Starting phenix.real_space_refine on Wed Sep 17 21:46:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ybj_39119/09_2025/8ybj_39119.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ybj_39119/09_2025/8ybj_39119.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ybj_39119/09_2025/8ybj_39119.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ybj_39119/09_2025/8ybj_39119.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ybj_39119/09_2025/8ybj_39119.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ybj_39119/09_2025/8ybj_39119.map" } resolution = 2.38 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 289 5.49 5 S 14 5.16 5 C 6606 2.51 5 N 2246 2.21 5 O 2798 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 86 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11953 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 844 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} 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} Time building chain proxies: 3.03, per 1000 atoms: 0.25 Number of scatterers: 11953 At special positions: 0 Unit cell: (75.26, 120.84, 116.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 289 15.00 O 2798 8.00 N 2246 7.00 C 6606 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 353.0 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1412 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 73.4% alpha, 2.9% beta 144 base pairs and 276 stacking pairs defined. Time for finding SS restraints: 2.02 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.709A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.772A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 124 removed outlier: 3.653A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.752A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.558A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.501A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.575A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.897A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.945A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (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 101 through 102 removed outlier: 6.551A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.907A 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: 7.095A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 414 hydrogen bonds defined for protein. 1215 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 368 hydrogen bonds 736 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 276 stacking parallelities Total time for adding SS restraints: 2.48 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1548 1.32 - 1.44: 4687 1.44 - 1.57: 5915 1.57 - 1.69: 579 1.69 - 1.81: 24 Bond restraints: 12753 Sorted by residual: bond pdb=" CZ ARG A 129 " pdb=" NH2 ARG A 129 " ideal model delta sigma weight residual 1.330 1.285 0.045 1.30e-02 5.92e+03 1.20e+01 bond pdb=" CA ALA C 103 " pdb=" CB ALA C 103 " ideal model delta sigma weight residual 1.529 1.471 0.058 1.69e-02 3.50e+03 1.18e+01 bond pdb=" ND1 HIS H 82 " pdb=" CE1 HIS H 82 " ideal model delta sigma weight residual 1.321 1.354 -0.033 1.00e-02 1.00e+04 1.11e+01 bond pdb=" CZ ARG A 134 " pdb=" NH2 ARG A 134 " ideal model delta sigma weight residual 1.330 1.287 0.043 1.30e-02 5.92e+03 1.09e+01 bond pdb=" CZ ARG E 131 " pdb=" NH2 ARG E 131 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 9.91e+00 ... (remaining 12748 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 16824 1.64 - 3.29: 1371 3.29 - 4.93: 233 4.93 - 6.58: 31 6.58 - 8.22: 5 Bond angle restraints: 18464 Sorted by residual: angle pdb=" C5' DC I 7 " pdb=" C4' DC I 7 " pdb=" O4' DC I 7 " ideal model delta sigma weight residual 109.40 115.29 -5.89 1.50e+00 4.44e-01 1.54e+01 angle pdb=" C PRO H 50 " pdb=" N ASP H 51 " pdb=" CA ASP H 51 " ideal model delta sigma weight residual 120.72 127.14 -6.42 1.67e+00 3.59e-01 1.48e+01 angle pdb=" CB HIS H 82 " pdb=" CG HIS H 82 " pdb=" CD2 HIS H 82 " ideal model delta sigma weight residual 131.20 126.26 4.94 1.30e+00 5.92e-01 1.44e+01 angle pdb=" O ASP G 72 " pdb=" C ASP G 72 " pdb=" N ASN G 73 " ideal model delta sigma weight residual 122.22 117.79 4.43 1.17e+00 7.31e-01 1.43e+01 angle pdb=" C GLY E 132 " pdb=" N GLU E 133 " pdb=" CA GLU E 133 " ideal model delta sigma weight residual 120.87 127.27 -6.40 1.69e+00 3.50e-01 1.43e+01 ... (remaining 18459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 4408 17.67 - 35.33: 1035 35.33 - 53.00: 1144 53.00 - 70.67: 319 70.67 - 88.33: 24 Dihedral angle restraints: 6930 sinusoidal: 4738 harmonic: 2192 Sorted by residual: dihedral pdb=" CA PRO H 103 " pdb=" C PRO H 103 " pdb=" N GLY H 104 " pdb=" CA GLY H 104 " ideal model delta harmonic sigma weight residual 180.00 151.86 28.14 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" CA LEU F 22 " pdb=" C LEU F 22 " pdb=" N ARG F 23 " pdb=" CA ARG F 23 " ideal model delta harmonic sigma weight residual -180.00 -158.06 -21.94 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA PRO D 103 " pdb=" C PRO D 103 " pdb=" N GLY D 104 " pdb=" CA GLY D 104 " ideal model delta harmonic sigma weight residual 180.00 158.42 21.58 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 6927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1797 0.069 - 0.138: 256 0.138 - 0.207: 31 0.207 - 0.275: 12 0.275 - 0.344: 4 Chirality restraints: 2100 Sorted by residual: chirality pdb=" CA LYS G 74 " pdb=" N LYS G 74 " pdb=" C LYS G 74 " pdb=" CB LYS G 74 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" C4' DC I -70 " pdb=" C5' DC I -70 " pdb=" O4' DC I -70 " pdb=" C3' DC I -70 " both_signs ideal model delta sigma weight residual False -2.53 -2.18 -0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" CA ASN G 73 " pdb=" N ASN G 73 " pdb=" C ASN G 73 " pdb=" CB ASN G 73 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.32e+00 ... (remaining 2097 not shown) Planarity restraints: 1335 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT J -24 " 0.050 2.00e-02 2.50e+03 6.62e-02 1.10e+02 pdb=" N1 DT J -24 " 0.046 2.00e-02 2.50e+03 pdb=" C2 DT J -24 " -0.018 2.00e-02 2.50e+03 pdb=" O2 DT J -24 " -0.117 2.00e-02 2.50e+03 pdb=" N3 DT J -24 " 0.013 2.00e-02 2.50e+03 pdb=" C4 DT J -24 " 0.027 2.00e-02 2.50e+03 pdb=" O4 DT J -24 " 0.080 2.00e-02 2.50e+03 pdb=" C5 DT J -24 " -0.005 2.00e-02 2.50e+03 pdb=" C7 DT J -24 " -0.125 2.00e-02 2.50e+03 pdb=" C6 DT J -24 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 55 " 0.095 2.00e-02 2.50e+03 6.04e-02 9.12e+01 pdb=" N1 DT I 55 " 0.038 2.00e-02 2.50e+03 pdb=" C2 DT I 55 " -0.020 2.00e-02 2.50e+03 pdb=" O2 DT I 55 " -0.093 2.00e-02 2.50e+03 pdb=" N3 DT I 55 " -0.015 2.00e-02 2.50e+03 pdb=" C4 DT I 55 " 0.021 2.00e-02 2.50e+03 pdb=" O4 DT I 55 " 0.100 2.00e-02 2.50e+03 pdb=" C5 DT I 55 " -0.033 2.00e-02 2.50e+03 pdb=" C7 DT I 55 " -0.063 2.00e-02 2.50e+03 pdb=" C6 DT I 55 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 5 " -0.101 2.00e-02 2.50e+03 6.31e-02 8.96e+01 pdb=" N1 DC I 5 " -0.023 2.00e-02 2.50e+03 pdb=" C2 DC I 5 " 0.008 2.00e-02 2.50e+03 pdb=" O2 DC I 5 " 0.067 2.00e-02 2.50e+03 pdb=" N3 DC I 5 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DC I 5 " 0.023 2.00e-02 2.50e+03 pdb=" N4 DC I 5 " -0.107 2.00e-02 2.50e+03 pdb=" C5 DC I 5 " 0.078 2.00e-02 2.50e+03 pdb=" C6 DC I 5 " 0.051 2.00e-02 2.50e+03 ... (remaining 1332 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 4264 2.93 - 3.43: 10430 3.43 - 3.92: 24382 3.92 - 4.41: 27712 4.41 - 4.90: 36602 Nonbonded interactions: 103390 Sorted by model distance: nonbonded pdb=" N ASP D 51 " pdb=" OD1 ASP D 51 " model vdw 2.443 3.120 nonbonded pdb=" OG SER G 18 " pdb=" O PHE G 25 " model vdw 2.467 3.040 nonbonded pdb=" OD2 ASP D 68 " pdb=" OH TYR F 98 " model vdw 2.486 3.040 nonbonded pdb=" OG SER C 40 " pdb=" O ARG C 42 " model vdw 2.504 3.040 nonbonded pdb=" NH2 ARG G 32 " pdb=" OE1 GLU H 35 " model vdw 2.521 3.120 ... (remaining 103385 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 40 through 135) } ncs_group { reference = (chain 'B' and resid 22 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 11 through 118) selection = (chain 'G' and resid 11 through 118) } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=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: 1.070 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.230 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:9.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 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 : 0.007 0.058 12753 Z= 0.386 Angle : 0.961 8.220 18464 Z= 0.616 Chirality : 0.054 0.344 2100 Planarity : 0.012 0.112 1335 Dihedral : 28.235 88.333 5518 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.32 (0.29), residues: 742 helix: 2.20 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -0.20 (0.36), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 35 TYR 0.036 0.003 TYR G 39 PHE 0.008 0.002 PHE E 67 HIS 0.007 0.002 HIS G 82 Details of bonding type rmsd covalent geometry : bond 0.00737 (12753) covalent geometry : angle 0.96133 (18464) hydrogen bonds : bond 0.12210 ( 782) hydrogen bonds : angle 3.69658 ( 1951) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8516 (ttt180) cc_final: 0.8312 (tpt90) REVERT: C 15 LYS cc_start: 0.7916 (mtpt) cc_final: 0.7683 (mtmt) REVERT: C 95 LYS cc_start: 0.8930 (ttmt) cc_final: 0.8498 (tttp) REVERT: E 97 GLU cc_start: 0.9069 (mt-10) cc_final: 0.8852 (mt-10) REVERT: G 95 LYS cc_start: 0.8499 (ttmt) cc_final: 0.7913 (tttt) REVERT: H 93 GLU cc_start: 0.8887 (mp0) cc_final: 0.8483 (mp0) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 1.1844 time to fit residues: 185.5100 Evaluate side-chains 137 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN B 25 ASN D 84 ASN E 68 GLN F 25 ASN H 84 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.166878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.118908 restraints weight = 10872.529| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.13 r_work: 0.3109 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12753 Z= 0.163 Angle : 0.550 5.191 18464 Z= 0.341 Chirality : 0.034 0.125 2100 Planarity : 0.004 0.034 1335 Dihedral : 30.389 95.899 4021 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 1.75 % Allowed : 12.44 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.06 (0.30), residues: 742 helix: 2.80 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.21 (0.38), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 92 TYR 0.010 0.001 TYR F 51 PHE 0.006 0.001 PHE E 67 HIS 0.004 0.001 HIS H 49 Details of bonding type rmsd covalent geometry : bond 0.00341 (12753) covalent geometry : angle 0.55005 (18464) hydrogen bonds : bond 0.04609 ( 782) hydrogen bonds : angle 2.82429 ( 1951) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 15 LYS cc_start: 0.7855 (mtpt) cc_final: 0.7433 (mtmt) REVERT: C 36 LYS cc_start: 0.8726 (mppt) cc_final: 0.8286 (mmtp) REVERT: C 91 GLU cc_start: 0.8067 (tt0) cc_final: 0.7698 (pm20) REVERT: G 95 LYS cc_start: 0.8490 (ttmt) cc_final: 0.7844 (tttt) outliers start: 11 outliers final: 3 residues processed: 149 average time/residue: 1.0800 time to fit residues: 168.6416 Evaluate side-chains 146 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 143 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 16 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 8 optimal weight: 0.3980 chunk 52 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 39 optimal weight: 0.0170 overall best weight: 0.5420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.167154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.119258 restraints weight = 11090.175| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.14 r_work: 0.3123 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12753 Z= 0.153 Angle : 0.539 5.061 18464 Z= 0.336 Chirality : 0.033 0.125 2100 Planarity : 0.004 0.058 1335 Dihedral : 30.372 95.836 4021 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 0.96 % Allowed : 13.72 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.17 (0.30), residues: 742 helix: 2.89 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.19 (0.38), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 92 TYR 0.010 0.001 TYR F 51 PHE 0.008 0.001 PHE E 67 HIS 0.004 0.001 HIS H 49 Details of bonding type rmsd covalent geometry : bond 0.00316 (12753) covalent geometry : angle 0.53862 (18464) hydrogen bonds : bond 0.04330 ( 782) hydrogen bonds : angle 2.80496 ( 1951) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 144 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: C 15 LYS cc_start: 0.7839 (mtpt) cc_final: 0.7415 (mtmt) REVERT: C 36 LYS cc_start: 0.8729 (mppt) cc_final: 0.8278 (mmtp) REVERT: C 91 GLU cc_start: 0.8008 (tt0) cc_final: 0.7790 (pm20) REVERT: G 95 LYS cc_start: 0.8465 (ttmt) cc_final: 0.7804 (tttt) REVERT: H 85 LYS cc_start: 0.8447 (mmtt) cc_final: 0.8245 (mptt) outliers start: 6 outliers final: 2 residues processed: 146 average time/residue: 1.1073 time to fit residues: 169.1522 Evaluate side-chains 144 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 142 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 72 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 95 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.162291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.113490 restraints weight = 11042.840| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.13 r_work: 0.3031 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 12753 Z= 0.283 Angle : 0.638 5.638 18464 Z= 0.384 Chirality : 0.041 0.146 2100 Planarity : 0.005 0.038 1335 Dihedral : 30.897 89.290 4021 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.39 % Allowed : 11.80 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.53 (0.29), residues: 742 helix: 2.43 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.46 (0.36), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 129 TYR 0.018 0.003 TYR B 88 PHE 0.009 0.002 PHE E 67 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00639 (12753) covalent geometry : angle 0.63752 (18464) hydrogen bonds : bond 0.06514 ( 782) hydrogen bonds : angle 3.00578 ( 1951) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: C 15 LYS cc_start: 0.8117 (mtpt) cc_final: 0.7545 (mtmt) REVERT: E 97 GLU cc_start: 0.9017 (mt-10) cc_final: 0.8792 (mt-10) REVERT: G 74 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7653 (mmmt) REVERT: G 95 LYS cc_start: 0.8490 (ttmt) cc_final: 0.7816 (tttt) REVERT: H 93 GLU cc_start: 0.8761 (mp0) cc_final: 0.8411 (mp0) outliers start: 15 outliers final: 5 residues processed: 142 average time/residue: 1.1163 time to fit residues: 165.9170 Evaluate side-chains 142 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 136 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 21 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 72 optimal weight: 10.0000 chunk 15 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.163629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.115120 restraints weight = 10975.622| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.14 r_work: 0.3056 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12753 Z= 0.180 Angle : 0.586 5.358 18464 Z= 0.359 Chirality : 0.035 0.130 2100 Planarity : 0.005 0.042 1335 Dihedral : 30.850 90.367 4021 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.71 % Allowed : 12.12 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.66 (0.30), residues: 742 helix: 2.54 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.46 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 52 TYR 0.012 0.002 TYR F 51 PHE 0.010 0.001 PHE E 67 HIS 0.005 0.001 HIS H 49 Details of bonding type rmsd covalent geometry : bond 0.00381 (12753) covalent geometry : angle 0.58579 (18464) hydrogen bonds : bond 0.05414 ( 782) hydrogen bonds : angle 2.97351 ( 1951) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: C 15 LYS cc_start: 0.8072 (mtpt) cc_final: 0.7540 (mtmt) REVERT: D 71 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8111 (mt-10) REVERT: E 97 GLU cc_start: 0.8977 (mt-10) cc_final: 0.8753 (mt-10) REVERT: G 95 LYS cc_start: 0.8482 (ttmt) cc_final: 0.7796 (tttt) REVERT: H 93 GLU cc_start: 0.8756 (mp0) cc_final: 0.8412 (mp0) outliers start: 17 outliers final: 10 residues processed: 142 average time/residue: 1.1260 time to fit residues: 167.2093 Evaluate side-chains 148 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 32 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.162111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.113296 restraints weight = 10972.109| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.13 r_work: 0.3029 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 12753 Z= 0.280 Angle : 0.636 5.370 18464 Z= 0.383 Chirality : 0.041 0.147 2100 Planarity : 0.005 0.040 1335 Dihedral : 30.804 89.557 4021 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.55 % Allowed : 12.28 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.35 (0.29), residues: 742 helix: 2.35 (0.22), residues: 539 sheet: None (None), residues: 0 loop : -0.66 (0.36), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 40 TYR 0.020 0.003 TYR B 88 PHE 0.010 0.002 PHE E 67 HIS 0.005 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00630 (12753) covalent geometry : angle 0.63633 (18464) hydrogen bonds : bond 0.06576 ( 782) hydrogen bonds : angle 3.00342 ( 1951) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: C 15 LYS cc_start: 0.8103 (mtpt) cc_final: 0.7530 (mtmt) REVERT: C 104 GLN cc_start: 0.8746 (mt0) cc_final: 0.8513 (mt0) REVERT: E 97 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8801 (mt-10) REVERT: G 95 LYS cc_start: 0.8453 (ttmt) cc_final: 0.7766 (tttt) REVERT: H 93 GLU cc_start: 0.8773 (mp0) cc_final: 0.8381 (mp0) outliers start: 16 outliers final: 9 residues processed: 143 average time/residue: 1.1354 time to fit residues: 169.9494 Evaluate side-chains 145 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 136 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 39 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.163461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.114996 restraints weight = 10932.499| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.12 r_work: 0.3055 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12753 Z= 0.179 Angle : 0.588 5.327 18464 Z= 0.360 Chirality : 0.035 0.128 2100 Planarity : 0.005 0.063 1335 Dihedral : 30.780 89.837 4021 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.91 % Allowed : 12.92 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.56 (0.30), residues: 742 helix: 2.49 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.57 (0.36), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 92 TYR 0.016 0.002 TYR B 88 PHE 0.009 0.001 PHE E 67 HIS 0.004 0.001 HIS H 49 Details of bonding type rmsd covalent geometry : bond 0.00381 (12753) covalent geometry : angle 0.58768 (18464) hydrogen bonds : bond 0.05461 ( 782) hydrogen bonds : angle 2.98327 ( 1951) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7965 (ttp80) cc_final: 0.7641 (ttt-90) REVERT: C 15 LYS cc_start: 0.8070 (mtpt) cc_final: 0.7527 (mtmt) REVERT: D 68 ASP cc_start: 0.9153 (t0) cc_final: 0.8813 (t0) REVERT: D 71 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8103 (mt-10) REVERT: E 97 GLU cc_start: 0.8978 (mt-10) cc_final: 0.8761 (mt-10) REVERT: G 95 LYS cc_start: 0.8441 (ttmt) cc_final: 0.7755 (tttt) REVERT: H 93 GLU cc_start: 0.8775 (mp0) cc_final: 0.8393 (mp0) outliers start: 12 outliers final: 10 residues processed: 140 average time/residue: 1.1143 time to fit residues: 163.2265 Evaluate side-chains 147 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 21 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 73 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.163722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.115275 restraints weight = 10949.388| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.12 r_work: 0.3060 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12753 Z= 0.188 Angle : 0.582 7.274 18464 Z= 0.355 Chirality : 0.035 0.141 2100 Planarity : 0.005 0.066 1335 Dihedral : 30.682 91.195 4021 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 1.91 % Allowed : 13.56 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.64 (0.30), residues: 742 helix: 2.54 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.50 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 92 TYR 0.015 0.002 TYR B 88 PHE 0.010 0.001 PHE E 67 HIS 0.004 0.001 HIS H 49 Details of bonding type rmsd covalent geometry : bond 0.00408 (12753) covalent geometry : angle 0.58182 (18464) hydrogen bonds : bond 0.05399 ( 782) hydrogen bonds : angle 2.90021 ( 1951) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7914 (ttp80) cc_final: 0.7561 (ttt-90) REVERT: C 15 LYS cc_start: 0.8093 (mtpt) cc_final: 0.7530 (mtmt) REVERT: D 71 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8146 (mt-10) REVERT: E 97 GLU cc_start: 0.8994 (mt-10) cc_final: 0.8766 (mt-10) REVERT: G 95 LYS cc_start: 0.8447 (ttmt) cc_final: 0.7763 (tttt) REVERT: H 93 GLU cc_start: 0.8775 (mp0) cc_final: 0.8390 (mp0) outliers start: 12 outliers final: 10 residues processed: 142 average time/residue: 1.0901 time to fit residues: 162.1244 Evaluate side-chains 147 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 16 optimal weight: 0.9980 chunk 68 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 73 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 chunk 86 optimal weight: 20.0000 chunk 14 optimal weight: 0.4980 chunk 24 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 24 GLN H 82 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.164189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.115769 restraints weight = 10981.904| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.13 r_work: 0.3067 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12753 Z= 0.170 Angle : 0.573 6.596 18464 Z= 0.351 Chirality : 0.034 0.130 2100 Planarity : 0.005 0.072 1335 Dihedral : 30.654 91.386 4021 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.75 % Allowed : 13.88 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.70 (0.30), residues: 742 helix: 2.58 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.46 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 92 TYR 0.015 0.002 TYR B 88 PHE 0.009 0.001 PHE E 67 HIS 0.004 0.001 HIS H 49 Details of bonding type rmsd covalent geometry : bond 0.00360 (12753) covalent geometry : angle 0.57269 (18464) hydrogen bonds : bond 0.05069 ( 782) hydrogen bonds : angle 2.89724 ( 1951) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 138 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: C 15 LYS cc_start: 0.8087 (mtpt) cc_final: 0.7514 (mtmt) REVERT: C 91 GLU cc_start: 0.8000 (tt0) cc_final: 0.7739 (pm20) REVERT: D 71 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8135 (mt-10) REVERT: E 97 GLU cc_start: 0.8979 (mt-10) cc_final: 0.8750 (mt-10) REVERT: G 95 LYS cc_start: 0.8441 (ttmt) cc_final: 0.7755 (tttt) REVERT: H 93 GLU cc_start: 0.8775 (mp0) cc_final: 0.8393 (mp0) outliers start: 11 outliers final: 9 residues processed: 140 average time/residue: 1.1083 time to fit residues: 162.4796 Evaluate side-chains 146 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 58 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN H 82 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.163475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.114899 restraints weight = 11027.419| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.13 r_work: 0.3056 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 12753 Z= 0.210 Angle : 0.587 6.620 18464 Z= 0.357 Chirality : 0.036 0.131 2100 Planarity : 0.004 0.040 1335 Dihedral : 30.544 91.281 4021 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 1.91 % Allowed : 13.88 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.63 (0.30), residues: 742 helix: 2.52 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.47 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 52 TYR 0.018 0.002 TYR B 88 PHE 0.009 0.001 PHE E 67 HIS 0.004 0.001 HIS H 49 Details of bonding type rmsd covalent geometry : bond 0.00461 (12753) covalent geometry : angle 0.58720 (18464) hydrogen bonds : bond 0.05522 ( 782) hydrogen bonds : angle 2.89857 ( 1951) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8013 (ttp80) cc_final: 0.7682 (ttt-90) REVERT: C 15 LYS cc_start: 0.8078 (mtpt) cc_final: 0.7534 (mtmt) REVERT: C 36 LYS cc_start: 0.8570 (mptt) cc_final: 0.8265 (mptm) REVERT: C 91 GLU cc_start: 0.8102 (tt0) cc_final: 0.7830 (pm20) REVERT: D 71 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8138 (mt-10) REVERT: E 97 GLU cc_start: 0.9000 (mt-10) cc_final: 0.8774 (mt-10) REVERT: G 95 LYS cc_start: 0.8451 (ttmt) cc_final: 0.7765 (tttt) REVERT: H 93 GLU cc_start: 0.8731 (mp0) cc_final: 0.8352 (mp0) outliers start: 12 outliers final: 10 residues processed: 143 average time/residue: 1.1037 time to fit residues: 165.1904 Evaluate side-chains 149 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 138 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 3 optimal weight: 0.4980 chunk 22 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 56 optimal weight: 0.4980 chunk 27 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.164206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.115781 restraints weight = 10989.894| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.13 r_work: 0.3068 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12753 Z= 0.166 Angle : 0.570 7.066 18464 Z= 0.349 Chirality : 0.034 0.127 2100 Planarity : 0.004 0.055 1335 Dihedral : 30.535 91.319 4021 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.75 % Allowed : 13.72 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.72 (0.30), residues: 742 helix: 2.58 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.42 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 92 TYR 0.018 0.002 TYR B 88 PHE 0.009 0.001 PHE E 67 HIS 0.004 0.001 HIS H 49 Details of bonding type rmsd covalent geometry : bond 0.00343 (12753) covalent geometry : angle 0.57044 (18464) hydrogen bonds : bond 0.05123 ( 782) hydrogen bonds : angle 2.89818 ( 1951) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6054.85 seconds wall clock time: 103 minutes 28.63 seconds (6208.63 seconds total)