Starting phenix.real_space_refine on Tue Feb 3 18:05:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ck4_45640/02_2026/9ck4_45640.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ck4_45640/02_2026/9ck4_45640.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ck4_45640/02_2026/9ck4_45640.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ck4_45640/02_2026/9ck4_45640.map" model { file = "/net/cci-nas-00/data/ceres_data/9ck4_45640/02_2026/9ck4_45640.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ck4_45640/02_2026/9ck4_45640.cif" } resolution = 3.1 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= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 3762 2.51 5 N 1008 2.21 5 O 1148 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5942 Number of models: 1 Model: "" Number of chains: 7 Chain: "W" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 626 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "A" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 940 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "B" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "E" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 940 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "F" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "C" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 940 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "D" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Time building chain proxies: 1.64, per 1000 atoms: 0.28 Number of scatterers: 5942 At special positions: 0 Unit cell: (68.928, 102.674, 108.418, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 1148 8.00 N 1008 7.00 C 3762 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.45 Conformation dependent library (CDL) restraints added in 331.6 milliseconds 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1372 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 19 sheets defined 4.4% alpha, 42.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 52 through 55 removed outlier: 3.648A pdb=" N SER A 55 " --> pdb=" O PHE A 52A" (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 87 removed outlier: 3.671A pdb=" N THR A 87 " --> pdb=" O ALA A 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 55 No H-bonds generated for 'chain 'E' and resid 53 through 55' Processing helix chain 'E' and resid 83 through 87 removed outlier: 3.615A pdb=" N THR E 87 " --> pdb=" O ALA E 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 83 removed outlier: 4.073A pdb=" N VAL F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 76 removed outlier: 3.708A pdb=" N ASN C 76 " --> pdb=" O ASN C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.591A pdb=" N THR C 87 " --> pdb=" O ALA C 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'W' and resid 7 through 12 Processing sheet with id=AA2, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.710A pdb=" N THR A 77 " --> pdb=" O ASP A 72 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.303A pdb=" N GLY A 10 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N MET A 34 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N TYR A 58 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 96 through 98 Processing sheet with id=AA5, first strand: chain 'B' and resid 4 through 6 Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.319A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.797A pdb=" N THR B 97 " --> pdb=" O GLU B 90 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.868A pdb=" N THR E 77 " --> pdb=" O ASP E 72 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.713A pdb=" N MET E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 96 through 97 removed outlier: 3.616A pdb=" N PHE E 96 " --> pdb=" O PHE E 100C" (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 4 through 5 Processing sheet with id=AB3, first strand: chain 'F' and resid 10 through 13 removed outlier: 5.820A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 10 through 13 removed outlier: 5.820A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR F 97 " --> pdb=" O GLU F 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.376A pdb=" N GLY C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N MET C 34 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 18 through 21 Processing sheet with id=AB7, first strand: chain 'C' and resid 96 through 97 Processing sheet with id=AB8, first strand: chain 'D' and resid 5 through 6 Processing sheet with id=AB9, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.512A pdb=" N ALA D 13 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.512A pdb=" N ALA D 13 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR D 97 " --> pdb=" O GLU D 90 " (cutoff:3.500A) 238 hydrogen bonds defined for protein. 561 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.96 Time building geometry restraints manager: 0.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1843 1.34 - 1.46: 1457 1.46 - 1.58: 2748 1.58 - 1.70: 0 1.70 - 1.82: 36 Bond restraints: 6084 Sorted by residual: bond pdb=" C GLN F 79 " pdb=" N PRO F 80 " ideal model delta sigma weight residual 1.336 1.373 -0.037 1.08e-02 8.57e+03 1.17e+01 bond pdb=" CG LEU F 33 " pdb=" CD2 LEU F 33 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.59e+00 bond pdb=" CB VAL E 48 " pdb=" CG2 VAL E 48 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.15e+00 bond pdb=" CA ASP E 53 " pdb=" CB ASP E 53 " ideal model delta sigma weight residual 1.530 1.560 -0.029 1.69e-02 3.50e+03 3.04e+00 bond pdb=" CB PHE C 67 " pdb=" CG PHE C 67 " ideal model delta sigma weight residual 1.502 1.541 -0.039 2.30e-02 1.89e+03 2.94e+00 ... (remaining 6079 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 7840 2.01 - 4.03: 320 4.03 - 6.04: 62 6.04 - 8.06: 14 8.06 - 10.07: 5 Bond angle restraints: 8241 Sorted by residual: angle pdb=" C PHE E 52A" pdb=" N ASP E 53 " pdb=" CA ASP E 53 " ideal model delta sigma weight residual 121.54 131.61 -10.07 1.91e+00 2.74e-01 2.78e+01 angle pdb=" N TYR C 102 " pdb=" CA TYR C 102 " pdb=" C TYR C 102 " ideal model delta sigma weight residual 111.02 116.59 -5.57 1.25e+00 6.40e-01 1.99e+01 angle pdb=" CA ASP D 82 " pdb=" CB ASP D 82 " pdb=" CG ASP D 82 " ideal model delta sigma weight residual 112.60 117.00 -4.40 1.00e+00 1.00e+00 1.94e+01 angle pdb=" N TYR E 102 " pdb=" CA TYR E 102 " pdb=" C TYR E 102 " ideal model delta sigma weight residual 111.24 117.02 -5.78 1.38e+00 5.25e-01 1.75e+01 angle pdb=" C SER F 7 " pdb=" N PRO F 8 " pdb=" CA PRO F 8 " ideal model delta sigma weight residual 119.84 114.78 5.06 1.25e+00 6.40e-01 1.64e+01 ... (remaining 8236 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 3335 17.75 - 35.51: 178 35.51 - 53.26: 37 53.26 - 71.01: 12 71.01 - 88.77: 5 Dihedral angle restraints: 3567 sinusoidal: 1402 harmonic: 2165 Sorted by residual: dihedral pdb=" CB CYS D 23 " pdb=" SG CYS D 23 " pdb=" SG CYS D 88 " pdb=" CB CYS D 88 " ideal model delta sinusoidal sigma weight residual 93.00 158.02 -65.02 1 1.00e+01 1.00e-02 5.55e+01 dihedral pdb=" CA ILE B 29 " pdb=" C ILE B 29 " pdb=" N SER B 30 " pdb=" CA SER B 30 " ideal model delta harmonic sigma weight residual 180.00 155.90 24.10 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA HIS C 35 " pdb=" C HIS C 35 " pdb=" N TRP C 36 " pdb=" CA TRP C 36 " ideal model delta harmonic sigma weight residual 180.00 156.78 23.22 0 5.00e+00 4.00e-02 2.16e+01 ... (remaining 3564 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 616 0.055 - 0.110: 196 0.110 - 0.165: 62 0.165 - 0.220: 7 0.220 - 0.275: 4 Chirality restraints: 885 Sorted by residual: chirality pdb=" CG LEU B 33 " pdb=" CB LEU B 33 " pdb=" CD1 LEU B 33 " pdb=" CD2 LEU B 33 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA ASP E 53 " pdb=" N ASP E 53 " pdb=" C ASP E 53 " pdb=" CB ASP E 53 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB ILE C 69 " pdb=" CA ILE C 69 " pdb=" CG1 ILE C 69 " pdb=" CG2 ILE C 69 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 882 not shown) Planarity restraints: 1052 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 89 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.65e+00 pdb=" CD GLN B 89 " -0.048 2.00e-02 2.50e+03 pdb=" OE1 GLN B 89 " 0.018 2.00e-02 2.50e+03 pdb=" NE2 GLN B 89 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 31 " -0.013 2.00e-02 2.50e+03 2.55e-02 6.50e+00 pdb=" C ARG B 31 " 0.044 2.00e-02 2.50e+03 pdb=" O ARG B 31 " -0.016 2.00e-02 2.50e+03 pdb=" N TRP B 32 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 82 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.89e+00 pdb=" C ASP D 82 " -0.042 2.00e-02 2.50e+03 pdb=" O ASP D 82 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL D 83 " 0.014 2.00e-02 2.50e+03 ... (remaining 1049 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 1448 2.81 - 3.33: 4676 3.33 - 3.85: 10122 3.85 - 4.38: 11829 4.38 - 4.90: 20526 Nonbonded interactions: 48601 Sorted by model distance: nonbonded pdb=" O TYR B 49 " pdb=" OH TYR B 91 " model vdw 2.283 3.040 nonbonded pdb=" OG SER D 63 " pdb=" OG1 THR D 74 " model vdw 2.294 3.040 nonbonded pdb=" NH2 ARG F 31 " pdb=" O PRO C 100B" model vdw 2.328 3.120 nonbonded pdb=" OG SER F 30 " pdb=" OD2 ASP C 98 " model vdw 2.351 3.040 nonbonded pdb=" NE2 GLN F 6 " pdb=" OG1 THR F 102 " model vdw 2.363 3.120 ... (remaining 48596 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 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.860 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.830 Find NCS groups from input model: 0.080 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 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 : 0.006 0.063 6090 Z= 0.255 Angle : 0.992 10.069 8253 Z= 0.562 Chirality : 0.060 0.275 885 Planarity : 0.008 0.056 1052 Dihedral : 12.442 88.768 2177 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.85 % Favored : 93.01 % Rotamer: Outliers : 0.15 % Allowed : 0.31 % Favored : 99.54 % 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: -0.92 (0.31), residues: 744 helix: None (None), residues: 0 sheet: -0.36 (0.26), residues: 389 loop : -0.78 (0.35), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 24 TYR 0.028 0.003 TYR C 97 PHE 0.027 0.004 PHE C 29 TRP 0.025 0.002 TRP A 36 HIS 0.007 0.002 HIS A 93 Details of bonding type rmsd covalent geometry : bond 0.00560 ( 6084) covalent geometry : angle 0.99033 ( 8241) SS BOND : bond 0.00557 ( 6) SS BOND : angle 1.67116 ( 12) hydrogen bonds : bond 0.13200 ( 221) hydrogen bonds : angle 7.81515 ( 561) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.233 Fit side-chains REVERT: B 24 ARG cc_start: 0.7815 (ttm110) cc_final: 0.7582 (ttm110) REVERT: E 97 TYR cc_start: 0.5160 (t80) cc_final: 0.4845 (t80) outliers start: 1 outliers final: 0 residues processed: 104 average time/residue: 0.1025 time to fit residues: 13.1629 Evaluate side-chains 97 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.0170 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.0570 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.0670 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 0.1980 overall best weight: 0.2474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 81 GLN C 95 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.193107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.167671 restraints weight = 6109.297| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 1.57 r_work: 0.3582 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6090 Z= 0.111 Angle : 0.554 5.849 8253 Z= 0.300 Chirality : 0.046 0.157 885 Planarity : 0.005 0.044 1052 Dihedral : 5.013 17.582 831 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.84 % Favored : 95.03 % Rotamer: Outliers : 0.77 % Allowed : 3.86 % Favored : 95.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.31), residues: 744 helix: None (None), residues: 0 sheet: 0.26 (0.28), residues: 336 loop : -0.89 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 24 TYR 0.013 0.001 TYR F 91 PHE 0.013 0.002 PHE C 29 TRP 0.009 0.001 TRP A 36 HIS 0.004 0.001 HIS A 93 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 6084) covalent geometry : angle 0.55308 ( 8241) SS BOND : bond 0.00244 ( 6) SS BOND : angle 1.00020 ( 12) hydrogen bonds : bond 0.03226 ( 221) hydrogen bonds : angle 6.05514 ( 561) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 118 time to evaluate : 0.168 Fit side-chains REVERT: W 28 ILE cc_start: 0.7018 (OUTLIER) cc_final: 0.6506 (tp) REVERT: W 42 ARG cc_start: 0.7629 (mmm160) cc_final: 0.7401 (mmm-85) REVERT: A 18 LEU cc_start: 0.7438 (tp) cc_final: 0.7101 (tt) REVERT: A 43 LYS cc_start: 0.7663 (mmtm) cc_final: 0.7425 (mppt) REVERT: B 9 SER cc_start: 0.8489 (m) cc_final: 0.8075 (p) REVERT: D 42 LYS cc_start: 0.8129 (mttp) cc_final: 0.7905 (mtmt) outliers start: 5 outliers final: 2 residues processed: 119 average time/residue: 0.0963 time to fit residues: 14.2796 Evaluate side-chains 108 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 105 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 28 ILE Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain F residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 54 optimal weight: 0.0070 chunk 51 optimal weight: 0.2980 chunk 7 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 15 optimal weight: 0.0670 chunk 64 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 81 GLN C 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.187562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.165498 restraints weight = 6235.304| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 1.60 r_work: 0.3611 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6090 Z= 0.122 Angle : 0.556 7.047 8253 Z= 0.295 Chirality : 0.047 0.158 885 Planarity : 0.004 0.044 1052 Dihedral : 4.810 16.704 831 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.51 % Favored : 94.35 % Rotamer: Outliers : 1.39 % Allowed : 6.02 % Favored : 92.59 % 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: -0.38 (0.32), residues: 744 helix: None (None), residues: 0 sheet: 0.33 (0.28), residues: 335 loop : -0.72 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 24 TYR 0.013 0.001 TYR B 49 PHE 0.020 0.002 PHE A 96 TRP 0.009 0.001 TRP A 36 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 6084) covalent geometry : angle 0.55589 ( 8241) SS BOND : bond 0.00309 ( 6) SS BOND : angle 0.84784 ( 12) hydrogen bonds : bond 0.03098 ( 221) hydrogen bonds : angle 5.72915 ( 561) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.140 Fit side-chains REVERT: A 43 LYS cc_start: 0.7738 (mmtm) cc_final: 0.7522 (mppt) REVERT: B 9 SER cc_start: 0.8421 (m) cc_final: 0.8068 (p) REVERT: C 16 ARG cc_start: 0.7261 (mmt-90) cc_final: 0.6359 (ttm-80) outliers start: 9 outliers final: 7 residues processed: 109 average time/residue: 0.1112 time to fit residues: 15.0347 Evaluate side-chains 113 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 79 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 0.0770 chunk 29 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.180882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.155589 restraints weight = 6308.596| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 1.55 r_work: 0.3468 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6090 Z= 0.162 Angle : 0.585 8.894 8253 Z= 0.311 Chirality : 0.048 0.167 885 Planarity : 0.004 0.048 1052 Dihedral : 4.968 17.196 831 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.51 % Favored : 94.35 % Rotamer: Outliers : 1.85 % Allowed : 7.87 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.37 (0.32), residues: 744 helix: None (None), residues: 0 sheet: 0.15 (0.28), residues: 349 loop : -0.55 (0.33), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 24 TYR 0.014 0.002 TYR B 49 PHE 0.013 0.002 PHE C 29 TRP 0.009 0.001 TRP A 36 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 6084) covalent geometry : angle 0.58454 ( 8241) SS BOND : bond 0.00463 ( 6) SS BOND : angle 0.79371 ( 12) hydrogen bonds : bond 0.03199 ( 221) hydrogen bonds : angle 5.84898 ( 561) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.244 Fit side-chains REVERT: E 97 TYR cc_start: 0.5506 (t80) cc_final: 0.4979 (t80) outliers start: 12 outliers final: 7 residues processed: 108 average time/residue: 0.0962 time to fit residues: 13.0371 Evaluate side-chains 111 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 79 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 44 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 19 optimal weight: 0.1980 chunk 46 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.178364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.154579 restraints weight = 6425.412| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 1.51 r_work: 0.3472 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6090 Z= 0.177 Angle : 0.608 7.781 8253 Z= 0.322 Chirality : 0.048 0.167 885 Planarity : 0.005 0.052 1052 Dihedral : 5.077 18.539 831 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.18 % Favored : 93.68 % Rotamer: Outliers : 2.01 % Allowed : 9.10 % Favored : 88.89 % 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: -0.48 (0.32), residues: 744 helix: None (None), residues: 0 sheet: -0.01 (0.27), residues: 360 loop : -0.54 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 24 TYR 0.014 0.002 TYR B 49 PHE 0.022 0.002 PHE A 96 TRP 0.010 0.001 TRP A 36 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 6084) covalent geometry : angle 0.60453 ( 8241) SS BOND : bond 0.00314 ( 6) SS BOND : angle 1.76721 ( 12) hydrogen bonds : bond 0.03264 ( 221) hydrogen bonds : angle 5.92191 ( 561) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.204 Fit side-chains REVERT: E 97 TYR cc_start: 0.5348 (t80) cc_final: 0.4841 (t80) REVERT: D 45 LYS cc_start: 0.8582 (tttt) cc_final: 0.8250 (tttp) outliers start: 13 outliers final: 9 residues processed: 109 average time/residue: 0.0991 time to fit residues: 13.5902 Evaluate side-chains 113 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 61 ARG Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain D residue 79 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 26 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 14 optimal weight: 0.1980 chunk 43 optimal weight: 0.3980 chunk 62 optimal weight: 3.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.180112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.156376 restraints weight = 6329.316| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 1.49 r_work: 0.3510 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6090 Z= 0.160 Angle : 0.590 7.565 8253 Z= 0.313 Chirality : 0.047 0.161 885 Planarity : 0.004 0.053 1052 Dihedral : 4.971 17.648 831 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.18 % Favored : 93.68 % Rotamer: Outliers : 2.16 % Allowed : 9.88 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.51 (0.32), residues: 744 helix: None (None), residues: 0 sheet: -0.03 (0.28), residues: 349 loop : -0.54 (0.34), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 24 TYR 0.014 0.002 TYR F 91 PHE 0.011 0.002 PHE C 29 TRP 0.013 0.001 TRP A 36 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 6084) covalent geometry : angle 0.58833 ( 8241) SS BOND : bond 0.00258 ( 6) SS BOND : angle 1.45128 ( 12) hydrogen bonds : bond 0.03130 ( 221) hydrogen bonds : angle 5.88099 ( 561) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.147 Fit side-chains REVERT: E 97 TYR cc_start: 0.5342 (t80) cc_final: 0.4835 (t80) REVERT: C 19 ARG cc_start: 0.6495 (tpp80) cc_final: 0.5803 (ttt-90) REVERT: D 45 LYS cc_start: 0.8570 (tttt) cc_final: 0.8238 (tttp) outliers start: 14 outliers final: 11 residues processed: 114 average time/residue: 0.0930 time to fit residues: 13.3741 Evaluate side-chains 121 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 61 ARG Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 68 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 36 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 20 optimal weight: 8.9990 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.176699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.152829 restraints weight = 6389.285| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 1.53 r_work: 0.3449 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 6090 Z= 0.188 Angle : 0.624 8.274 8253 Z= 0.330 Chirality : 0.048 0.163 885 Planarity : 0.005 0.056 1052 Dihedral : 5.128 18.759 831 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.72 % Favored : 93.15 % Rotamer: Outliers : 2.62 % Allowed : 10.34 % Favored : 87.04 % 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: -0.60 (0.32), residues: 744 helix: None (None), residues: 0 sheet: -0.12 (0.28), residues: 360 loop : -0.59 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 24 TYR 0.014 0.002 TYR F 91 PHE 0.021 0.002 PHE A 96 TRP 0.015 0.002 TRP A 36 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 6084) covalent geometry : angle 0.62228 ( 8241) SS BOND : bond 0.00350 ( 6) SS BOND : angle 1.51108 ( 12) hydrogen bonds : bond 0.03314 ( 221) hydrogen bonds : angle 6.01838 ( 561) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.195 Fit side-chains REVERT: E 97 TYR cc_start: 0.5403 (t80) cc_final: 0.4899 (t80) REVERT: C 19 ARG cc_start: 0.6492 (tpp80) cc_final: 0.5738 (ttt-90) REVERT: D 45 LYS cc_start: 0.8560 (tttt) cc_final: 0.8236 (tttp) outliers start: 17 outliers final: 12 residues processed: 108 average time/residue: 0.0870 time to fit residues: 11.6163 Evaluate side-chains 115 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 61 ARG Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 68 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 44 optimal weight: 0.1980 chunk 18 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 61 optimal weight: 0.0010 chunk 19 optimal weight: 0.0470 chunk 42 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.3284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.180430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.157258 restraints weight = 6363.767| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 1.47 r_work: 0.3589 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6090 Z= 0.119 Angle : 0.562 11.743 8253 Z= 0.293 Chirality : 0.046 0.145 885 Planarity : 0.004 0.048 1052 Dihedral : 4.743 16.728 831 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.32 % Favored : 93.55 % Rotamer: Outliers : 2.01 % Allowed : 11.11 % Favored : 86.88 % 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: -0.40 (0.32), residues: 744 helix: None (None), residues: 0 sheet: 0.02 (0.29), residues: 340 loop : -0.44 (0.33), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 24 TYR 0.013 0.001 TYR F 91 PHE 0.011 0.001 PHE C 29 TRP 0.016 0.001 TRP A 36 HIS 0.003 0.001 HIS A 93 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 6084) covalent geometry : angle 0.56154 ( 8241) SS BOND : bond 0.00154 ( 6) SS BOND : angle 0.92251 ( 12) hydrogen bonds : bond 0.02947 ( 221) hydrogen bonds : angle 5.71017 ( 561) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.156 Fit side-chains REVERT: E 97 TYR cc_start: 0.5315 (t80) cc_final: 0.4804 (t80) REVERT: C 19 ARG cc_start: 0.6238 (tpp80) cc_final: 0.5937 (ttt-90) REVERT: D 42 LYS cc_start: 0.8152 (mtmt) cc_final: 0.7796 (mtmm) REVERT: D 45 LYS cc_start: 0.8549 (tttt) cc_final: 0.8213 (tttp) outliers start: 13 outliers final: 10 residues processed: 111 average time/residue: 0.0839 time to fit residues: 11.6860 Evaluate side-chains 118 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 61 ARG Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 68 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 25 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 2 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 30 optimal weight: 0.0270 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.183392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.160164 restraints weight = 6344.297| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 1.47 r_work: 0.3480 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6090 Z= 0.141 Angle : 0.585 11.180 8253 Z= 0.304 Chirality : 0.047 0.151 885 Planarity : 0.004 0.050 1052 Dihedral : 4.800 16.936 831 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.32 % Favored : 93.55 % Rotamer: Outliers : 1.85 % Allowed : 11.88 % Favored : 86.27 % 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: -0.42 (0.32), residues: 744 helix: None (None), residues: 0 sheet: 0.04 (0.29), residues: 340 loop : -0.49 (0.33), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 24 TYR 0.014 0.002 TYR F 91 PHE 0.028 0.002 PHE A 96 TRP 0.018 0.001 TRP A 36 HIS 0.003 0.001 HIS A 93 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 6084) covalent geometry : angle 0.58389 ( 8241) SS BOND : bond 0.00211 ( 6) SS BOND : angle 0.98065 ( 12) hydrogen bonds : bond 0.03045 ( 221) hydrogen bonds : angle 5.74372 ( 561) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.195 Fit side-chains REVERT: E 97 TYR cc_start: 0.5405 (t80) cc_final: 0.4884 (t80) REVERT: C 19 ARG cc_start: 0.6217 (tpp80) cc_final: 0.5905 (ttt-90) REVERT: D 42 LYS cc_start: 0.8181 (mtmt) cc_final: 0.7823 (mtmm) REVERT: D 45 LYS cc_start: 0.8567 (tttt) cc_final: 0.8234 (tttp) outliers start: 12 outliers final: 11 residues processed: 109 average time/residue: 0.0893 time to fit residues: 12.2059 Evaluate side-chains 117 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 61 ARG Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 68 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 40 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 39 optimal weight: 0.1980 chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 57 optimal weight: 0.2980 chunk 43 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.178795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.152940 restraints weight = 6446.517| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 1.58 r_work: 0.3494 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6090 Z= 0.159 Angle : 0.606 11.167 8253 Z= 0.316 Chirality : 0.047 0.151 885 Planarity : 0.005 0.053 1052 Dihedral : 4.900 17.370 831 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.59 % Favored : 93.28 % Rotamer: Outliers : 2.47 % Allowed : 11.27 % Favored : 86.27 % 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: -0.46 (0.32), residues: 744 helix: None (None), residues: 0 sheet: 0.01 (0.29), residues: 340 loop : -0.51 (0.33), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 24 TYR 0.014 0.002 TYR F 91 PHE 0.029 0.002 PHE A 96 TRP 0.021 0.001 TRP A 36 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 6084) covalent geometry : angle 0.60484 ( 8241) SS BOND : bond 0.00261 ( 6) SS BOND : angle 1.06973 ( 12) hydrogen bonds : bond 0.03165 ( 221) hydrogen bonds : angle 5.84078 ( 561) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.233 Fit side-chains REVERT: E 97 TYR cc_start: 0.5816 (t80) cc_final: 0.5215 (t80) REVERT: C 16 ARG cc_start: 0.7234 (mmt-90) cc_final: 0.6376 (ttm-80) REVERT: C 19 ARG cc_start: 0.6184 (tpp80) cc_final: 0.5822 (ttt-90) REVERT: D 42 LYS cc_start: 0.8319 (mtmt) cc_final: 0.7945 (mtmm) REVERT: D 45 LYS cc_start: 0.8691 (tttt) cc_final: 0.8370 (tttp) outliers start: 16 outliers final: 13 residues processed: 111 average time/residue: 0.0967 time to fit residues: 13.4580 Evaluate side-chains 122 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 61 ARG Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 68 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 3 optimal weight: 0.9990 chunk 12 optimal weight: 0.0070 chunk 5 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 42 optimal weight: 0.4980 chunk 19 optimal weight: 0.8980 chunk 34 optimal weight: 0.0870 chunk 45 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.185077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.161750 restraints weight = 6229.933| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 1.45 r_work: 0.3506 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6090 Z= 0.131 Angle : 0.571 10.498 8253 Z= 0.298 Chirality : 0.046 0.147 885 Planarity : 0.004 0.049 1052 Dihedral : 4.714 16.718 831 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.59 % Favored : 93.28 % Rotamer: Outliers : 2.01 % Allowed : 12.04 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.43 (0.32), residues: 744 helix: None (None), residues: 0 sheet: 0.04 (0.29), residues: 340 loop : -0.50 (0.33), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 24 TYR 0.015 0.002 TYR B 91 PHE 0.029 0.002 PHE A 96 TRP 0.021 0.001 TRP A 36 HIS 0.004 0.001 HIS A 93 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 6084) covalent geometry : angle 0.57026 ( 8241) SS BOND : bond 0.00182 ( 6) SS BOND : angle 0.83678 ( 12) hydrogen bonds : bond 0.02997 ( 221) hydrogen bonds : angle 5.72202 ( 561) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1614.28 seconds wall clock time: 28 minutes 24.05 seconds (1704.05 seconds total)