Starting phenix.real_space_refine on Fri Sep 11 20:14:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wlr_32591/09_2026/7wlr_32591.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wlr_32591/09_2026/7wlr_32591.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wlr_32591/09_2026/7wlr_32591.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wlr_32591/09_2026/7wlr_32591.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wlr_32591/09_2026/7wlr_32591.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wlr_32591/09_2026/7wlr_32591.map" } resolution = 3.54 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= 1.000 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 6 5.16 5 C 6588 2.51 5 N 2222 2.21 5 O 2817 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11922 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 794 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "B" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 666 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 802 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 740 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 794 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "F" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 813 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 714 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: 2.54, per 1000 atoms: 0.21 Number of scatterers: 11922 At special positions: 0 Unit cell: (118.72, 86.92, 119.78, 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 6 16.00 P 289 15.00 O 2817 8.00 N 2222 7.00 C 6588 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 296.3 milliseconds 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1420 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 10 sheets defined 74.5% alpha, 3.2% beta 144 base pairs and 260 stacking pairs defined. Time for finding SS restraints: 2.47 Creating SS restraints... Processing helix chain 'A' and resid 45 through 58 Processing helix chain 'A' and resid 64 through 80 removed outlier: 4.142A pdb=" N ASP A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 115 removed outlier: 3.688A pdb=" N ALA A 115 " --> pdb=" O CYS A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 133 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.755A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.815A 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 45 through 73 removed outlier: 4.439A pdb=" N VAL C 49 " --> pdb=" O SER C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 41 through 53 removed outlier: 3.925A pdb=" N LYS D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 88 removed outlier: 3.510A pdb=" N ASN D 88 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 106 Processing helix chain 'D' and resid 107 through 129 Processing helix chain 'E' and resid 45 through 58 Processing helix chain 'E' and resid 64 through 78 removed outlier: 3.880A pdb=" N ASP E 78 " --> pdb=" O GLU E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 115 removed outlier: 3.642A pdb=" N ALA E 115 " --> pdb=" O CYS E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 132 removed outlier: 3.507A pdb=" N ILE E 125 " --> pdb=" O GLN E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.999A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.426A pdb=" N VAL G 49 " --> pdb=" O SER G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 41 through 53 Processing helix chain 'H' and resid 59 through 88 Processing helix chain 'H' and resid 94 through 106 Processing helix chain 'H' and resid 107 through 129 Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.306A pdb=" N ARG A 84 " --> 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 119 through 120 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.520A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.377A pdb=" N ARG C 42 " --> pdb=" O ILE D 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 84 through 85 removed outlier: 7.067A pdb=" N ARG E 84 " --> 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 119 through 120 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.113A pdb=" N ARG G 42 " --> pdb=" O ILE H 93 " (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 78 418 hydrogen bonds defined for protein. 1233 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 367 hydrogen bonds 730 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 260 stacking parallelities Total time for adding SS restraints: 2.62 Time building geometry restraints manager: 1.39 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: 1476 1.32 - 1.44: 4699 1.44 - 1.56: 5959 1.56 - 1.69: 577 1.69 - 1.81: 10 Bond restraints: 12721 Sorted by residual: bond pdb=" N ARG B 23 " pdb=" CA ARG B 23 " ideal model delta sigma weight residual 1.457 1.511 -0.054 1.29e-02 6.01e+03 1.75e+01 bond pdb=" C6 DA I 97 " pdb=" N6 DA I 97 " ideal model delta sigma weight residual 1.335 1.304 0.031 8.00e-03 1.56e+04 1.54e+01 bond pdb=" C3' DC I 122 " pdb=" C2' DC I 122 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.46e+01 bond pdb=" C3' DC I 11 " pdb=" C2' DC I 11 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.21e+01 bond pdb=" C5' DA I 123 " pdb=" C4' DA I 123 " ideal model delta sigma weight residual 1.512 1.536 -0.024 7.00e-03 2.04e+04 1.21e+01 ... (remaining 12716 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 16238 1.55 - 3.10: 1878 3.10 - 4.65: 251 4.65 - 6.20: 44 6.20 - 7.74: 13 Bond angle restraints: 18424 Sorted by residual: angle pdb=" O5' DA I 123 " pdb=" C5' DA I 123 " pdb=" C4' DA I 123 " ideal model delta sigma weight residual 109.40 113.48 -4.08 8.00e-01 1.56e+00 2.60e+01 angle pdb=" O4' DA I 130 " pdb=" C1' DA I 130 " pdb=" N9 DA I 130 " ideal model delta sigma weight residual 108.00 104.63 3.37 7.00e-01 2.04e+00 2.31e+01 angle pdb=" O4' DA I 28 " pdb=" C4' DA I 28 " pdb=" C3' DA I 28 " ideal model delta sigma weight residual 106.00 103.12 2.88 6.00e-01 2.78e+00 2.31e+01 angle pdb=" N3 DT J 14 " pdb=" C4 DT J 14 " pdb=" O4 DT J 14 " ideal model delta sigma weight residual 119.90 122.74 -2.84 6.00e-01 2.78e+00 2.24e+01 angle pdb=" C THR A 59 " pdb=" N GLU A 60 " pdb=" CA GLU A 60 " ideal model delta sigma weight residual 120.82 127.74 -6.92 1.47e+00 4.63e-01 2.22e+01 ... (remaining 18419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.23: 4488 21.23 - 42.46: 1286 42.46 - 63.69: 1085 63.69 - 84.92: 46 84.92 - 106.15: 8 Dihedral angle restraints: 6913 sinusoidal: 4719 harmonic: 2194 Sorted by residual: dihedral pdb=" CA GLY E 45 " pdb=" C GLY E 45 " pdb=" N THR E 46 " pdb=" CA THR E 46 " ideal model delta harmonic sigma weight residual 180.00 -154.28 -25.72 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA GLY A 45 " pdb=" C GLY A 45 " pdb=" N THR A 46 " pdb=" CA THR A 46 " ideal model delta harmonic sigma weight residual 180.00 -154.53 -25.47 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA ARG B 23 " pdb=" C ARG B 23 " pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta harmonic sigma weight residual 180.00 -156.82 -23.18 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 6910 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1727 0.062 - 0.124: 339 0.124 - 0.187: 27 0.187 - 0.249: 10 0.249 - 0.311: 4 Chirality restraints: 2107 Sorted by residual: chirality pdb=" CA ARG F 23 " pdb=" N ARG F 23 " pdb=" C ARG F 23 " pdb=" CB ARG F 23 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CA LYS G 118 " pdb=" N LYS G 118 " pdb=" C LYS G 118 " pdb=" CB LYS G 118 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA THR A 46 " pdb=" N THR A 46 " pdb=" C THR A 46 " pdb=" CB THR A 46 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.28 2.00e-01 2.50e+01 1.95e+00 ... (remaining 2104 not shown) Planarity restraints: 1323 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 44 " 0.045 2.00e-02 2.50e+03 3.82e-02 2.92e+01 pdb=" CG TYR D 44 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR D 44 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TYR D 44 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR D 44 " -0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR D 44 " -0.049 2.00e-02 2.50e+03 pdb=" CZ TYR D 44 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR D 44 " 0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 101 " -0.020 2.00e-02 2.50e+03 4.02e-02 1.62e+01 pdb=" C GLY B 101 " 0.070 2.00e-02 2.50e+03 pdb=" O GLY B 101 " -0.026 2.00e-02 2.50e+03 pdb=" N GLY B 102 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS H 53 " 0.014 2.00e-02 2.50e+03 3.24e-02 1.57e+01 pdb=" CG HIS H 53 " -0.005 2.00e-02 2.50e+03 pdb=" ND1 HIS H 53 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 HIS H 53 " -0.040 2.00e-02 2.50e+03 pdb=" CE1 HIS H 53 " -0.035 2.00e-02 2.50e+03 pdb=" NE2 HIS H 53 " 0.055 2.00e-02 2.50e+03 ... (remaining 1320 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1741 2.77 - 3.30: 10480 3.30 - 3.83: 23372 3.83 - 4.37: 27505 4.37 - 4.90: 39362 Nonbonded interactions: 102460 Sorted by model distance: nonbonded pdb=" O2 DC I 50 " pdb=" N2 DG J 96 " model vdw 2.232 2.496 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 72 " model vdw 2.287 3.040 nonbonded pdb=" OG SER H 94 " pdb=" OE1 GLU H 97 " model vdw 2.346 3.040 nonbonded pdb=" OG SER C 18 " pdb=" O PHE C 25 " model vdw 2.365 3.040 nonbonded pdb=" OG SER G 18 " pdb=" O PHE G 25 " model vdw 2.383 3.040 ... (remaining 102455 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 15 through 118) } ncs_group { reference = (chain 'D' and resid 38 through 129) 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.380 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.120 Find NCS groups from input model: 0.150 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 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 0.060 12721 Z= 0.594 Angle : 1.012 7.744 18424 Z= 0.829 Chirality : 0.052 0.311 2107 Planarity : 0.010 0.124 1323 Dihedral : 29.271 106.152 5493 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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 are not related in a simple way. whole: 1.65 (0.29), residues: 738 helix: 1.78 (0.21), residues: 539 sheet: None (None), residues: 0 loop : -0.77 (0.40), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 35 TYR 0.068 0.004 TYR D 44 PHE 0.008 0.001 PHE D 74 HIS 0.047 0.003 HIS H 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00722 / 0.59 (12721) covalent geometry : angle 1.01221 / 0.83 (18424) hydrogen bonds : bond 0.11505 / 7.63 ( 785) hydrogen bonds : angle 3.72291 / 2.73 ( 1963) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.326 Fit side-chains REVERT: B 91 LYS cc_start: 0.7799 (tttp) cc_final: 0.7209 (ttmm) REVERT: C 41 GLN cc_start: 0.7720 (mm-40) cc_final: 0.7399 (mt0) REVERT: C 95 LYS cc_start: 0.7478 (ttmt) cc_final: 0.7248 (tttm) REVERT: D 38 LYS cc_start: 0.7201 (tptm) cc_final: 0.6778 (tppt) REVERT: D 89 LYS cc_start: 0.8368 (mmmt) cc_final: 0.7467 (mttm) REVERT: E 111 CYS cc_start: 0.6645 (p) cc_final: 0.6432 (p) REVERT: G 36 ARG cc_start: 0.6975 (tpp80) cc_final: 0.6569 (mmt90) REVERT: G 107 VAL cc_start: 0.8850 (p) cc_final: 0.8621 (m) REVERT: H 75 GLU cc_start: 0.6979 (tp30) cc_final: 0.6624 (mt-10) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1839 time to fit residues: 25.1646 Evaluate side-chains 61 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.302 ------------------------------------------------------------------------------- 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: 0.6980 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN D 51 GLN D 53 HIS D 88 ASN E 77 GLN E 94 GLN F 25 ASN G 73 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.167631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.115830 restraints weight = 14637.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.114683 restraints weight = 20226.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.115628 restraints weight = 19425.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.115753 restraints weight = 16164.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.116047 restraints weight = 17065.070| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12721 Z= 0.143 Angle : 0.637 6.141 18424 Z= 0.375 Chirality : 0.045 0.218 2107 Planarity : 0.005 0.056 1323 Dihedral : 31.892 97.993 4005 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.10 % Allowed : 5.02 % Favored : 93.89 % 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 are not related in a simple way. whole: 2.45 (0.29), residues: 738 helix: 2.33 (0.21), residues: 549 sheet: None (None), residues: 0 loop : -0.54 (0.40), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 96 TYR 0.010 0.001 TYR G 57 PHE 0.006 0.001 PHE H 74 HIS 0.008 0.001 HIS H 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.14 (12721) covalent geometry : angle 0.63730 / 0.38 (18424) hydrogen bonds : bond 0.05412 / 3.45 ( 785) hydrogen bonds : angle 2.92475 / 2.12 ( 1963) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.349 Fit side-chains REVERT: A 77 GLN cc_start: 0.8023 (tm-30) cc_final: 0.7768 (tm-30) REVERT: B 91 LYS cc_start: 0.8240 (tttp) cc_final: 0.7691 (ttmm) REVERT: D 89 LYS cc_start: 0.8432 (mmmt) cc_final: 0.7783 (mttm) REVERT: G 36 ARG cc_start: 0.6895 (tpp80) cc_final: 0.6615 (mmt90) REVERT: G 73 ASN cc_start: 0.8106 (OUTLIER) cc_final: 0.7788 (t0) REVERT: G 107 VAL cc_start: 0.9055 (p) cc_final: 0.8759 (m) outliers start: 7 outliers final: 2 residues processed: 71 average time/residue: 0.1284 time to fit residues: 12.8387 Evaluate side-chains 62 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain H residue 86 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 98 optimal weight: 40.0000 chunk 97 optimal weight: 20.0000 chunk 78 optimal weight: 30.0000 chunk 99 optimal weight: 50.0000 chunk 7 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN D 51 GLN D 53 HIS F 25 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.163758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.110736 restraints weight = 14693.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.109745 restraints weight = 21383.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.110683 restraints weight = 19967.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.110869 restraints weight = 16849.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.111453 restraints weight = 17178.757| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12721 Z= 0.165 Angle : 0.627 5.924 18424 Z= 0.366 Chirality : 0.045 0.213 2107 Planarity : 0.004 0.037 1323 Dihedral : 31.731 100.316 4005 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.78 % Allowed : 6.90 % Favored : 92.32 % 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 are not related in a simple way. whole: 2.61 (0.30), residues: 738 helix: 2.51 (0.21), residues: 549 sheet: None (None), residues: 0 loop : -0.73 (0.40), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG D 96 TYR 0.013 0.001 TYR G 57 PHE 0.009 0.002 PHE G 25 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.17 (12721) covalent geometry : angle 0.62691 / 0.37 (18424) hydrogen bonds : bond 0.05532 / 3.55 ( 785) hydrogen bonds : angle 2.82640 / 2.05 ( 1963) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.315 Fit side-chains REVERT: A 77 GLN cc_start: 0.8002 (tm-30) cc_final: 0.7548 (tm-30) REVERT: B 91 LYS cc_start: 0.8371 (tttp) cc_final: 0.7824 (ttmm) REVERT: D 46 TYR cc_start: 0.8240 (t80) cc_final: 0.7397 (t80) REVERT: D 75 GLU cc_start: 0.7362 (tm-30) cc_final: 0.7136 (tm-30) REVERT: D 89 LYS cc_start: 0.8388 (mmmt) cc_final: 0.7813 (mttm) REVERT: G 36 ARG cc_start: 0.6964 (tpp80) cc_final: 0.6651 (mmt90) outliers start: 5 outliers final: 4 residues processed: 68 average time/residue: 0.1345 time to fit residues: 12.7485 Evaluate side-chains 61 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain H residue 86 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.4980 chunk 3 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 87 optimal weight: 40.0000 chunk 84 optimal weight: 30.0000 chunk 99 optimal weight: 50.0000 chunk 85 optimal weight: 30.0000 chunk 70 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 98 optimal weight: 30.0000 chunk 53 optimal weight: 0.0670 overall best weight: 1.4722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 51 GLN E 77 GLN F 25 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.163496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.111004 restraints weight = 14591.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.109851 restraints weight = 21479.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.110771 restraints weight = 19957.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.110940 restraints weight = 16660.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.111531 restraints weight = 17177.562| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12721 Z= 0.139 Angle : 0.589 5.715 18424 Z= 0.348 Chirality : 0.043 0.196 2107 Planarity : 0.004 0.034 1323 Dihedral : 31.399 105.240 4005 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.41 % Allowed : 9.25 % Favored : 89.34 % 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 are not related in a simple way. whole: 2.83 (0.30), residues: 738 helix: 2.70 (0.21), residues: 549 sheet: None (None), residues: 0 loop : -0.73 (0.40), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 78 TYR 0.010 0.001 TYR G 57 PHE 0.006 0.001 PHE H 69 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.14 (12721) covalent geometry : angle 0.58895 / 0.35 (18424) hydrogen bonds : bond 0.04977 / 3.14 ( 785) hydrogen bonds : angle 2.64832 / 1.92 ( 1963) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.313 Fit side-chains REVERT: A 77 GLN cc_start: 0.7985 (tm-30) cc_final: 0.7694 (tm-30) REVERT: B 91 LYS cc_start: 0.8361 (tttp) cc_final: 0.7954 (ttmm) REVERT: D 46 TYR cc_start: 0.8200 (t80) cc_final: 0.7373 (t80) REVERT: D 89 LYS cc_start: 0.8415 (mmmt) cc_final: 0.7812 (mttm) REVERT: G 36 ARG cc_start: 0.6894 (tpp80) cc_final: 0.6571 (mmt90) outliers start: 9 outliers final: 4 residues processed: 79 average time/residue: 0.1289 time to fit residues: 14.3326 Evaluate side-chains 66 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain H residue 86 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 71 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 83 optimal weight: 20.0000 chunk 90 optimal weight: 30.0000 chunk 34 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN E 77 GLN F 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.160230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.110078 restraints weight = 14814.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.109011 restraints weight = 22660.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.109821 restraints weight = 20995.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.109981 restraints weight = 16821.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.110275 restraints weight = 16249.066| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12721 Z= 0.182 Angle : 0.644 7.016 18424 Z= 0.367 Chirality : 0.045 0.199 2107 Planarity : 0.004 0.035 1323 Dihedral : 31.510 105.179 4005 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.41 % Allowed : 10.82 % Favored : 87.77 % 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 are not related in a simple way. whole: 2.54 (0.30), residues: 738 helix: 2.53 (0.21), residues: 550 sheet: None (None), residues: 0 loop : -1.01 (0.39), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 96 TYR 0.015 0.002 TYR G 57 PHE 0.012 0.002 PHE G 25 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 (12721) covalent geometry : angle 0.64377 / 0.37 (18424) hydrogen bonds : bond 0.05832 / 3.75 ( 785) hydrogen bonds : angle 2.81047 / 2.04 ( 1963) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.307 Fit side-chains REVERT: A 77 GLN cc_start: 0.8000 (tm-30) cc_final: 0.7683 (tm-30) REVERT: B 91 LYS cc_start: 0.8506 (tttp) cc_final: 0.8137 (ttmm) REVERT: D 46 TYR cc_start: 0.8347 (t80) cc_final: 0.7513 (t80) REVERT: D 63 MET cc_start: 0.8896 (tpp) cc_final: 0.8138 (tpp) REVERT: D 89 LYS cc_start: 0.8404 (mmmt) cc_final: 0.7897 (mttm) REVERT: G 36 ARG cc_start: 0.6913 (tpp80) cc_final: 0.6476 (mmt90) REVERT: G 83 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8747 (mt) REVERT: H 38 LYS cc_start: 0.7758 (tppt) cc_final: 0.7158 (mtpt) outliers start: 9 outliers final: 7 residues processed: 77 average time/residue: 0.1447 time to fit residues: 15.1064 Evaluate side-chains 75 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain H residue 86 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 65 optimal weight: 2.9990 chunk 82 optimal weight: 30.0000 chunk 60 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 85 optimal weight: 40.0000 chunk 36 optimal weight: 10.0000 chunk 92 optimal weight: 20.0000 chunk 74 optimal weight: 40.0000 chunk 23 optimal weight: 0.4980 chunk 87 optimal weight: 30.0000 chunk 91 optimal weight: 20.0000 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN E 77 GLN E 94 GLN F 25 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.158520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.102700 restraints weight = 14725.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.101292 restraints weight = 17012.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.102070 restraints weight = 17116.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.102351 restraints weight = 14886.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.102584 restraints weight = 15034.805| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12721 Z= 0.201 Angle : 0.657 7.225 18424 Z= 0.371 Chirality : 0.046 0.207 2107 Planarity : 0.005 0.038 1323 Dihedral : 31.457 110.475 4005 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.72 % Allowed : 10.97 % Favored : 87.30 % 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 are not related in a simple way. whole: 2.34 (0.30), residues: 738 helix: 2.44 (0.21), residues: 549 sheet: None (None), residues: 0 loop : -1.27 (0.38), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 120 TYR 0.015 0.002 TYR G 57 PHE 0.011 0.002 PHE E 68 HIS 0.005 0.001 HIS H 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.20 (12721) covalent geometry : angle 0.65656 / 0.37 (18424) hydrogen bonds : bond 0.05823 / 3.70 ( 785) hydrogen bonds : angle 2.84720 / 2.09 ( 1963) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.317 Fit side-chains REVERT: A 77 GLN cc_start: 0.7968 (tm-30) cc_final: 0.7624 (tm-30) REVERT: B 91 LYS cc_start: 0.8532 (tttp) cc_final: 0.8167 (ttmm) REVERT: C 45 SER cc_start: 0.9009 (m) cc_final: 0.8789 (p) REVERT: D 46 TYR cc_start: 0.8281 (t80) cc_final: 0.7500 (t80) REVERT: D 63 MET cc_start: 0.9064 (tpp) cc_final: 0.8450 (tpp) REVERT: D 89 LYS cc_start: 0.8411 (mmmt) cc_final: 0.7948 (mttm) REVERT: G 36 ARG cc_start: 0.7069 (tpp80) cc_final: 0.6635 (mmt90) REVERT: H 38 LYS cc_start: 0.7754 (tppt) cc_final: 0.7256 (mtpt) outliers start: 11 outliers final: 9 residues processed: 81 average time/residue: 0.1313 time to fit residues: 14.9742 Evaluate side-chains 78 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain E residue 111 CYS Chi-restraints excluded: chain H residue 86 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 17 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 97 optimal weight: 30.0000 chunk 82 optimal weight: 30.0000 chunk 58 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 81 optimal weight: 20.0000 chunk 21 optimal weight: 0.9990 chunk 89 optimal weight: 30.0000 chunk 24 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.160954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.108576 restraints weight = 14596.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.107070 restraints weight = 18843.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.107848 restraints weight = 20307.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.107735 restraints weight = 18006.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.107845 restraints weight = 16493.344| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12721 Z= 0.127 Angle : 0.573 6.853 18424 Z= 0.341 Chirality : 0.042 0.194 2107 Planarity : 0.004 0.038 1323 Dihedral : 31.212 111.184 4005 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.63 % Allowed : 12.38 % Favored : 86.99 % 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 are not related in a simple way. whole: 2.93 (0.30), residues: 738 helix: 2.87 (0.21), residues: 548 sheet: None (None), residues: 0 loop : -1.02 (0.39), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 120 TYR 0.010 0.001 TYR B 51 PHE 0.006 0.001 PHE E 68 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.13 (12721) covalent geometry : angle 0.57333 / 0.34 (18424) hydrogen bonds : bond 0.04853 / 3.06 ( 785) hydrogen bonds : angle 2.63231 / 1.94 ( 1963) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.341 Fit side-chains REVERT: A 77 GLN cc_start: 0.7928 (tm-30) cc_final: 0.7603 (tm-30) REVERT: B 91 LYS cc_start: 0.8469 (tttp) cc_final: 0.8043 (ttmm) REVERT: C 45 SER cc_start: 0.8897 (m) cc_final: 0.8696 (p) REVERT: D 46 TYR cc_start: 0.8119 (t80) cc_final: 0.7290 (t80) REVERT: D 63 MET cc_start: 0.8895 (tpp) cc_final: 0.8649 (tpp) REVERT: D 89 LYS cc_start: 0.8444 (mmmt) cc_final: 0.7829 (mttm) REVERT: G 36 ARG cc_start: 0.7056 (tpp80) cc_final: 0.6601 (mmt90) REVERT: H 38 LYS cc_start: 0.7682 (tppt) cc_final: 0.7214 (mtpt) outliers start: 4 outliers final: 4 residues processed: 74 average time/residue: 0.1254 time to fit residues: 13.2527 Evaluate side-chains 73 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain D residue 92 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 65 optimal weight: 0.5980 chunk 91 optimal weight: 30.0000 chunk 83 optimal weight: 20.0000 chunk 35 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 23 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN E 77 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.159936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.107223 restraints weight = 14605.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.106076 restraints weight = 19327.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.106828 restraints weight = 20372.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.106782 restraints weight = 17891.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.106883 restraints weight = 16456.031| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12721 Z= 0.151 Angle : 0.599 6.653 18424 Z= 0.347 Chirality : 0.043 0.196 2107 Planarity : 0.004 0.039 1323 Dihedral : 31.294 111.212 4005 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.41 % Allowed : 12.07 % Favored : 86.52 % 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 are not related in a simple way. whole: 2.83 (0.30), residues: 738 helix: 2.80 (0.21), residues: 550 sheet: None (None), residues: 0 loop : -1.08 (0.40), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 23 TYR 0.010 0.001 TYR G 57 PHE 0.009 0.001 PHE A 68 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (12721) covalent geometry : angle 0.59947 / 0.35 (18424) hydrogen bonds : bond 0.05261 / 3.34 ( 785) hydrogen bonds : angle 2.69985 / 1.99 ( 1963) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.320 Fit side-chains REVERT: A 77 GLN cc_start: 0.7914 (tm-30) cc_final: 0.7563 (tm-30) REVERT: B 91 LYS cc_start: 0.8489 (tttp) cc_final: 0.8115 (ttmm) REVERT: C 45 SER cc_start: 0.8936 (m) cc_final: 0.8729 (p) REVERT: D 46 TYR cc_start: 0.8223 (t80) cc_final: 0.7390 (t80) REVERT: D 63 MET cc_start: 0.8986 (tpp) cc_final: 0.8673 (tpp) REVERT: D 89 LYS cc_start: 0.8429 (mmmt) cc_final: 0.7926 (mttm) REVERT: G 36 ARG cc_start: 0.7135 (tpp80) cc_final: 0.6643 (mmt90) REVERT: G 83 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8732 (mt) REVERT: H 38 LYS cc_start: 0.7753 (tppt) cc_final: 0.7259 (mtpt) outliers start: 9 outliers final: 8 residues processed: 77 average time/residue: 0.1412 time to fit residues: 14.9552 Evaluate side-chains 76 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain H residue 86 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 5.9990 chunk 96 optimal weight: 30.0000 chunk 85 optimal weight: 40.0000 chunk 80 optimal weight: 20.0000 chunk 48 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 94 optimal weight: 20.0000 chunk 4 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN E 77 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.159887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.106945 restraints weight = 14658.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.104881 restraints weight = 25200.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.105783 restraints weight = 22943.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.106083 restraints weight = 18199.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.106342 restraints weight = 18620.530| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12721 Z= 0.151 Angle : 0.592 6.298 18424 Z= 0.345 Chirality : 0.043 0.199 2107 Planarity : 0.004 0.039 1323 Dihedral : 31.259 113.072 4005 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.41 % Allowed : 12.38 % Favored : 86.21 % 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 are not related in a simple way. whole: 2.82 (0.30), residues: 738 helix: 2.78 (0.21), residues: 550 sheet: None (None), residues: 0 loop : -1.07 (0.40), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 23 TYR 0.009 0.001 TYR G 57 PHE 0.009 0.001 PHE E 68 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 (12721) covalent geometry : angle 0.59179 / 0.34 (18424) hydrogen bonds : bond 0.05213 / 3.30 ( 785) hydrogen bonds : angle 2.68099 / 1.97 ( 1963) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.336 Fit side-chains REVERT: A 77 GLN cc_start: 0.7917 (tm-30) cc_final: 0.7572 (tm-30) REVERT: B 91 LYS cc_start: 0.8502 (tttp) cc_final: 0.8135 (ttmm) REVERT: C 45 SER cc_start: 0.8946 (m) cc_final: 0.8733 (p) REVERT: D 46 TYR cc_start: 0.8199 (t80) cc_final: 0.7365 (t80) REVERT: D 63 MET cc_start: 0.8955 (tpp) cc_final: 0.8624 (tpp) REVERT: D 89 LYS cc_start: 0.8415 (mmmt) cc_final: 0.7954 (mttm) REVERT: G 36 ARG cc_start: 0.7226 (tpp80) cc_final: 0.6731 (mmt90) REVERT: G 83 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8692 (mt) REVERT: H 38 LYS cc_start: 0.7781 (tppt) cc_final: 0.7323 (mtpt) outliers start: 9 outliers final: 8 residues processed: 75 average time/residue: 0.1251 time to fit residues: 13.4190 Evaluate side-chains 75 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain H residue 86 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 27 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 77 optimal weight: 30.0000 chunk 39 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 63 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 86 optimal weight: 50.0000 chunk 20 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN E 77 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.162309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.109463 restraints weight = 14593.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.107834 restraints weight = 21363.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.108843 restraints weight = 22060.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.108904 restraints weight = 18169.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.109017 restraints weight = 16723.763| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12721 Z= 0.124 Angle : 0.555 7.078 18424 Z= 0.332 Chirality : 0.040 0.204 2107 Planarity : 0.004 0.038 1323 Dihedral : 31.115 113.983 4005 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.94 % Allowed : 12.70 % Favored : 86.36 % 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 are not related in a simple way. whole: 3.17 (0.30), residues: 738 helix: 3.04 (0.21), residues: 549 sheet: None (None), residues: 0 loop : -0.92 (0.40), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 120 TYR 0.008 0.001 TYR H 41 PHE 0.007 0.001 PHE E 68 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.12 (12721) covalent geometry : angle 0.55475 / 0.33 (18424) hydrogen bonds : bond 0.04661 / 2.93 ( 785) hydrogen bonds : angle 2.58004 / 1.90 ( 1963) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.254 Fit side-chains REVERT: A 77 GLN cc_start: 0.7891 (tm-30) cc_final: 0.7570 (tm-30) REVERT: B 91 LYS cc_start: 0.8466 (tttp) cc_final: 0.8123 (ttmm) REVERT: D 46 TYR cc_start: 0.8120 (t80) cc_final: 0.7260 (t80) REVERT: D 89 LYS cc_start: 0.8476 (mmmt) cc_final: 0.7916 (mttm) REVERT: G 36 ARG cc_start: 0.7090 (tpp80) cc_final: 0.6627 (mmt90) REVERT: G 83 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8643 (mt) REVERT: H 38 LYS cc_start: 0.7843 (tppt) cc_final: 0.7408 (mtpt) outliers start: 6 outliers final: 5 residues processed: 75 average time/residue: 0.1304 time to fit residues: 13.8120 Evaluate side-chains 74 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain G residue 83 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 94 optimal weight: 20.0000 chunk 49 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 48 optimal weight: 0.9980 chunk 84 optimal weight: 30.0000 chunk 65 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN E 77 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.162118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.109683 restraints weight = 14746.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.107902 restraints weight = 21840.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.108901 restraints weight = 22149.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.109098 restraints weight = 18006.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.109206 restraints weight = 16743.744| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12721 Z= 0.122 Angle : 0.553 7.428 18424 Z= 0.330 Chirality : 0.040 0.204 2107 Planarity : 0.004 0.038 1323 Dihedral : 31.131 113.828 4005 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.94 % Allowed : 13.01 % Favored : 86.05 % 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 are not related in a simple way. whole: 3.26 (0.30), residues: 738 helix: 3.10 (0.21), residues: 550 sheet: None (None), residues: 0 loop : -0.89 (0.40), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 120 TYR 0.008 0.001 TYR G 57 PHE 0.007 0.001 PHE E 68 HIS 0.003 0.000 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.12 (12721) covalent geometry : angle 0.55329 / 0.33 (18424) hydrogen bonds : bond 0.04685 / 2.95 ( 785) hydrogen bonds : angle 2.56436 / 1.89 ( 1963) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1611.28 seconds wall clock time: 28 minutes 43.25 seconds (1723.25 seconds total)