 - 78: 46.835 distance: 78 - 79: 14.894 distance: 78 - 81: 41.931 distance: 79 - 80: 5.452 distance: 79 - 91: 15.899 distance: 81 - 82: 36.568 distance: 82 - 83: 30.125 distance: 82 - 84: 36.907 distance: 83 - 85: 21.667 distance: 84 - 86: 44.126 distance: 84 - 87: 30.624 distance: 85 - 86: 54.596 distance: 86 - 88: 38.638 distance: 87 - 89: 15.027 distance: 88 - 90: 27.659 distance: 89 - 90: 10.116