Starting phenix.real_space_refine on Sat Oct 24 02:51:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10gk_75153/10_2026/10gk_75153.cif Found real_map, /net/cci-nas-00/data/ceres_data/10gk_75153/10_2026/10gk_75153.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/10gk_75153/10_2026/10gk_75153.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10gk_75153/10_2026/10gk_75153.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/10gk_75153/10_2026/10gk_75153.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10gk_75153/10_2026/10gk_75153.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 294 5.49 5 S 10 5.16 5 C 6639 2.51 5 N 2255 2.21 5 O 2821 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12019 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 805 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "B" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 832 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 789 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} 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: 2997 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 147, 2997 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "J" Number of atoms: 3033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3033 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" P B8OG I 34 " occ=0.96 ... (21 atoms not shown) pdb=" O8 B8OG I 34 " occ=0.96 Time building chain proxies: 2.45, per 1000 atoms: 0.20 Number of scatterers: 12019 At special positions: 0 Unit cell: (75.648, 115.048, 120.958, 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 10 16.00 P 294 15.00 O 2821 8.00 N 2255 7.00 C 6639 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 476.6 milliseconds 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 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: 35 helices and 9 sheets defined 72.2% alpha, 2.6% beta 146 base pairs and 260 stacking pairs defined. Time for finding SS restraints: 2.14 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 4.105A pdb=" N GLU A 50 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ARG A 53 " --> pdb=" O ARG A 49 " (cutoff:3.500A) 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 removed outlier: 3.552A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.501A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 36 removed outlier: 3.740A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.365A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) 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 47 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 removed outlier: 3.729A pdb=" N LYS D 116 " --> pdb=" O SER D 112 " (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: 3.746A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 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: 4.432A pdb=" N VAL G 49 " --> pdb=" O ALA 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 '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 124 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.069A 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 removed outlier: 6.705A 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: 7.312A 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 'E' and resid 83 through 84 removed outlier: 7.265A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.076A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 398 hydrogen bonds defined for protein. 1173 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 373 hydrogen bonds 746 hydrogen bond angles 0 basepair planarities 146 basepair parallelities 260 stacking parallelities Total time for adding SS restraints: 2.17 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: 1.21 - 1.33: 2500 1.33 - 1.45: 4168 1.45 - 1.57: 5560 1.57 - 1.69: 585 1.69 - 1.82: 20 Bond restraints: 12833 Sorted by residual: bond pdb=" P B8OG I 34 " pdb=" O5'B8OG I 34 " ideal model delta sigma weight residual 1.708 1.562 0.146 2.00e-02 2.50e+03 5.31e+01 bond pdb=" P B8OG I 34 " pdb=" OP2B8OG I 34 " ideal model delta sigma weight residual 1.545 1.459 0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" N LEU A 61 " pdb=" CA LEU A 61 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.29e-02 6.01e+03 1.05e+01 bond pdb=" C3' DC J 81 " pdb=" O3' DC J 81 " ideal model delta sigma weight residual 1.435 1.395 0.040 1.30e-02 5.92e+03 9.40e+00 bond pdb=" N LEU B 22 " pdb=" CA LEU B 22 " ideal model delta sigma weight residual 1.457 1.497 -0.039 1.29e-02 6.01e+03 9.30e+00 ... (remaining 12828 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 17421 2.00 - 4.00: 1073 4.00 - 5.99: 78 5.99 - 7.99: 20 7.99 - 9.99: 2 Bond angle restraints: 18594 Sorted by residual: angle pdb=" N SER C 18 " pdb=" CA SER C 18 " pdb=" C SER C 18 " ideal model delta sigma weight residual 111.71 117.44 -5.73 1.15e+00 7.56e-01 2.49e+01 angle pdb=" CA ASP F 24 " pdb=" CB ASP F 24 " pdb=" CG ASP F 24 " ideal model delta sigma weight residual 112.60 117.57 -4.97 1.00e+00 1.00e+00 2.47e+01 angle pdb=" N ARG A 49 " pdb=" CA ARG A 49 " pdb=" C ARG A 49 " ideal model delta sigma weight residual 110.35 103.57 6.78 1.38e+00 5.25e-01 2.42e+01 angle pdb=" CA ARG A 49 " pdb=" C ARG A 49 " pdb=" O ARG A 49 " ideal model delta sigma weight residual 121.88 116.66 5.22 1.13e+00 7.83e-01 2.13e+01 angle pdb=" N3 DT J 83 " pdb=" C4 DT J 83 " pdb=" O4 DT J 83 " ideal model delta sigma weight residual 119.90 122.67 -2.77 6.00e-01 2.78e+00 2.13e+01 ... (remaining 18589 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.08: 5122 29.08 - 58.16: 1746 58.16 - 87.25: 102 87.25 - 116.33: 1 116.33 - 145.41: 5 Dihedral angle restraints: 6976 sinusoidal: 4786 harmonic: 2190 Sorted by residual: dihedral pdb=" CD ARG B 95 " pdb=" NE ARG B 95 " pdb=" CZ ARG B 95 " pdb=" NH1 ARG B 95 " ideal model delta sinusoidal sigma weight residual 0.00 84.62 -84.62 1 1.00e+01 1.00e-02 8.70e+01 dihedral pdb=" CD ARG A 134 " pdb=" NE ARG A 134 " pdb=" CZ ARG A 134 " pdb=" NH1 ARG A 134 " ideal model delta sinusoidal sigma weight residual 0.00 50.10 -50.10 1 1.00e+01 1.00e-02 3.44e+01 dihedral pdb=" CD ARG C 81 " pdb=" NE ARG C 81 " pdb=" CZ ARG C 81 " pdb=" NH1 ARG C 81 " ideal model delta sinusoidal sigma weight residual 0.00 -48.14 48.14 1 1.00e+01 1.00e-02 3.19e+01 ... (remaining 6973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 2003 0.110 - 0.220: 100 0.220 - 0.330: 11 0.330 - 0.440: 1 0.440 - 0.549: 2 Chirality restraints: 2117 Sorted by residual: chirality pdb=" P DT J 128 " pdb=" OP1 DT J 128 " pdb=" OP2 DT J 128 " pdb=" O5' DT J 128 " both_signs ideal model delta sigma weight residual True 2.34 -2.88 -0.55 2.00e-01 2.50e+01 7.55e+00 chirality pdb=" CG LEU E 60 " pdb=" CB LEU E 60 " pdb=" CD1 LEU E 60 " pdb=" CD2 LEU E 60 " both_signs ideal model delta sigma weight residual False -2.59 -2.07 -0.52 2.00e-01 2.50e+01 6.65e+00 chirality pdb=" CA ASP F 24 " pdb=" N ASP F 24 " pdb=" C ASP F 24 " pdb=" CB ASP F 24 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.21e+00 ... (remaining 2114 not shown) Planarity restraints: 1331 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 95 " 1.096 9.50e-02 1.11e+02 4.91e-01 1.46e+02 pdb=" NE ARG B 95 " -0.067 2.00e-02 2.50e+03 pdb=" CZ ARG B 95 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG B 95 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG B 95 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 134 " -0.845 9.50e-02 1.11e+02 3.79e-01 8.72e+01 pdb=" NE ARG A 134 " 0.050 2.00e-02 2.50e+03 pdb=" CZ ARG A 134 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 134 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 134 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 81 " 0.825 9.50e-02 1.11e+02 3.70e-01 8.31e+01 pdb=" NE ARG C 81 " -0.049 2.00e-02 2.50e+03 pdb=" CZ ARG C 81 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG C 81 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 81 " 0.024 2.00e-02 2.50e+03 ... (remaining 1328 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3033 2.83 - 3.34: 10161 3.34 - 3.86: 24823 3.86 - 4.38: 28457 4.38 - 4.90: 39270 Nonbonded interactions: 105744 Sorted by model distance: nonbonded pdb=" OD2 ASP D 68 " pdb=" OH TYR F 98 " model vdw 2.308 3.040 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 68 " model vdw 2.343 3.040 nonbonded pdb=" NH1 ARG C 32 " pdb=" OP1 DA I 30 " model vdw 2.347 3.120 nonbonded pdb=" OG SER E 57 " pdb=" OE1 GLU E 59 " model vdw 2.347 3.040 nonbonded pdb=" OH TYR A 99 " pdb=" OE1 GLU A 133 " model vdw 2.358 3.040 ... (remaining 105739 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 133) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 11 through 117) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 33 through 124) 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=0.96 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: 21.630 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: 0.710 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.820 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:8.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 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 : 0.008 0.146 12833 Z= 0.627 Angle : 0.964 9.990 18594 Z= 0.788 Chirality : 0.059 0.549 2117 Planarity : 0.026 0.491 1331 Dihedral : 28.496 145.412 5564 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 14.99 % Favored : 85.01 % Cbeta Deviations : 0.14 % 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: 0.63 (0.29), residues: 740 helix: 0.95 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -0.88 (0.38), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 42 TYR 0.014 0.002 TYR H 40 PHE 0.010 0.002 PHE G 25 HIS 0.004 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00785 / 0.63 (12833) covalent geometry : angle 0.96377 / 0.79 (18594) hydrogen bonds : bond 0.11393 / 7.54 ( 771) hydrogen bonds : angle 3.92232 / 2.76 ( 1919) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.377 Fit side-chains REVERT: A 59 GLU cc_start: 0.7661 (pm20) cc_final: 0.7319 (pm20) REVERT: A 129 ARG cc_start: 0.8488 (tpt90) cc_final: 0.8243 (tpt90) REVERT: B 74 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8519 (mm-30) REVERT: C 76 THR cc_start: 0.8965 (m) cc_final: 0.8668 (p) REVERT: D 85 LYS cc_start: 0.9483 (mppt) cc_final: 0.9266 (mttm) REVERT: E 60 LEU cc_start: 0.8206 (mp) cc_final: 0.7765 (mt) REVERT: F 79 LYS cc_start: 0.8394 (mttm) cc_final: 0.8079 (mttt) REVERT: F 91 LYS cc_start: 0.9055 (tttp) cc_final: 0.8818 (ttmt) REVERT: G 73 ASN cc_start: 0.9115 (t0) cc_final: 0.8898 (m-40) REVERT: G 74 LYS cc_start: 0.9190 (mtmm) cc_final: 0.8933 (mtmm) REVERT: H 68 ASP cc_start: 0.9075 (t0) cc_final: 0.8664 (t0) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.7914 time to fit residues: 152.0495 Evaluate side-chains 168 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [49, 97, 53, 5, 33, 65, 62, 51, 38, 61, 45] chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN C 24 GLN C 73 ASN D 84 ASN H 63 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.102409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.065876 restraints weight = 21955.565| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.62 r_work: 0.2794 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2818 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2818 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12833 Z= 0.157 Angle : 0.666 7.177 18594 Z= 0.389 Chirality : 0.044 0.223 2117 Planarity : 0.005 0.079 1331 Dihedral : 30.993 145.648 4073 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.91 % Allowed : 16.91 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.96 (0.30), residues: 740 helix: 2.00 (0.22), residues: 551 sheet: None (None), residues: 0 loop : -0.82 (0.40), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 134 TYR 0.015 0.001 TYR F 51 PHE 0.011 0.001 PHE E 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.16 (12833) covalent geometry : angle 0.66599 / 0.39 (18594) hydrogen bonds : bond 0.04385 / 2.99 ( 771) hydrogen bonds : angle 3.12632 / 2.18 ( 1919) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 172 time to evaluate : 0.347 Fit side-chains REVERT: A 59 GLU cc_start: 0.7563 (pm20) cc_final: 0.7298 (pm20) REVERT: A 129 ARG cc_start: 0.8525 (tpt90) cc_final: 0.8324 (tpt90) REVERT: B 74 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8528 (mm-30) REVERT: D 68 ASP cc_start: 0.8985 (t0) cc_final: 0.8770 (t0) REVERT: D 85 LYS cc_start: 0.9466 (OUTLIER) cc_final: 0.9224 (mttm) REVERT: E 59 GLU cc_start: 0.8143 (pm20) cc_final: 0.7801 (pm20) REVERT: E 64 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.7959 (mmtp) REVERT: F 79 LYS cc_start: 0.8347 (mttm) cc_final: 0.8058 (mttt) REVERT: F 91 LYS cc_start: 0.9014 (tttp) cc_final: 0.8787 (ttmt) REVERT: G 73 ASN cc_start: 0.9008 (t0) cc_final: 0.8790 (m-40) REVERT: G 74 LYS cc_start: 0.9202 (mtmm) cc_final: 0.8965 (mtmm) REVERT: H 68 ASP cc_start: 0.8927 (t0) cc_final: 0.8663 (t0) outliers start: 12 outliers final: 5 residues processed: 176 average time/residue: 0.8050 time to fit residues: 149.5126 Evaluate side-chains 171 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 164 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain H residue 71 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [76, 43, 18, 58, 13, 98, 94, 89, 95, 87, 79] chunk 76 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 98 optimal weight: 20.0000 chunk 94 optimal weight: 10.0000 chunk 89 optimal weight: 20.0000 chunk 95 optimal weight: 10.0000 chunk 87 optimal weight: 40.0000 chunk 79 optimal weight: 10.0000 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN F 75 HIS G 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.099429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.062480 restraints weight = 22073.094| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 1.65 r_work: 0.2706 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2726 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2726 r_free = 0.2726 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2726 r_free = 0.2726 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2726 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 12833 Z= 0.337 Angle : 0.725 7.253 18594 Z= 0.404 Chirality : 0.049 0.258 2117 Planarity : 0.005 0.051 1331 Dihedral : 31.476 146.084 4073 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.71 % Allowed : 17.07 % Favored : 80.22 % 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: 2.06 (0.31), residues: 740 helix: 2.12 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.88 (0.39), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 40 TYR 0.015 0.002 TYR E 54 PHE 0.015 0.002 PHE E 67 HIS 0.004 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00732 / 0.34 (12833) covalent geometry : angle 0.72495 / 0.40 (18594) hydrogen bonds : bond 0.05305 / 3.66 ( 771) hydrogen bonds : angle 2.96833 / 2.07 ( 1919) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 165 time to evaluate : 0.293 Fit side-chains REVERT: A 120 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8178 (mtm) REVERT: D 85 LYS cc_start: 0.9429 (mppt) cc_final: 0.9148 (mttm) REVERT: D 93 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8124 (mp0) REVERT: E 64 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.7948 (mmtp) REVERT: F 91 LYS cc_start: 0.8991 (tttp) cc_final: 0.8740 (ttmt) REVERT: G 73 ASN cc_start: 0.8982 (t0) cc_final: 0.8745 (m-40) REVERT: H 68 ASP cc_start: 0.8944 (t0) cc_final: 0.8737 (t0) outliers start: 17 outliers final: 6 residues processed: 170 average time/residue: 0.8081 time to fit residues: 144.9732 Evaluate side-chains 168 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 159 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain H residue 39 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [15, 41, 8, 37, 1, 50, 10, 70, 74, 64, 5] chunk 15 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 74 optimal weight: 20.0000 chunk 64 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN C 73 ASN D 63 ASN G 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.101209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.064164 restraints weight = 22042.801| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.67 r_work: 0.2761 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2777 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2777 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 12833 Z= 0.142 Angle : 0.645 7.045 18594 Z= 0.371 Chirality : 0.045 0.284 2117 Planarity : 0.004 0.043 1331 Dihedral : 31.444 147.422 4073 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.23 % Allowed : 19.46 % Favored : 78.31 % 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: 2.36 (0.31), residues: 740 helix: 2.33 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.73 (0.40), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 71 TYR 0.010 0.001 TYR D 40 PHE 0.009 0.001 PHE A 67 HIS 0.002 0.000 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.14 (12833) covalent geometry : angle 0.64500 / 0.37 (18594) hydrogen bonds : bond 0.03824 / 2.61 ( 771) hydrogen bonds : angle 2.81482 / 1.97 ( 1919) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 168 time to evaluate : 0.262 Fit side-chains REVERT: A 59 GLU cc_start: 0.7726 (pm20) cc_final: 0.7351 (pm20) REVERT: D 35 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7856 (mt-10) REVERT: D 68 ASP cc_start: 0.8938 (t0) cc_final: 0.8729 (t0) REVERT: D 85 LYS cc_start: 0.9426 (mppt) cc_final: 0.9162 (mttm) REVERT: D 93 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8123 (mp0) REVERT: E 59 GLU cc_start: 0.8140 (pm20) cc_final: 0.7781 (pm20) REVERT: E 64 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.7947 (mmtp) REVERT: F 79 LYS cc_start: 0.8210 (mttm) cc_final: 0.7894 (mttt) REVERT: F 91 LYS cc_start: 0.8969 (tttp) cc_final: 0.8721 (ttmt) REVERT: F 92 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8290 (ttp80) REVERT: G 73 ASN cc_start: 0.8982 (t0) cc_final: 0.8717 (m-40) REVERT: H 68 ASP cc_start: 0.8904 (t0) cc_final: 0.8586 (t0) outliers start: 14 outliers final: 6 residues processed: 175 average time/residue: 0.7793 time to fit residues: 144.3751 Evaluate side-chains 173 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 163 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain H residue 39 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [87, 77, 8, 49, 16, 57, 84, 70, 19, 18, 82] chunk 87 optimal weight: 40.0000 chunk 77 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 84 optimal weight: 20.0000 chunk 70 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.099836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.062755 restraints weight = 21964.720| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 1.64 r_work: 0.2732 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2757 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2757 r_free = 0.2757 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2757 r_free = 0.2757 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2757 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12833 Z= 0.225 Angle : 0.660 7.219 18594 Z= 0.374 Chirality : 0.045 0.288 2117 Planarity : 0.004 0.045 1331 Dihedral : 31.486 145.134 4073 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.39 % Allowed : 19.46 % Favored : 78.15 % 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: 2.43 (0.31), residues: 740 helix: 2.40 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.78 (0.40), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 71 TYR 0.011 0.002 TYR D 40 PHE 0.013 0.002 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.22 (12833) covalent geometry : angle 0.66043 / 0.37 (18594) hydrogen bonds : bond 0.04362 / 3.00 ( 771) hydrogen bonds : angle 2.76770 / 1.93 ( 1919) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 165 time to evaluate : 0.244 Fit side-chains REVERT: A 59 GLU cc_start: 0.7991 (pm20) cc_final: 0.7603 (pm20) REVERT: A 120 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8159 (mtm) REVERT: C 74 LYS cc_start: 0.9415 (OUTLIER) cc_final: 0.9111 (mtmm) REVERT: D 35 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7885 (mt-10) REVERT: D 85 LYS cc_start: 0.9426 (mppt) cc_final: 0.9186 (mttm) REVERT: D 93 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8107 (mp0) REVERT: E 59 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7839 (pm20) REVERT: E 64 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.7925 (mmtp) REVERT: F 91 LYS cc_start: 0.9008 (tttp) cc_final: 0.8769 (ttmt) REVERT: F 92 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.8355 (ttp80) REVERT: G 73 ASN cc_start: 0.9024 (t0) cc_final: 0.8757 (m-40) REVERT: G 76 THR cc_start: 0.9020 (p) cc_final: 0.8724 (t) REVERT: H 68 ASP cc_start: 0.8934 (t0) cc_final: 0.8631 (t0) outliers start: 15 outliers final: 8 residues processed: 169 average time/residue: 0.7933 time to fit residues: 141.7829 Evaluate side-chains 178 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 163 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain H residue 39 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [68, 49, 85, 14, 10, 84, 8, 6, 65, 5, 7] chunk 68 optimal weight: 0.2980 chunk 49 optimal weight: 2.9990 chunk 85 optimal weight: 40.0000 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 84 optimal weight: 20.0000 chunk 8 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.101058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.064247 restraints weight = 22035.635| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.65 r_work: 0.2755 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2780 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2780 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 12833 Z= 0.139 Angle : 0.640 7.463 18594 Z= 0.367 Chirality : 0.044 0.290 2117 Planarity : 0.004 0.043 1331 Dihedral : 31.480 145.666 4073 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.35 % Allowed : 18.34 % Favored : 78.31 % 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: 2.60 (0.31), residues: 740 helix: 2.52 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.69 (0.41), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 71 TYR 0.013 0.001 TYR D 40 PHE 0.011 0.001 PHE E 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.14 (12833) covalent geometry : angle 0.64045 / 0.37 (18594) hydrogen bonds : bond 0.03913 / 2.68 ( 771) hydrogen bonds : angle 2.72186 / 1.91 ( 1919) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 170 time to evaluate : 0.325 Fit side-chains REVERT: A 59 GLU cc_start: 0.7860 (pm20) cc_final: 0.7453 (pm20) REVERT: A 122 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8115 (pttp) REVERT: C 74 LYS cc_start: 0.9401 (OUTLIER) cc_final: 0.9101 (mtmm) REVERT: D 35 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7849 (mt-10) REVERT: D 71 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8100 (tm-30) REVERT: D 85 LYS cc_start: 0.9418 (mppt) cc_final: 0.9184 (mttm) REVERT: D 93 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8064 (mp0) REVERT: E 59 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7716 (pm20) REVERT: F 79 LYS cc_start: 0.8228 (mttm) cc_final: 0.7905 (mttt) REVERT: F 91 LYS cc_start: 0.8982 (tttp) cc_final: 0.8740 (ttmt) REVERT: F 92 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.8281 (ttp80) REVERT: G 73 ASN cc_start: 0.9002 (t0) cc_final: 0.8728 (m-40) REVERT: G 76 THR cc_start: 0.8986 (p) cc_final: 0.8697 (t) REVERT: G 95 LYS cc_start: 0.9324 (OUTLIER) cc_final: 0.8861 (tptp) REVERT: H 68 ASP cc_start: 0.8901 (t0) cc_final: 0.8567 (t0) outliers start: 21 outliers final: 7 residues processed: 178 average time/residue: 0.7779 time to fit residues: 146.5766 Evaluate side-chains 181 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 167 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 39 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [11, 79, 60, 13, 94, 80, 46, 92, 19, 76, 99] chunk 11 optimal weight: 4.9990 chunk 79 optimal weight: 10.0000 chunk 60 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 94 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 46 optimal weight: 0.7980 chunk 92 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 76 optimal weight: 20.0000 chunk 99 optimal weight: 30.0000 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN G 104 GLN H 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.099855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.062870 restraints weight = 21976.218| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 1.65 r_work: 0.2731 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2760 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2760 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12833 Z= 0.211 Angle : 0.652 7.224 18594 Z= 0.371 Chirality : 0.045 0.302 2117 Planarity : 0.004 0.044 1331 Dihedral : 31.499 144.942 4073 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.39 % Allowed : 18.98 % Favored : 78.63 % 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: 2.55 (0.31), residues: 740 helix: 2.48 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.70 (0.41), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 42 TYR 0.011 0.001 TYR C 57 PHE 0.012 0.002 PHE E 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.21 (12833) covalent geometry : angle 0.65244 / 0.37 (18594) hydrogen bonds : bond 0.04186 / 2.87 ( 771) hydrogen bonds : angle 2.72523 / 1.90 ( 1919) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 164 time to evaluate : 0.329 Fit side-chains REVERT: A 59 GLU cc_start: 0.7961 (pm20) cc_final: 0.7612 (pm20) REVERT: A 122 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8176 (pttp) REVERT: D 35 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7871 (mt-10) REVERT: D 85 LYS cc_start: 0.9419 (mppt) cc_final: 0.9181 (mttm) REVERT: D 105 GLU cc_start: 0.8518 (tp30) cc_final: 0.8308 (mm-30) REVERT: F 79 LYS cc_start: 0.8294 (mttm) cc_final: 0.7975 (mttt) REVERT: F 91 LYS cc_start: 0.9004 (tttp) cc_final: 0.8773 (ttmt) REVERT: F 92 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8370 (ttp80) REVERT: G 76 THR cc_start: 0.8999 (p) cc_final: 0.8723 (t) REVERT: H 68 ASP cc_start: 0.8915 (t0) cc_final: 0.8614 (t0) outliers start: 15 outliers final: 7 residues processed: 169 average time/residue: 0.7915 time to fit residues: 141.3760 Evaluate side-chains 170 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 160 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain H residue 39 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [52, 77, 85, 79, 56, 64, 21, 81, 31, 4, 71] chunk 52 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 85 optimal weight: 40.0000 chunk 79 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 81 optimal weight: 20.0000 chunk 31 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.100668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.064054 restraints weight = 21985.109| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.62 r_work: 0.2752 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2763 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2763 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12833 Z= 0.168 Angle : 0.647 7.354 18594 Z= 0.368 Chirality : 0.044 0.305 2117 Planarity : 0.004 0.043 1331 Dihedral : 31.502 144.941 4073 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.07 % Allowed : 19.94 % Favored : 77.99 % 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: 2.63 (0.31), residues: 740 helix: 2.53 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.67 (0.41), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 71 TYR 0.011 0.001 TYR D 40 PHE 0.011 0.001 PHE E 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.17 (12833) covalent geometry : angle 0.64653 / 0.37 (18594) hydrogen bonds : bond 0.03943 / 2.70 ( 771) hydrogen bonds : angle 2.70370 / 1.89 ( 1919) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 162 time to evaluate : 0.262 Fit side-chains REVERT: A 59 GLU cc_start: 0.7924 (pm20) cc_final: 0.7593 (pm20) REVERT: A 122 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8134 (pttp) REVERT: D 35 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7858 (mt-10) REVERT: D 85 LYS cc_start: 0.9416 (mppt) cc_final: 0.9177 (mttm) REVERT: E 59 GLU cc_start: 0.8128 (pm20) cc_final: 0.7683 (pm20) REVERT: F 79 LYS cc_start: 0.8266 (mttm) cc_final: 0.7945 (mttt) REVERT: F 91 LYS cc_start: 0.8991 (tttp) cc_final: 0.8758 (ttmt) REVERT: F 92 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8351 (ttp80) REVERT: G 76 THR cc_start: 0.8983 (p) cc_final: 0.8710 (t) REVERT: H 68 ASP cc_start: 0.8889 (t0) cc_final: 0.8601 (t0) outliers start: 13 outliers final: 7 residues processed: 167 average time/residue: 0.8008 time to fit residues: 141.2543 Evaluate side-chains 171 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 161 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain H residue 39 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [23, 22, 18, 61, 37, 10, 99, 79, 55, 62, 40] chunk 23 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 99 optimal weight: 20.0000 chunk 79 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.101156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.064552 restraints weight = 21861.842| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.62 r_work: 0.2759 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2770 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2770 r_free = 0.2770 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2770 r_free = 0.2770 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2770 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12833 Z= 0.150 Angle : 0.636 7.191 18594 Z= 0.364 Chirality : 0.044 0.307 2117 Planarity : 0.004 0.043 1331 Dihedral : 31.484 144.911 4073 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.75 % Allowed : 20.26 % Favored : 77.99 % 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: 2.68 (0.31), residues: 740 helix: 2.58 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.66 (0.41), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 71 TYR 0.015 0.001 TYR B 88 PHE 0.010 0.001 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.15 (12833) covalent geometry : angle 0.63633 / 0.36 (18594) hydrogen bonds : bond 0.03810 / 2.61 ( 771) hydrogen bonds : angle 2.68395 / 1.87 ( 1919) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 163 time to evaluate : 0.336 Fit side-chains REVERT: A 59 GLU cc_start: 0.7919 (pm20) cc_final: 0.7564 (pm20) REVERT: A 122 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8125 (pttp) REVERT: D 35 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7847 (mt-10) REVERT: D 85 LYS cc_start: 0.9415 (mppt) cc_final: 0.9177 (mttm) REVERT: D 93 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.7924 (mp0) REVERT: E 59 GLU cc_start: 0.8116 (pm20) cc_final: 0.7686 (pm20) REVERT: F 79 LYS cc_start: 0.8255 (mttm) cc_final: 0.7936 (mttt) REVERT: F 91 LYS cc_start: 0.8990 (tttp) cc_final: 0.8760 (ttmt) REVERT: F 92 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8312 (ttp80) REVERT: G 76 THR cc_start: 0.8979 (p) cc_final: 0.8708 (t) REVERT: H 68 ASP cc_start: 0.8875 (t0) cc_final: 0.8551 (t0) outliers start: 11 outliers final: 7 residues processed: 167 average time/residue: 0.7972 time to fit residues: 140.4518 Evaluate side-chains 174 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 163 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain H residue 39 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [20, 78, 67, 55, 97, 92, 6, 15, 23, 87, 29] chunk 20 optimal weight: 0.0970 chunk 78 optimal weight: 10.0000 chunk 67 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 6 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 87 optimal weight: 40.0000 chunk 29 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.101188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.064619 restraints weight = 22044.332| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 1.64 r_work: 0.2714 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2780 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2780 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.080 12833 Z= 0.139 Angle : 0.639 8.079 18594 Z= 0.365 Chirality : 0.043 0.308 2117 Planarity : 0.004 0.042 1331 Dihedral : 31.466 144.904 4073 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.44 % Allowed : 20.41 % Favored : 78.15 % 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: 2.72 (0.31), residues: 740 helix: 2.60 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.65 (0.41), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 71 TYR 0.015 0.001 TYR B 88 PHE 0.010 0.001 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.14 (12833) covalent geometry : angle 0.63883 / 0.37 (18594) hydrogen bonds : bond 0.03710 / 2.53 ( 771) hydrogen bonds : angle 2.66804 / 1.86 ( 1919) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 163 time to evaluate : 0.358 Fit side-chains REVERT: A 59 GLU cc_start: 0.7926 (pm20) cc_final: 0.7577 (pm20) REVERT: D 85 LYS cc_start: 0.9425 (mppt) cc_final: 0.9190 (mttm) REVERT: D 93 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.7955 (mp0) REVERT: E 59 GLU cc_start: 0.8119 (pm20) cc_final: 0.7702 (pm20) REVERT: F 79 LYS cc_start: 0.8299 (mttm) cc_final: 0.7985 (mttt) REVERT: F 91 LYS cc_start: 0.9019 (tttp) cc_final: 0.8790 (ttmt) REVERT: F 92 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.8309 (ttp80) REVERT: G 76 THR cc_start: 0.8989 (p) cc_final: 0.8723 (t) REVERT: H 68 ASP cc_start: 0.8883 (t0) cc_final: 0.8611 (t0) outliers start: 9 outliers final: 5 residues processed: 167 average time/residue: 0.7987 time to fit residues: 140.8234 Evaluate side-chains 169 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 162 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain H residue 39 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [94, 49, 53, 14, 20, 30, 89, 58, 41, 17, 10] chunk 94 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.101266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.064662 restraints weight = 21974.197| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 1.63 r_work: 0.2761 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2775 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2775 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12833 Z= 0.174 Angle : 0.629 7.091 18594 Z= 0.361 Chirality : 0.044 0.313 2117 Planarity : 0.004 0.042 1331 Dihedral : 31.427 145.076 4073 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.12 % Allowed : 20.73 % Favored : 78.15 % 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: 2.69 (0.31), residues: 740 helix: 2.59 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.69 (0.41), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 71 TYR 0.011 0.001 TYR D 40 PHE 0.011 0.001 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.17 (12833) covalent geometry : angle 0.62897 / 0.36 (18594) hydrogen bonds : bond 0.03832 / 2.62 ( 771) hydrogen bonds : angle 2.63244 / 1.84 ( 1919) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5224.92 seconds wall clock time: 89 minutes 24.83 seconds (5364.83 seconds total)