Starting phenix.real_space_refine on Wed Jun 11 03:29:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v28_42901/06_2025/8v28_42901_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v28_42901/06_2025/8v28_42901.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v28_42901/06_2025/8v28_42901.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v28_42901/06_2025/8v28_42901.map" model { file = "/net/cci-nas-00/data/ceres_data/8v28_42901/06_2025/8v28_42901_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v28_42901/06_2025/8v28_42901_neut.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.019 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 288 5.49 5 S 15 5.16 5 C 7046 2.51 5 N 2380 2.21 5 O 2930 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-5710/modules/chem_data/mon_lib" Total number of atoms: 12659 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 859 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "D" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 764 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "E" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 817 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 841 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 754 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 574 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Time building chain proxies: 8.35, per 1000 atoms: 0.66 Number of scatterers: 12659 At special positions: 0 Unit cell: (100.88, 122.22, 118.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 P 288 15.00 O 2930 8.00 N 2380 7.00 C 7046 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.62 Conformation dependent library (CDL) restraints added in 1.1 seconds 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1586 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 67.0% alpha, 4.3% beta 139 base pairs and 250 stacking pairs defined. Time for finding SS restraints: 6.58 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.829A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.772A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.653A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.171A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.562A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.631A pdb=" N ARG C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.518A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.657A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 121 Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.645A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.564A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.717A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.520A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.176A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 removed outlier: 3.551A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.595A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.545A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.576A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 Processing helix chain 'K' and resid 22 through 35 Processing helix chain 'K' and resid 37 through 41 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.952A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.330A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.738A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.385A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'K' and resid 12 through 16 421 hydrogen bonds defined for protein. 1236 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 357 hydrogen bonds 714 hydrogen bond angles 0 basepair planarities 139 basepair parallelities 250 stacking parallelities Total time for adding SS restraints: 5.07 Time building geometry restraints manager: 4.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2434 1.33 - 1.45: 4277 1.45 - 1.57: 6155 1.57 - 1.69: 576 1.69 - 1.81: 26 Bond restraints: 13468 Sorted by residual: bond pdb=" C1' DG I -70 " pdb=" N9 DG I -70 " ideal model delta sigma weight residual 1.460 1.384 0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" C1' DG J -70 " pdb=" N9 DG J -70 " ideal model delta sigma weight residual 1.460 1.386 0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" C1' DA I 72 " pdb=" N9 DA I 72 " ideal model delta sigma weight residual 1.460 1.390 0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" N TYR B 98 " pdb=" CA TYR B 98 " ideal model delta sigma weight residual 1.455 1.483 -0.028 1.21e-02 6.83e+03 5.20e+00 bond pdb=" N ASP H 65 " pdb=" CA ASP H 65 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.19e-02 7.06e+03 5.20e+00 ... (remaining 13463 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 19164 2.13 - 4.26: 239 4.26 - 6.39: 17 6.39 - 8.52: 1 8.52 - 10.65: 5 Bond angle restraints: 19426 Sorted by residual: angle pdb=" C3' DG J 71 " pdb=" O3' DG J 71 " pdb=" P DA J 72 " ideal model delta sigma weight residual 120.20 109.55 10.65 1.50e+00 4.44e-01 5.05e+01 angle pdb=" C3' DC J 70 " pdb=" O3' DC J 70 " pdb=" P DG J 71 " ideal model delta sigma weight residual 120.20 109.76 10.44 1.50e+00 4.44e-01 4.84e+01 angle pdb=" C3' DT J 69 " pdb=" O3' DT J 69 " pdb=" P DC J 70 " ideal model delta sigma weight residual 120.20 110.58 9.62 1.50e+00 4.44e-01 4.12e+01 angle pdb=" CB ARG K 42 " pdb=" CG ARG K 42 " pdb=" CD ARG K 42 " ideal model delta sigma weight residual 111.30 120.88 -9.58 2.30e+00 1.89e-01 1.73e+01 angle pdb=" CA LYS C 118 " pdb=" CB LYS C 118 " pdb=" CG LYS C 118 " ideal model delta sigma weight residual 114.10 121.09 -6.99 2.00e+00 2.50e-01 1.22e+01 ... (remaining 19421 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.66: 6009 35.66 - 71.32: 1362 71.32 - 106.98: 13 106.98 - 142.65: 4 142.65 - 178.31: 1 Dihedral angle restraints: 7389 sinusoidal: 4936 harmonic: 2453 Sorted by residual: dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual -140.00 38.31 -178.31 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT J 54 " pdb=" C3' DT J 54 " pdb=" O3' DT J 54 " pdb=" P DC J 55 " ideal model delta sinusoidal sigma weight residual 220.00 91.35 128.65 1 3.50e+01 8.16e-04 1.27e+01 dihedral pdb=" C4' DC J 34 " pdb=" C3' DC J 34 " pdb=" O3' DC J 34 " pdb=" P DT J 35 " ideal model delta sinusoidal sigma weight residual 220.00 95.57 124.43 1 3.50e+01 8.16e-04 1.23e+01 ... (remaining 7386 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2164 0.093 - 0.186: 48 0.186 - 0.279: 0 0.279 - 0.373: 0 0.373 - 0.466: 3 Chirality restraints: 2215 Sorted by residual: chirality pdb=" P DC J 70 " pdb=" OP1 DC J 70 " pdb=" OP2 DC J 70 " pdb=" O5' DC J 70 " both_signs ideal model delta sigma weight residual True 2.35 -2.81 -0.47 2.00e-01 2.50e+01 5.42e+00 chirality pdb=" P DG J 71 " pdb=" OP1 DG J 71 " pdb=" OP2 DG J 71 " pdb=" O5' DG J 71 " both_signs ideal model delta sigma weight residual True 2.35 -2.80 -0.45 2.00e-01 2.50e+01 5.17e+00 chirality pdb=" P DA J 72 " pdb=" OP1 DA J 72 " pdb=" OP2 DA J 72 " pdb=" O5' DA J 72 " both_signs ideal model delta sigma weight residual True 2.35 -2.80 -0.45 2.00e-01 2.50e+01 5.10e+00 ... (remaining 2212 not shown) Planarity restraints: 1457 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP F 24 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.45e+00 pdb=" C ASP F 24 " -0.044 2.00e-02 2.50e+03 pdb=" O ASP F 24 " 0.017 2.00e-02 2.50e+03 pdb=" N ASN F 25 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP F 24 " 0.010 2.00e-02 2.50e+03 2.04e-02 4.18e+00 pdb=" CG ASP F 24 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASP F 24 " 0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP F 24 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 47 " -0.024 2.00e-02 2.50e+03 1.00e-02 3.01e+00 pdb=" N9 DG I 47 " 0.022 2.00e-02 2.50e+03 pdb=" C8 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" N7 DG I 47 " 0.006 2.00e-02 2.50e+03 pdb=" C5 DG I 47 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 47 " -0.005 2.00e-02 2.50e+03 pdb=" O6 DG I 47 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DG I 47 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 47 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 47 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DG I 47 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DG I 47 " 0.002 2.00e-02 2.50e+03 ... (remaining 1454 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 2842 2.82 - 3.34: 10531 3.34 - 3.86: 22604 3.86 - 4.38: 26544 4.38 - 4.90: 38192 Nonbonded interactions: 100713 Sorted by model distance: nonbonded pdb=" O THR E 58 " pdb=" OG1 THR E 58 " model vdw 2.295 3.040 nonbonded pdb=" O GLN K 2 " pdb=" N GLU K 64 " model vdw 2.347 3.120 nonbonded pdb=" O ARG A 129 " pdb=" NH1 ARG A 129 " model vdw 2.361 3.120 nonbonded pdb=" N ASP F 85 " pdb=" OD1 ASP F 85 " model vdw 2.362 3.120 nonbonded pdb=" OG SER G 18 " pdb=" O PHE G 25 " model vdw 2.376 3.040 ... (remaining 100708 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' and resid 37 through 134) } ncs_group { reference = (chain 'B' and resid 23 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 10 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 26 through 121) 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.290 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: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 37.960 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 13468 Z= 0.196 Angle : 0.582 10.654 19426 Z= 0.351 Chirality : 0.038 0.466 2215 Planarity : 0.004 0.037 1457 Dihedral : 27.274 178.308 5803 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.56 % Allowed : 19.15 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.30), residues: 827 helix: 3.33 (0.22), residues: 530 sheet: 1.37 (1.73), residues: 12 loop : -1.10 (0.33), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.010 0.001 PHE F 61 TYR 0.017 0.001 TYR H 80 ARG 0.008 0.000 ARG D 96 Details of bonding type rmsd hydrogen bonds : bond 0.11556 ( 778) hydrogen bonds : angle 3.58914 ( 1950) covalent geometry : bond 0.00422 (13468) covalent geometry : angle 0.58220 (19426) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 113 time to evaluate : 0.951 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 114 average time/residue: 0.4010 time to fit residues: 59.6036 Evaluate side-chains 110 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 108 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 98 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 98 optimal weight: 6.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN E 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.092187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.060778 restraints weight = 29951.183| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 2.11 r_work: 0.2651 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.0675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13468 Z= 0.197 Angle : 0.547 7.287 19426 Z= 0.331 Chirality : 0.034 0.133 2215 Planarity : 0.004 0.035 1457 Dihedral : 29.358 178.217 4112 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.55 % Allowed : 19.44 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.03 (0.30), residues: 827 helix: 3.44 (0.22), residues: 531 sheet: 1.27 (1.31), residues: 20 loop : -1.02 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 106 PHE 0.010 0.001 PHE F 61 TYR 0.015 0.001 TYR B 98 ARG 0.004 0.000 ARG D 96 Details of bonding type rmsd hydrogen bonds : bond 0.06209 ( 778) hydrogen bonds : angle 3.08602 ( 1950) covalent geometry : bond 0.00437 (13468) covalent geometry : angle 0.54718 (19426) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 1.043 Fit side-chains REVERT: A 83 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8374 (mtp180) REVERT: D 73 GLU cc_start: 0.9147 (tp30) cc_final: 0.8828 (tp30) REVERT: E 118 THR cc_start: 0.9469 (m) cc_final: 0.9267 (p) REVERT: F 24 ASP cc_start: 0.8484 (p0) cc_final: 0.8217 (p0) REVERT: H 65 ASP cc_start: 0.8782 (t0) cc_final: 0.8569 (t0) outliers start: 11 outliers final: 5 residues processed: 123 average time/residue: 0.3754 time to fit residues: 59.9010 Evaluate side-chains 114 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 108 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain H residue 98 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 26 optimal weight: 3.9990 chunk 82 optimal weight: 7.9990 chunk 88 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 4 optimal weight: 0.0370 chunk 94 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 100 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 overall best weight: 3.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.089516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.057803 restraints weight = 29860.253| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 2.05 r_work: 0.2587 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 13468 Z= 0.256 Angle : 0.595 6.821 19426 Z= 0.358 Chirality : 0.037 0.140 2215 Planarity : 0.005 0.061 1457 Dihedral : 29.607 178.779 4110 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.39 % Allowed : 20.42 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.66 (0.30), residues: 827 helix: 3.17 (0.22), residues: 532 sheet: 1.11 (1.35), residues: 20 loop : -1.21 (0.34), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 106 PHE 0.013 0.002 PHE D 67 TYR 0.016 0.002 TYR B 98 ARG 0.007 0.001 ARG D 96 Details of bonding type rmsd hydrogen bonds : bond 0.07714 ( 778) hydrogen bonds : angle 3.29187 ( 1950) covalent geometry : bond 0.00588 (13468) covalent geometry : angle 0.59525 (19426) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.895 Fit side-chains REVERT: A 59 GLU cc_start: 0.8430 (pm20) cc_final: 0.8056 (pm20) REVERT: A 83 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8371 (mtp180) REVERT: C 118 LYS cc_start: 0.8646 (tmtt) cc_final: 0.8411 (tmtt) REVERT: D 73 GLU cc_start: 0.9196 (tp30) cc_final: 0.8849 (tp30) REVERT: E 118 THR cc_start: 0.9487 (m) cc_final: 0.9271 (p) REVERT: F 24 ASP cc_start: 0.8599 (p0) cc_final: 0.8343 (p0) REVERT: F 74 GLU cc_start: 0.9076 (tp30) cc_final: 0.8704 (mt-10) outliers start: 17 outliers final: 11 residues processed: 125 average time/residue: 0.3340 time to fit residues: 55.9125 Evaluate side-chains 122 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 8 optimal weight: 0.2980 chunk 100 optimal weight: 8.9990 chunk 47 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 73 optimal weight: 10.0000 chunk 41 optimal weight: 0.0000 chunk 49 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.095568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.064257 restraints weight = 29982.684| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 2.11 r_work: 0.2733 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13468 Z= 0.145 Angle : 0.510 5.485 19426 Z= 0.309 Chirality : 0.032 0.125 2215 Planarity : 0.004 0.039 1457 Dihedral : 29.416 178.231 4110 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.54 % Allowed : 20.56 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.17 (0.30), residues: 827 helix: 3.58 (0.22), residues: 531 sheet: 1.83 (1.36), residues: 19 loop : -1.04 (0.34), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 39 PHE 0.008 0.001 PHE H 67 TYR 0.006 0.001 TYR B 98 ARG 0.007 0.000 ARG D 96 Details of bonding type rmsd hydrogen bonds : bond 0.04401 ( 778) hydrogen bonds : angle 2.72502 ( 1950) covalent geometry : bond 0.00301 (13468) covalent geometry : angle 0.50956 (19426) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.949 Fit side-chains REVERT: A 59 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7946 (pm20) REVERT: A 83 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.8646 (mtp85) REVERT: B 91 LYS cc_start: 0.9355 (tptm) cc_final: 0.9103 (tptm) REVERT: C 118 LYS cc_start: 0.8653 (tmtt) cc_final: 0.8445 (tmtt) REVERT: D 73 GLU cc_start: 0.9220 (tp30) cc_final: 0.8950 (tp30) REVERT: F 24 ASP cc_start: 0.8523 (p0) cc_final: 0.8216 (p0) outliers start: 18 outliers final: 11 residues processed: 134 average time/residue: 0.3294 time to fit residues: 59.4159 Evaluate side-chains 119 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 43 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 95 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 18 optimal weight: 0.0980 chunk 40 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.095219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.063718 restraints weight = 29998.506| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 2.11 r_work: 0.2721 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13468 Z= 0.149 Angle : 0.506 5.179 19426 Z= 0.308 Chirality : 0.032 0.127 2215 Planarity : 0.004 0.036 1457 Dihedral : 29.474 178.559 4110 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.83 % Allowed : 22.25 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.26 (0.30), residues: 827 helix: 3.64 (0.22), residues: 532 sheet: 1.77 (1.33), residues: 19 loop : -1.00 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 39 PHE 0.008 0.001 PHE F 61 TYR 0.008 0.001 TYR H 80 ARG 0.007 0.000 ARG D 96 Details of bonding type rmsd hydrogen bonds : bond 0.04707 ( 778) hydrogen bonds : angle 2.71762 ( 1950) covalent geometry : bond 0.00314 (13468) covalent geometry : angle 0.50624 (19426) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.885 Fit side-chains REVERT: A 59 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7894 (pm20) REVERT: B 91 LYS cc_start: 0.9361 (tptm) cc_final: 0.9131 (tptm) REVERT: D 73 GLU cc_start: 0.9239 (tp30) cc_final: 0.8896 (tp30) REVERT: F 24 ASP cc_start: 0.8487 (p0) cc_final: 0.8166 (p0) outliers start: 13 outliers final: 8 residues processed: 121 average time/residue: 0.3254 time to fit residues: 52.3408 Evaluate side-chains 118 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 70 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 88 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.094342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.062564 restraints weight = 30289.110| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 2.13 r_work: 0.2694 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13468 Z= 0.162 Angle : 0.520 6.813 19426 Z= 0.314 Chirality : 0.033 0.129 2215 Planarity : 0.004 0.039 1457 Dihedral : 29.477 178.094 4110 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.97 % Allowed : 22.82 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.18 (0.30), residues: 827 helix: 3.59 (0.22), residues: 536 sheet: 1.74 (1.33), residues: 19 loop : -1.13 (0.34), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 39 PHE 0.009 0.001 PHE F 61 TYR 0.010 0.001 TYR H 80 ARG 0.007 0.000 ARG D 96 Details of bonding type rmsd hydrogen bonds : bond 0.05245 ( 778) hydrogen bonds : angle 2.77364 ( 1950) covalent geometry : bond 0.00351 (13468) covalent geometry : angle 0.51956 (19426) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.930 Fit side-chains REVERT: A 59 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7923 (pm20) REVERT: B 91 LYS cc_start: 0.9401 (tptm) cc_final: 0.9137 (tptm) REVERT: D 73 GLU cc_start: 0.9233 (tp30) cc_final: 0.8881 (tp30) REVERT: F 24 ASP cc_start: 0.8493 (p0) cc_final: 0.8155 (p0) REVERT: F 39 ARG cc_start: 0.9181 (OUTLIER) cc_final: 0.8887 (mmt90) outliers start: 14 outliers final: 11 residues processed: 117 average time/residue: 0.3193 time to fit residues: 49.8152 Evaluate side-chains 122 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 24 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.091877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.059582 restraints weight = 29714.774| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 2.10 r_work: 0.2626 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 13468 Z= 0.206 Angle : 0.554 7.475 19426 Z= 0.333 Chirality : 0.035 0.136 2215 Planarity : 0.004 0.041 1457 Dihedral : 29.556 178.497 4110 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.39 % Allowed : 22.39 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.92 (0.30), residues: 827 helix: 3.45 (0.22), residues: 533 sheet: 1.87 (1.38), residues: 19 loop : -1.36 (0.33), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 106 PHE 0.010 0.001 PHE F 61 TYR 0.012 0.001 TYR H 80 ARG 0.008 0.000 ARG D 96 Details of bonding type rmsd hydrogen bonds : bond 0.06533 ( 778) hydrogen bonds : angle 3.00585 ( 1950) covalent geometry : bond 0.00463 (13468) covalent geometry : angle 0.55404 (19426) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 1.298 Fit side-chains REVERT: A 59 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8076 (pm20) REVERT: B 91 LYS cc_start: 0.9406 (tptm) cc_final: 0.9139 (tptm) REVERT: D 32 GLU cc_start: 0.8513 (mp0) cc_final: 0.8208 (mp0) REVERT: D 73 GLU cc_start: 0.9210 (tp30) cc_final: 0.8884 (tp30) REVERT: E 118 THR cc_start: 0.9487 (m) cc_final: 0.9248 (p) REVERT: F 24 ASP cc_start: 0.8536 (p0) cc_final: 0.8304 (p0) outliers start: 17 outliers final: 15 residues processed: 120 average time/residue: 0.3369 time to fit residues: 54.3430 Evaluate side-chains 122 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.5325 > 50: distance: 14 - 19: 3.023 distance: 25 - 34: 3.006 distance: 61 - 66: 31.870 distance: 66 - 67: 40.487 distance: 67 - 68: 21.199 distance: 67 - 70: 22.899 distance: 68 - 69: 6.591 distance: 68 - 73: 51.845 distance: 70 - 71: 27.294 distance: 70 - 72: 33.988 distance: 73 - 74: 5.524 distance: 74 - 75: 40.508 distance: 74 - 77: 38.780 distance: 75 - 76: 26.584 distance: 75 - 78: 17.037 distance: 76 - 101: 35.214 distance: 78 - 79: 32.910 distance: 80 - 81: 27.938 distance: 80 - 86: 8.784 distance: 81 - 108: 17.070 distance: 82 - 83: 39.841 distance: 83 - 84: 36.460 distance: 84 - 85: 41.568 distance: 86 - 87: 9.683 distance: 87 - 88: 27.588 distance: 87 - 90: 27.610 distance: 88 - 89: 13.775 distance: 88 - 94: 38.624 distance: 89 - 120: 36.703 distance: 90 - 91: 44.588 distance: 91 - 93: 22.042 distance: 94 - 95: 47.600 distance: 95 - 96: 51.382 distance: 95 - 98: 33.414 distance: 96 - 101: 18.744 distance: 97 - 125: 41.625 distance: 98 - 99: 36.408 distance: 98 - 100: 18.438 distance: 101 - 102: 8.030 distance: 102 - 103: 21.746 distance: 102 - 105: 11.144 distance: 103 - 104: 12.407 distance: 103 - 108: 9.662 distance: 104 - 133: 18.572 distance: 105 - 107: 47.540 distance: 108 - 109: 27.906 distance: 109 - 110: 17.589 distance: 109 - 112: 33.891 distance: 110 - 111: 21.475 distance: 110 - 120: 15.042 distance: 111 - 142: 29.232 distance: 112 - 113: 19.441 distance: 113 - 114: 24.109 distance: 113 - 115: 17.256 distance: 114 - 116: 10.908 distance: 115 - 117: 26.987 distance: 116 - 118: 12.814 distance: 117 - 118: 8.021 distance: 118 - 119: 28.528 distance: 120 - 121: 7.364 distance: 121 - 122: 16.580 distance: 121 - 124: 25.015 distance: 122 - 123: 32.843 distance: 122 - 125: 10.517 distance: 125 - 126: 23.364 distance: 126 - 127: 37.907 distance: 126 - 129: 42.179 distance: 127 - 128: 16.792 distance: 127 - 133: 13.328 distance: 133 - 134: 8.713 distance: 134 - 135: 7.998 distance: 134 - 137: 9.554 distance: 135 - 136: 12.071 distance: 135 - 142: 25.530 distance: 137 - 138: 9.025 distance: 138 - 139: 13.965 distance: 139 - 140: 17.457 distance: 140 - 141: 32.124