Starting phenix.real_space_refine on Tue Jul 29 19:10:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ybj_39119/07_2025/8ybj_39119.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ybj_39119/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ybj_39119/07_2025/8ybj_39119.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ybj_39119/07_2025/8ybj_39119.map" model { file = "/net/cci-nas-00/data/ceres_data/8ybj_39119/07_2025/8ybj_39119.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ybj_39119/07_2025/8ybj_39119.cif" } resolution = 2.38 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= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.36, per 1000 atoms: 0.62 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: 2.92 Conformation dependent library (CDL) restraints added in 875.6 milliseconds 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: 5.24 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: 4.17 Time building geometry restraints manager: 3.51 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: 0.790 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: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 31.860 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.610 ------------------------------------------------------------------------------- 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 (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: 2.32 (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 HIS 0.007 0.002 HIS G 82 PHE 0.008 0.002 PHE E 67 TYR 0.036 0.003 TYR G 39 ARG 0.013 0.001 ARG F 35 Details of bonding type rmsd hydrogen bonds : bond 0.12210 ( 782) hydrogen bonds : angle 3.69658 ( 1951) covalent geometry : bond 0.00737 (12753) covalent geometry : angle 0.96133 (18464) *********************** 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 : 0.833 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: 2.2184 time to fit residues: 347.9087 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 : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3954 r_free = 0.3954 target = 0.166303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.118265 restraints weight = 10814.119| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.13 r_work: 0.3100 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 12753 Z= 0.168 Angle : 0.555 5.500 18464 Z= 0.343 Chirality : 0.034 0.127 2100 Planarity : 0.004 0.034 1335 Dihedral : 30.426 96.089 4021 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 1.59 % Allowed : 12.44 % Favored : 85.96 % 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: 3.00 (0.30), residues: 742 helix: 2.76 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.24 (0.38), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 49 PHE 0.008 0.001 PHE E 67 TYR 0.011 0.001 TYR F 51 ARG 0.005 0.000 ARG D 92 Details of bonding type rmsd hydrogen bonds : bond 0.04767 ( 782) hydrogen bonds : angle 2.83164 ( 1951) covalent geometry : bond 0.00355 (12753) covalent geometry : angle 0.55468 (18464) *********************** 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 157 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 147 time to evaluate : 0.846 Fit side-chains revert: symmetry clash REVERT: A 134 ARG cc_start: 0.7358 (ttt90) cc_final: 0.7104 (mtt180) REVERT: C 15 LYS cc_start: 0.7878 (mtpt) cc_final: 0.7445 (mtmt) REVERT: C 36 LYS cc_start: 0.8718 (mppt) cc_final: 0.8270 (mmtp) REVERT: C 91 GLU cc_start: 0.8081 (tt0) cc_final: 0.7702 (pm20) REVERT: E 97 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8670 (mt-10) REVERT: G 95 LYS cc_start: 0.8484 (ttmt) cc_final: 0.7828 (tttt) outliers start: 10 outliers final: 3 residues processed: 148 average time/residue: 2.0662 time to fit residues: 320.7849 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 : 1.128 ------------------------------------------------------------------------------- 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 75 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- 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 = 0.3908 r_free = 0.3908 target = 0.162048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.113147 restraints weight = 11053.263| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.15 r_work: 0.3027 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 12753 Z= 0.291 Angle : 0.646 6.018 18464 Z= 0.389 Chirality : 0.042 0.149 2100 Planarity : 0.006 0.039 1335 Dihedral : 30.908 89.429 4021 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.55 % Allowed : 11.96 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.29), residues: 742 helix: 2.36 (0.22), residues: 539 sheet: None (None), residues: 0 loop : -0.54 (0.36), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 75 PHE 0.010 0.002 PHE E 67 TYR 0.016 0.003 TYR B 88 ARG 0.007 0.001 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.06690 ( 782) hydrogen bonds : angle 3.03276 ( 1951) covalent geometry : bond 0.00658 (12753) covalent geometry : angle 0.64582 (18464) *********************** 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 153 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.940 Fit side-chains revert: symmetry clash REVERT: A 122 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8809 (pttt) REVERT: C 15 LYS cc_start: 0.8123 (mtpt) cc_final: 0.7564 (mtmt) REVERT: E 97 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8800 (mt-10) REVERT: G 64 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8245 (tt0) REVERT: G 95 LYS cc_start: 0.8505 (ttmt) cc_final: 0.7844 (tttt) REVERT: H 93 GLU cc_start: 0.8761 (mp0) cc_final: 0.8427 (mp0) outliers start: 16 outliers final: 7 residues processed: 142 average time/residue: 2.1025 time to fit residues: 313.1267 Evaluate side-chains 144 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 135 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 76 THR 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 6 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 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 = 0.3921 r_free = 0.3921 target = 0.163295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.114713 restraints weight = 10869.353| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.13 r_work: 0.3049 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12753 Z= 0.190 Angle : 0.596 8.254 18464 Z= 0.364 Chirality : 0.036 0.129 2100 Planarity : 0.005 0.077 1335 Dihedral : 30.868 90.254 4021 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.23 % Allowed : 12.12 % Favored : 85.65 % 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: 2.53 (0.30), residues: 742 helix: 2.45 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.53 (0.36), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS H 49 PHE 0.010 0.001 PHE E 67 TYR 0.013 0.002 TYR F 51 ARG 0.004 0.000 ARG C 35 Details of bonding type rmsd hydrogen bonds : bond 0.05674 ( 782) hydrogen bonds : angle 2.99790 ( 1951) covalent geometry : bond 0.00408 (12753) covalent geometry : angle 0.59609 (18464) *********************** 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 150 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 0.873 Fit side-chains revert: symmetry clash REVERT: C 15 LYS cc_start: 0.8102 (mtpt) cc_final: 0.7528 (mtmt) REVERT: C 36 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8157 (mptm) REVERT: D 71 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8091 (mt-10) REVERT: E 97 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8765 (mt-10) REVERT: G 64 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8236 (tt0) REVERT: G 95 LYS cc_start: 0.8477 (ttmt) cc_final: 0.7783 (tttt) REVERT: H 93 GLU cc_start: 0.8752 (mp0) cc_final: 0.8421 (mp0) outliers start: 14 outliers final: 9 residues processed: 140 average time/residue: 2.1766 time to fit residues: 319.1683 Evaluate side-chains 147 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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 C residue 95 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain G residue 64 GLU 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 97 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 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 = 0.163640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.115071 restraints weight = 10885.010| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.12 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: 0.8173 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12753 Z= 0.191 Angle : 0.584 5.320 18464 Z= 0.358 Chirality : 0.036 0.129 2100 Planarity : 0.005 0.051 1335 Dihedral : 30.782 91.661 4021 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.59 % Allowed : 13.40 % Favored : 85.01 % 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: 2.63 (0.30), residues: 742 helix: 2.52 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.49 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 49 PHE 0.010 0.001 PHE E 67 TYR 0.014 0.002 TYR F 51 ARG 0.004 0.000 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.05497 ( 782) hydrogen bonds : angle 2.93447 ( 1951) covalent geometry : bond 0.00414 (12753) covalent geometry : angle 0.58368 (18464) *********************** 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 148 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 138 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 15 LYS cc_start: 0.8082 (mtpt) cc_final: 0.7548 (mtmt) REVERT: D 68 ASP cc_start: 0.9150 (t0) cc_final: 0.8809 (t0) REVERT: D 71 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8123 (mt-10) REVERT: E 97 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8773 (mt-10) REVERT: G 64 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8232 (tt0) REVERT: G 95 LYS cc_start: 0.8481 (ttmt) cc_final: 0.7788 (tttt) REVERT: H 93 GLU cc_start: 0.8762 (mp0) cc_final: 0.8420 (mp0) outliers start: 10 outliers final: 6 residues processed: 143 average time/residue: 2.1101 time to fit residues: 316.2821 Evaluate side-chains 144 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 136 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain G residue 64 GLU 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 3 optimal weight: 0.5980 chunk 91 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3928 r_free = 0.3928 target = 0.164067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.115666 restraints weight = 11061.783| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.13 r_work: 0.3066 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12753 Z= 0.173 Angle : 0.569 5.147 18464 Z= 0.351 Chirality : 0.035 0.128 2100 Planarity : 0.004 0.055 1335 Dihedral : 30.723 92.273 4021 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 2.23 % Allowed : 12.92 % Favored : 84.85 % 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: 2.70 (0.30), residues: 742 helix: 2.57 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.46 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 49 PHE 0.009 0.001 PHE E 67 TYR 0.015 0.002 TYR B 88 ARG 0.004 0.000 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.05162 ( 782) hydrogen bonds : angle 2.91531 ( 1951) covalent geometry : bond 0.00369 (12753) covalent geometry : angle 0.56872 (18464) *********************** 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 151 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.796 Fit side-chains revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7800 (ttt-90) cc_final: 0.7527 (tmt-80) REVERT: A 56 LYS cc_start: 0.8375 (mtpt) cc_final: 0.8155 (ttmt) REVERT: C 15 LYS cc_start: 0.8066 (mtpt) cc_final: 0.7529 (mtmt) REVERT: C 36 LYS cc_start: 0.8445 (mptt) cc_final: 0.8155 (mptm) REVERT: D 71 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8105 (mt-10) REVERT: E 97 GLU cc_start: 0.8986 (mt-10) cc_final: 0.8770 (mt-10) REVERT: G 64 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8231 (tt0) REVERT: G 95 LYS cc_start: 0.8479 (ttmt) cc_final: 0.7788 (tttt) REVERT: H 93 GLU cc_start: 0.8771 (mp0) cc_final: 0.8411 (mp0) outliers start: 14 outliers final: 9 residues processed: 142 average time/residue: 2.0808 time to fit residues: 309.5481 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 : 0.944 ------------------------------------------------------------------------------- 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 112 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain G residue 64 GLU 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 53 optimal weight: 10.0000 chunk 42 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 31 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3932 r_free = 0.3932 target = 0.164402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.116069 restraints weight = 10988.363| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.13 r_work: 0.3072 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12753 Z= 0.169 Angle : 0.565 7.559 18464 Z= 0.348 Chirality : 0.034 0.126 2100 Planarity : 0.004 0.048 1335 Dihedral : 30.678 92.815 4021 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 2.07 % Allowed : 12.76 % 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 (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: 2.75 (0.30), residues: 742 helix: 2.61 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.44 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 49 PHE 0.009 0.001 PHE E 67 TYR 0.012 0.001 TYR B 88 ARG 0.004 0.000 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.05052 ( 782) hydrogen bonds : angle 2.88859 ( 1951) covalent geometry : bond 0.00359 (12753) covalent geometry : angle 0.56547 (18464) *********************** 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 149 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.8387 (mtpt) cc_final: 0.8110 (ttmt) REVERT: C 15 LYS cc_start: 0.8079 (mtpt) cc_final: 0.7543 (mtmt) REVERT: C 36 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8153 (mptm) REVERT: D 71 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8115 (mt-10) REVERT: E 97 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8767 (mt-10) REVERT: G 64 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8229 (tt0) REVERT: G 95 LYS cc_start: 0.8477 (ttmt) cc_final: 0.7786 (tttt) REVERT: H 93 GLU cc_start: 0.8770 (mp0) cc_final: 0.8394 (mp0) outliers start: 13 outliers final: 9 residues processed: 141 average time/residue: 2.4624 time to fit residues: 363.2694 Evaluate side-chains 149 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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 D residue 71 GLU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 76 THR 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 49 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 = 0.3934 r_free = 0.3934 target = 0.164532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.116115 restraints weight = 11057.548| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.13 r_work: 0.3072 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 12753 Z= 0.181 Angle : 0.560 5.098 18464 Z= 0.345 Chirality : 0.035 0.127 2100 Planarity : 0.004 0.040 1335 Dihedral : 30.485 94.332 4021 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 2.07 % Allowed : 12.44 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.79 (0.30), residues: 742 helix: 2.64 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.41 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS H 49 PHE 0.008 0.001 PHE E 67 TYR 0.018 0.002 TYR B 88 ARG 0.006 0.000 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.05018 ( 782) hydrogen bonds : angle 2.83365 ( 1951) covalent geometry : bond 0.00390 (12753) covalent geometry : angle 0.56006 (18464) *********************** 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 154 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 15 LYS cc_start: 0.8027 (mtpt) cc_final: 0.7502 (mtmt) REVERT: C 91 GLU cc_start: 0.8176 (tt0) cc_final: 0.7866 (pm20) REVERT: D 71 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8106 (mt-10) REVERT: E 97 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8754 (mt-10) REVERT: G 64 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8246 (tt0) REVERT: G 92 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7137 (mt-10) REVERT: G 95 LYS cc_start: 0.8478 (ttmt) cc_final: 0.7794 (tttt) REVERT: H 93 GLU cc_start: 0.8771 (mp0) cc_final: 0.8358 (mp0) outliers start: 13 outliers final: 7 residues processed: 144 average time/residue: 2.0931 time to fit residues: 316.0580 Evaluate side-chains 148 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 138 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ARG 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 E residue 65 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 92 GLU 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 4 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.163377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.114667 restraints weight = 11006.293| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.15 r_work: 0.3051 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 12753 Z= 0.220 Angle : 0.590 6.693 18464 Z= 0.359 Chirality : 0.037 0.130 2100 Planarity : 0.005 0.039 1335 Dihedral : 30.585 91.555 4021 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 2.23 % Allowed : 12.76 % Favored : 85.01 % 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: 2.63 (0.30), residues: 742 helix: 2.52 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.48 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS H 49 PHE 0.009 0.002 PHE E 67 TYR 0.022 0.002 TYR B 88 ARG 0.008 0.001 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.05709 ( 782) hydrogen bonds : angle 2.89138 ( 1951) covalent geometry : bond 0.00487 (12753) covalent geometry : angle 0.59043 (18464) *********************** 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 154 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8012 (ttp80) cc_final: 0.7603 (ttt-90) REVERT: C 15 LYS cc_start: 0.8117 (mtpt) cc_final: 0.7558 (mtmt) REVERT: C 91 GLU cc_start: 0.8128 (tt0) cc_final: 0.7813 (pm20) REVERT: D 68 ASP cc_start: 0.9177 (t0) cc_final: 0.8848 (t0) REVERT: D 71 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8123 (mt-10) REVERT: E 97 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8778 (mt-10) REVERT: G 64 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8247 (tt0) REVERT: G 95 LYS cc_start: 0.8454 (ttmt) cc_final: 0.7764 (tttt) REVERT: H 93 GLU cc_start: 0.8783 (mp0) cc_final: 0.8374 (mp0) outliers start: 14 outliers final: 10 residues processed: 143 average time/residue: 2.1017 time to fit residues: 315.6857 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 : 0.889 ------------------------------------------------------------------------------- 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 C residue 104 GLN Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 85 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 64 GLU Chi-restraints excluded: chain G residue 76 THR 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 91 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 84 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 11 optimal weight: 0.1980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN G 24 GLN H 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.164611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.116179 restraints weight = 10950.156| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.14 r_work: 0.3072 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 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 : 0.004 0.084 12753 Z= 0.171 Angle : 0.571 8.895 18464 Z= 0.350 Chirality : 0.034 0.126 2100 Planarity : 0.004 0.048 1335 Dihedral : 30.541 92.286 4021 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 1.75 % Allowed : 13.40 % Favored : 84.85 % 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: 2.78 (0.30), residues: 742 helix: 2.63 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.42 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 49 PHE 0.009 0.001 PHE E 67 TYR 0.019 0.002 TYR B 88 ARG 0.004 0.000 ARG H 92 Details of bonding type rmsd hydrogen bonds : bond 0.05023 ( 782) hydrogen bonds : angle 2.85508 ( 1951) covalent geometry : bond 0.00365 (12753) covalent geometry : angle 0.57091 (18464) ********************** 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 149 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 138 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7976 (ttp80) cc_final: 0.7609 (ttt-90) REVERT: C 15 LYS cc_start: 0.8081 (mtpt) cc_final: 0.7533 (mtmt) REVERT: C 91 GLU cc_start: 0.8176 (tt0) cc_final: 0.7870 (pm20) REVERT: D 71 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8120 (mt-10) REVERT: E 97 GLU cc_start: 0.8974 (mt-10) cc_final: 0.8741 (mt-10) REVERT: G 64 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8233 (tt0) REVERT: G 95 LYS cc_start: 0.8466 (ttmt) cc_final: 0.7775 (tttt) REVERT: H 93 GLU cc_start: 0.8771 (mp0) cc_final: 0.8369 (mp0) outliers start: 11 outliers final: 6 residues processed: 140 average time/residue: 2.1136 time to fit residues: 310.1624 Evaluate side-chains 146 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 138 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 76 THR 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 59 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 86 optimal weight: 20.0000 chunk 34 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN G 24 GLN H 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.164906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.116655 restraints weight = 11005.704| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.12 r_work: 0.3078 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12753 Z= 0.169 Angle : 0.566 7.571 18464 Z= 0.347 Chirality : 0.034 0.125 2100 Planarity : 0.005 0.066 1335 Dihedral : 30.503 92.758 4021 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.59 % Allowed : 13.56 % Favored : 84.85 % 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: 2.82 (0.30), residues: 742 helix: 2.66 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.40 (0.38), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 49 PHE 0.009 0.001 PHE E 67 TYR 0.016 0.002 TYR B 88 ARG 0.003 0.000 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.04922 ( 782) hydrogen bonds : angle 2.83716 ( 1951) covalent geometry : bond 0.00357 (12753) covalent geometry : angle 0.56575 (18464) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11255.91 seconds wall clock time: 195 minutes 22.06 seconds (11722.06 seconds total)