Starting phenix.real_space_refine on Sat Sep 12 10:23:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pfd_13372/09_2026/7pfd_13372.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pfd_13372/09_2026/7pfd_13372.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pfd_13372/09_2026/7pfd_13372.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pfd_13372/09_2026/7pfd_13372.map" model { file = "/net/cci-nas-00/data/ceres_data/7pfd_13372/09_2026/7pfd_13372.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pfd_13372/09_2026/7pfd_13372.cif" } resolution = 4.4 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= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2230 atoms to isotropic. 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 344 5.49 5 S 10 5.16 5 C 7520 2.51 5 N 2563 2.21 5 O 3238 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13675 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 798 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 798 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "J" Number of atoms: 3541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 3541 Classifications: {'DNA': 172} Link IDs: {'rna3p': 171} Chain: "I" Number of atoms: 3511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 3511 Classifications: {'DNA': 172} Link IDs: {'rna3p': 171} Chain: "U" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 535 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Time building chain proxies: 2.85, per 1000 atoms: 0.21 Number of scatterers: 13675 At special positions: 0 Unit cell: (111.3, 160.65, 114.45, 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 344 15.00 O 3238 8.00 N 2563 7.00 C 7520 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: 1.02 Conformation dependent library (CDL) restraints added in 377.9 milliseconds 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1566 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 68.8% alpha, 2.8% beta 169 base pairs and 294 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.842A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.537A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.533A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.507A pdb=" N ASN C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.564A pdb=" N VAL D 41 " --> pdb=" O TYR D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.796A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.544A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.641A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.313A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.573A pdb=" N VAL H 41 " --> pdb=" O TYR H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 123 Processing helix chain 'U' and resid 38 through 49 removed outlier: 3.967A pdb=" N LEU U 42 " --> pdb=" O PRO U 38 " (cutoff:3.500A) Processing helix chain 'U' and resid 57 through 69 Processing helix chain 'U' and resid 75 through 90 removed outlier: 3.971A pdb=" N LYS U 84 " --> pdb=" O LYS U 80 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL U 87 " --> pdb=" O LEU U 83 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.283A 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 97 removed outlier: 6.192A 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: 6.846A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.967A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.503A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'U' and resid 92 through 94 429 hydrogen bonds defined for protein. 1284 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 431 hydrogen bonds 862 hydrogen bond angles 0 basepair planarities 169 basepair parallelities 294 stacking parallelities Total time for adding SS restraints: 2.41 Time building geometry restraints manager: 1.42 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: 2420 1.33 - 1.45: 5050 1.45 - 1.57: 6440 1.57 - 1.69: 686 1.69 - 1.82: 20 Bond restraints: 14616 Sorted by residual: bond pdb=" C3' DG J 763 " pdb=" O3' DG J 763 " ideal model delta sigma weight residual 1.435 1.497 -0.062 1.30e-02 5.92e+03 2.27e+01 bond pdb=" C5' DA I 182 " pdb=" C4' DA I 182 " ideal model delta sigma weight residual 1.512 1.544 -0.032 7.00e-03 2.04e+04 2.04e+01 bond pdb=" C3' DC I 168 " pdb=" O3' DC I 168 " ideal model delta sigma weight residual 1.435 1.380 0.055 1.30e-02 5.92e+03 1.80e+01 bond pdb=" C3' DC I 136 " pdb=" O3' DC I 136 " ideal model delta sigma weight residual 1.435 1.387 0.048 1.30e-02 5.92e+03 1.36e+01 bond pdb=" C5' DA I 84 " pdb=" C4' DA I 84 " ideal model delta sigma weight residual 1.512 1.538 -0.026 7.00e-03 2.04e+04 1.35e+01 ... (remaining 14611 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.99: 20849 2.99 - 5.98: 324 5.98 - 8.97: 30 8.97 - 11.96: 2 11.96 - 14.95: 3 Bond angle restraints: 21208 Sorted by residual: angle pdb=" O4' DA I 166 " pdb=" C4' DA I 166 " pdb=" C3' DA I 166 " ideal model delta sigma weight residual 106.00 101.66 4.34 6.00e-01 2.78e+00 5.24e+01 angle pdb=" O4' DG I 127 " pdb=" C4' DG I 127 " pdb=" C3' DG I 127 " ideal model delta sigma weight residual 106.00 102.41 3.59 6.00e-01 2.78e+00 3.59e+01 angle pdb=" O4' DC J 688 " pdb=" C1' DC J 688 " pdb=" N1 DC J 688 " ideal model delta sigma weight residual 108.00 112.17 -4.17 7.00e-01 2.04e+00 3.55e+01 angle pdb=" N GLU H 113 " pdb=" CA GLU H 113 " pdb=" CB GLU H 113 " ideal model delta sigma weight residual 110.28 119.29 -9.01 1.55e+00 4.16e-01 3.38e+01 angle pdb=" O4' DA I 45 " pdb=" C4' DA I 45 " pdb=" C3' DA I 45 " ideal model delta sigma weight residual 106.00 102.53 3.47 6.00e-01 2.78e+00 3.35e+01 ... (remaining 21203 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 6098 35.86 - 71.73: 1769 71.73 - 107.59: 49 107.59 - 143.46: 1 143.46 - 179.32: 2 Dihedral angle restraints: 7919 sinusoidal: 5488 harmonic: 2431 Sorted by residual: dihedral pdb=" CA LEU B 22 " pdb=" C LEU B 22 " pdb=" N ARG B 23 " pdb=" CA ARG B 23 " ideal model delta harmonic sigma weight residual 180.00 -159.60 -20.40 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" C4' DG I 119 " pdb=" C3' DG I 119 " pdb=" O3' DG I 119 " pdb=" P DC I 120 " ideal model delta sinusoidal sigma weight residual 220.00 40.68 179.32 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA PHE A 84 " pdb=" C PHE A 84 " pdb=" N GLN A 85 " pdb=" CA GLN A 85 " ideal model delta harmonic sigma weight residual 180.00 160.32 19.68 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 7916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1611 0.047 - 0.094: 636 0.094 - 0.142: 136 0.142 - 0.189: 24 0.189 - 0.236: 9 Chirality restraints: 2416 Sorted by residual: chirality pdb=" CB THR G 59 " pdb=" CA THR G 59 " pdb=" OG1 THR G 59 " pdb=" CG2 THR G 59 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA PHE E 104 " pdb=" N PHE E 104 " pdb=" C PHE E 104 " pdb=" CB PHE E 104 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA ASP A 81 " pdb=" N ASP A 81 " pdb=" C ASP A 81 " pdb=" CB ASP A 81 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 2413 not shown) Planarity restraints: 1488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.052 5.00e-02 4.00e+02 7.88e-02 9.94e+00 pdb=" N PRO G 80 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU H 113 " 0.015 2.00e-02 2.50e+03 3.14e-02 9.87e+00 pdb=" CD GLU H 113 " -0.054 2.00e-02 2.50e+03 pdb=" OE1 GLU H 113 " 0.019 2.00e-02 2.50e+03 pdb=" OE2 GLU H 113 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 70 " -0.015 2.00e-02 2.50e+03 2.91e-02 8.49e+00 pdb=" C VAL F 70 " 0.050 2.00e-02 2.50e+03 pdb=" O VAL F 70 " -0.019 2.00e-02 2.50e+03 pdb=" N THR F 71 " -0.017 2.00e-02 2.50e+03 ... (remaining 1485 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 2628 2.78 - 3.31: 12748 3.31 - 3.84: 30087 3.84 - 4.37: 33559 4.37 - 4.90: 45685 Nonbonded interactions: 124707 Sorted by model distance: nonbonded pdb=" O VAL D 118 " pdb=" OG1 THR D 122 " model vdw 2.245 3.040 nonbonded pdb=" O LYS G 15 " pdb=" NH1 ARG G 20 " model vdw 2.279 3.120 nonbonded pdb=" NH1 ARG C 81 " pdb=" O VAL C 107 " model vdw 2.290 3.120 nonbonded pdb=" OH TYR C 39 " pdb=" OE1 GLU D 71 " model vdw 2.293 3.040 nonbonded pdb=" NH2 ARG D 33 " pdb=" O2 DC I 51 " model vdw 2.296 3.120 ... (remaining 124702 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.740 Find NCS groups from input model: 0.140 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 14616 Z= 0.616 Angle : 1.048 14.946 21208 Z= 0.847 Chirality : 0.052 0.236 2416 Planarity : 0.007 0.079 1488 Dihedral : 29.935 179.324 6353 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: -0.57 (0.26), residues: 825 helix: 0.04 (0.20), residues: 560 sheet: -3.84 (0.84), residues: 10 loop : -0.91 (0.32), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 67 TYR 0.023 0.003 TYR G 50 PHE 0.020 0.003 PHE C 25 HIS 0.010 0.003 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00687 / 0.62 (14616) covalent geometry : angle 1.04777 / 0.85 (21208) hydrogen bonds : bond 0.11370 / 7.79 ( 860) hydrogen bonds : angle 4.75167 / 3.44 ( 2146) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.8488 (t80) cc_final: 0.8221 (t80) REVERT: A 104 PHE cc_start: 0.9578 (m-10) cc_final: 0.9329 (m-80) REVERT: E 105 GLU cc_start: 0.9361 (mt-10) cc_final: 0.8961 (mm-30) REVERT: G 34 LEU cc_start: 0.8427 (mt) cc_final: 0.8216 (mt) REVERT: H 98 VAL cc_start: 0.9711 (t) cc_final: 0.9467 (p) REVERT: H 102 LEU cc_start: 0.8816 (mp) cc_final: 0.8425 (tp) REVERT: H 106 LEU cc_start: 0.9767 (mt) cc_final: 0.9410 (mt) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.1015 time to fit residues: 16.2909 Evaluate side-chains 70 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 30.0000 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 20.0000 chunk 106 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN E 108 ASN H 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.039790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.031858 restraints weight = 196235.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.032910 restraints weight = 115255.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.033643 restraints weight = 81043.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.034179 restraints weight = 62606.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.034475 restraints weight = 51449.812| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14616 Z= 0.201 Angle : 0.780 9.137 21208 Z= 0.450 Chirality : 0.050 0.306 2416 Planarity : 0.005 0.071 1488 Dihedral : 33.630 174.881 4701 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.43 % Allowed : 3.17 % Favored : 96.39 % 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: 0.27 (0.27), residues: 825 helix: 0.71 (0.21), residues: 578 sheet: -4.09 (0.84), residues: 10 loop : -0.75 (0.34), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 32 TYR 0.013 0.002 TYR G 39 PHE 0.016 0.002 PHE D 70 HIS 0.006 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.20 (14616) covalent geometry : angle 0.77993 / 0.45 (21208) hydrogen bonds : bond 0.08430 / 5.75 ( 860) hydrogen bonds : angle 3.69652 / 2.69 ( 2146) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 96 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.8118 (t80) cc_final: 0.7891 (t80) REVERT: E 105 GLU cc_start: 0.9080 (mt-10) cc_final: 0.8816 (mm-30) REVERT: F 97 LEU cc_start: 0.7826 (tp) cc_final: 0.7551 (tp) REVERT: H 98 VAL cc_start: 0.9530 (t) cc_final: 0.9273 (t) outliers start: 3 outliers final: 1 residues processed: 99 average time/residue: 0.1062 time to fit residues: 16.1292 Evaluate side-chains 65 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 4 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 93 optimal weight: 30.0000 chunk 86 optimal weight: 30.0000 chunk 10 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN E 108 ASN H 82 HIS U 75 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.039755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.033555 restraints weight = 215223.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.034416 restraints weight = 133827.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.035023 restraints weight = 95055.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.035427 restraints weight = 73666.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.035722 restraints weight = 61039.093| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14616 Z= 0.169 Angle : 0.722 8.798 21208 Z= 0.420 Chirality : 0.048 0.326 2416 Planarity : 0.005 0.066 1488 Dihedral : 33.565 178.831 4701 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.14 % Allowed : 3.61 % Favored : 96.25 % 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 (0.27), residues: 825 helix: 0.96 (0.21), residues: 576 sheet: -3.90 (1.00), residues: 10 loop : -0.74 (0.35), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 33 TYR 0.036 0.002 TYR D 42 PHE 0.011 0.002 PHE A 67 HIS 0.004 0.001 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.17 (14616) covalent geometry : angle 0.72193 / 0.42 (21208) hydrogen bonds : bond 0.06882 / 4.69 ( 860) hydrogen bonds : angle 3.55758 / 2.60 ( 2146) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.8483 (t80) cc_final: 0.8241 (t80) REVERT: A 100 LEU cc_start: 0.9782 (mm) cc_final: 0.9517 (mm) REVERT: A 104 PHE cc_start: 0.9640 (m-10) cc_final: 0.9416 (m-80) REVERT: B 68 ASP cc_start: 0.9479 (m-30) cc_final: 0.9276 (m-30) REVERT: E 105 GLU cc_start: 0.9343 (mt-10) cc_final: 0.8861 (mm-30) REVERT: G 73 ASN cc_start: 0.8947 (t0) cc_final: 0.8684 (t0) REVERT: H 102 LEU cc_start: 0.8656 (tp) cc_final: 0.8347 (tp) outliers start: 1 outliers final: 0 residues processed: 95 average time/residue: 0.1094 time to fit residues: 15.8191 Evaluate side-chains 70 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 30.0000 chunk 48 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 103 optimal weight: 30.0000 chunk 44 optimal weight: 5.9990 chunk 86 optimal weight: 30.0000 chunk 21 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 87 optimal weight: 30.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN H 47 GLN H 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.036072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.028834 restraints weight = 206413.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.029762 restraints weight = 124062.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.030427 restraints weight = 87338.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.030900 restraints weight = 67654.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.031231 restraints weight = 55747.598| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 14616 Z= 0.229 Angle : 0.778 8.804 21208 Z= 0.445 Chirality : 0.049 0.318 2416 Planarity : 0.005 0.066 1488 Dihedral : 33.632 179.182 4701 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 18.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % 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: 0.39 (0.27), residues: 825 helix: 0.81 (0.21), residues: 580 sheet: -3.20 (1.34), residues: 10 loop : -0.78 (0.36), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 32 TYR 0.019 0.003 TYR C 57 PHE 0.022 0.003 PHE E 104 HIS 0.006 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.23 (14616) covalent geometry : angle 0.77849 / 0.44 (21208) hydrogen bonds : bond 0.11014 / 7.45 ( 860) hydrogen bonds : angle 3.73272 / 2.72 ( 2146) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.8062 (t80) cc_final: 0.7828 (t80) REVERT: B 66 ILE cc_start: 0.9563 (tp) cc_final: 0.9249 (pt) REVERT: E 104 PHE cc_start: 0.9020 (m-80) cc_final: 0.8686 (m-80) REVERT: E 105 GLU cc_start: 0.9047 (mt-10) cc_final: 0.8737 (mm-30) REVERT: F 52 GLU cc_start: 0.9785 (tp30) cc_final: 0.9581 (pm20) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1067 time to fit residues: 14.6380 Evaluate side-chains 66 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 55 optimal weight: 0.0970 chunk 79 optimal weight: 30.0000 chunk 84 optimal weight: 40.0000 chunk 54 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 19 optimal weight: 0.0980 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN E 108 ASN G 84 GLN H 47 GLN H 82 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.038778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.032615 restraints weight = 211603.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.033481 restraints weight = 131693.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.034068 restraints weight = 93485.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.034527 restraints weight = 72435.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.034809 restraints weight = 59426.565| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 14616 Z= 0.163 Angle : 0.723 8.547 21208 Z= 0.417 Chirality : 0.048 0.332 2416 Planarity : 0.005 0.070 1488 Dihedral : 33.621 178.187 4701 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.14 % Allowed : 2.45 % Favored : 97.40 % 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: 0.54 (0.28), residues: 825 helix: 0.94 (0.21), residues: 588 sheet: -2.83 (1.61), residues: 10 loop : -0.87 (0.36), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 77 TYR 0.031 0.002 TYR H 42 PHE 0.029 0.002 PHE A 104 HIS 0.004 0.001 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.16 (14616) covalent geometry : angle 0.72284 / 0.42 (21208) hydrogen bonds : bond 0.06545 / 4.47 ( 860) hydrogen bonds : angle 3.65880 / 2.67 ( 2146) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.8400 (t80) cc_final: 0.8189 (t80) REVERT: A 100 LEU cc_start: 0.9783 (mm) cc_final: 0.9345 (pp) REVERT: A 104 PHE cc_start: 0.9482 (m-80) cc_final: 0.9025 (m-80) REVERT: B 66 ILE cc_start: 0.9786 (tp) cc_final: 0.9570 (pt) REVERT: B 68 ASP cc_start: 0.9577 (m-30) cc_final: 0.9348 (m-30) REVERT: E 104 PHE cc_start: 0.9600 (m-80) cc_final: 0.9248 (m-80) REVERT: E 105 GLU cc_start: 0.9367 (mt-10) cc_final: 0.8833 (mm-30) REVERT: F 52 GLU cc_start: 0.9642 (tp30) cc_final: 0.9345 (pm20) REVERT: H 102 LEU cc_start: 0.8802 (tp) cc_final: 0.8570 (tp) REVERT: H 108 LYS cc_start: 0.9711 (ptpp) cc_final: 0.9453 (ptpp) REVERT: H 109 HIS cc_start: 0.9794 (m90) cc_final: 0.9474 (m90) outliers start: 1 outliers final: 0 residues processed: 95 average time/residue: 0.1148 time to fit residues: 16.5432 Evaluate side-chains 71 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 49 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 102 optimal weight: 30.0000 chunk 108 optimal weight: 30.0000 chunk 73 optimal weight: 40.0000 chunk 18 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 chunk 95 optimal weight: 40.0000 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN H 82 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.037637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.031643 restraints weight = 215707.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.032465 restraints weight = 134238.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.033004 restraints weight = 95976.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.033422 restraints weight = 75318.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.033756 restraints weight = 62116.073| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14616 Z= 0.194 Angle : 0.736 8.341 21208 Z= 0.422 Chirality : 0.048 0.323 2416 Planarity : 0.005 0.078 1488 Dihedral : 33.571 178.309 4701 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % 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 (0.27), residues: 825 helix: 1.00 (0.20), residues: 584 sheet: -2.17 (1.94), residues: 10 loop : -1.04 (0.35), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 55 TYR 0.015 0.002 TYR F 51 PHE 0.028 0.002 PHE A 104 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.19 (14616) covalent geometry : angle 0.73556 / 0.42 (21208) hydrogen bonds : bond 0.08974 / 6.10 ( 860) hydrogen bonds : angle 3.70926 / 2.70 ( 2146) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.8530 (t80) cc_final: 0.8309 (t80) REVERT: A 104 PHE cc_start: 0.9551 (m-80) cc_final: 0.9346 (m-80) REVERT: B 66 ILE cc_start: 0.9774 (tp) cc_final: 0.9567 (pt) REVERT: B 68 ASP cc_start: 0.9574 (m-30) cc_final: 0.9344 (m-30) REVERT: E 104 PHE cc_start: 0.9650 (m-80) cc_final: 0.9243 (m-80) REVERT: E 105 GLU cc_start: 0.9436 (mt-10) cc_final: 0.8954 (mm-30) REVERT: H 102 LEU cc_start: 0.8749 (tp) cc_final: 0.8538 (tp) REVERT: H 109 HIS cc_start: 0.9790 (m90) cc_final: 0.9191 (m90) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1054 time to fit residues: 13.9989 Evaluate side-chains 65 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 34 optimal weight: 0.9980 chunk 96 optimal weight: 40.0000 chunk 21 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 65 optimal weight: 30.0000 chunk 40 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 17 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN H 82 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.037919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.030331 restraints weight = 196839.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.031317 restraints weight = 115678.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.031976 restraints weight = 81674.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.032490 restraints weight = 63838.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.032820 restraints weight = 52763.976| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14616 Z= 0.169 Angle : 0.724 9.315 21208 Z= 0.416 Chirality : 0.047 0.330 2416 Planarity : 0.005 0.070 1488 Dihedral : 33.571 178.050 4701 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % 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: 0.50 (0.28), residues: 825 helix: 0.93 (0.21), residues: 590 sheet: -2.43 (1.88), residues: 10 loop : -0.99 (0.36), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 77 TYR 0.015 0.002 TYR H 42 PHE 0.025 0.002 PHE A 104 HIS 0.007 0.001 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.17 (14616) covalent geometry : angle 0.72415 / 0.42 (21208) hydrogen bonds : bond 0.06675 / 4.56 ( 860) hydrogen bonds : angle 3.76007 / 2.74 ( 2146) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 82 LEU cc_start: 0.7639 (tp) cc_final: 0.7282 (tp) REVERT: E 104 PHE cc_start: 0.9109 (m-80) cc_final: 0.8813 (m-80) REVERT: E 105 GLU cc_start: 0.9088 (mt-10) cc_final: 0.8780 (mm-30) REVERT: F 52 GLU cc_start: 0.9768 (tp30) cc_final: 0.9553 (pm20) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1050 time to fit residues: 14.1474 Evaluate side-chains 64 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 100 optimal weight: 20.0000 chunk 55 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 85 optimal weight: 30.0000 chunk 109 optimal weight: 0.0770 chunk 112 optimal weight: 9.9990 chunk 5 optimal weight: 0.8980 overall best weight: 2.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN G 112 GLN H 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.037811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.030258 restraints weight = 196835.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.031232 restraints weight = 116711.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.031896 restraints weight = 82751.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.032356 restraints weight = 64435.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.032699 restraints weight = 53894.433| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14616 Z= 0.168 Angle : 0.712 7.863 21208 Z= 0.408 Chirality : 0.047 0.326 2416 Planarity : 0.005 0.073 1488 Dihedral : 33.476 178.919 4701 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % 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: 0.59 (0.28), residues: 825 helix: 1.03 (0.21), residues: 586 sheet: -2.25 (1.95), residues: 10 loop : -1.04 (0.35), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 32 TYR 0.016 0.002 TYR E 99 PHE 0.019 0.002 PHE D 65 HIS 0.004 0.001 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.17 (14616) covalent geometry : angle 0.71214 / 0.41 (21208) hydrogen bonds : bond 0.06933 / 4.73 ( 860) hydrogen bonds : angle 3.70388 / 2.70 ( 2146) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 104 PHE cc_start: 0.9119 (m-80) cc_final: 0.8663 (m-80) REVERT: E 105 GLU cc_start: 0.9085 (mt-10) cc_final: 0.8740 (mm-30) REVERT: F 52 GLU cc_start: 0.9776 (tp30) cc_final: 0.9562 (pm20) REVERT: F 97 LEU cc_start: 0.7532 (tp) cc_final: 0.7263 (tp) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1149 time to fit residues: 14.9934 Evaluate side-chains 65 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 34 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 100 optimal weight: 30.0000 chunk 102 optimal weight: 30.0000 chunk 92 optimal weight: 30.0000 chunk 83 optimal weight: 40.0000 chunk 77 optimal weight: 40.0000 chunk 87 optimal weight: 30.0000 chunk 35 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 79 optimal weight: 30.0000 overall best weight: 10.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN D 67 ASN D 84 ASN E 76 GLN E 108 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.032154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.025860 restraints weight = 217366.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.026776 restraints weight = 119825.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.027414 restraints weight = 80186.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.027881 restraints weight = 59939.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.028202 restraints weight = 48014.526| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 14616 Z= 0.388 Angle : 0.989 12.209 21208 Z= 0.546 Chirality : 0.058 0.326 2416 Planarity : 0.009 0.101 1488 Dihedral : 34.140 179.159 4701 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 40.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.08 (0.26), residues: 825 helix: -0.21 (0.19), residues: 582 sheet: -2.53 (1.85), residues: 10 loop : -1.66 (0.35), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 77 TYR 0.044 0.005 TYR H 42 PHE 0.032 0.004 PHE E 78 HIS 0.014 0.003 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00667 / 0.39 (14616) covalent geometry : angle 0.98874 / 0.55 (21208) hydrogen bonds : bond 0.19028 / 12.86 ( 860) hydrogen bonds : angle 4.72022 / 3.42 ( 2146) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 81 ASP cc_start: 0.9442 (p0) cc_final: 0.9196 (m-30) REVERT: E 82 LEU cc_start: 0.6930 (tp) cc_final: 0.6116 (tp) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1023 time to fit residues: 12.2424 Evaluate side-chains 56 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 47 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 80 optimal weight: 40.0000 chunk 33 optimal weight: 6.9990 chunk 99 optimal weight: 40.0000 chunk 93 optimal weight: 30.0000 chunk 25 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN E 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.033445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.026828 restraints weight = 216210.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.027715 restraints weight = 125038.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.028344 restraints weight = 86911.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.028781 restraints weight = 67149.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.029085 restraints weight = 55273.179| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14616 Z= 0.218 Angle : 0.816 10.687 21208 Z= 0.460 Chirality : 0.052 0.332 2416 Planarity : 0.006 0.072 1488 Dihedral : 34.208 174.676 4701 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 23.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % 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: -0.65 (0.27), residues: 825 helix: 0.18 (0.20), residues: 584 sheet: -2.69 (1.81), residues: 10 loop : -1.71 (0.34), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 116 TYR 0.039 0.003 TYR D 42 PHE 0.019 0.002 PHE B 100 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.22 (14616) covalent geometry : angle 0.81613 / 0.46 (21208) hydrogen bonds : bond 0.09274 / 6.35 ( 860) hydrogen bonds : angle 4.29932 / 3.11 ( 2146) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 81 ASP cc_start: 0.9506 (p0) cc_final: 0.9297 (m-30) REVERT: E 82 LEU cc_start: 0.7989 (tp) cc_final: 0.7556 (tp) REVERT: F 97 LEU cc_start: 0.7500 (tp) cc_final: 0.7288 (tp) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1054 time to fit residues: 13.1618 Evaluate side-chains 64 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 6 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 97 optimal weight: 30.0000 chunk 59 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 87 optimal weight: 30.0000 chunk 22 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN E 108 ASN H 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.033447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.026811 restraints weight = 211549.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.027699 restraints weight = 122806.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.028341 restraints weight = 84657.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.028766 restraints weight = 64582.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.029087 restraints weight = 53252.372| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.4600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14616 Z= 0.208 Angle : 0.788 9.608 21208 Z= 0.445 Chirality : 0.050 0.320 2416 Planarity : 0.005 0.070 1488 Dihedral : 34.011 177.855 4701 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 21.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.36 (0.27), residues: 825 helix: 0.41 (0.20), residues: 584 sheet: -2.38 (1.90), residues: 10 loop : -1.66 (0.34), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 116 TYR 0.015 0.002 TYR D 42 PHE 0.026 0.003 PHE A 104 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.21 (14616) covalent geometry : angle 0.78755 / 0.45 (21208) hydrogen bonds : bond 0.09532 / 6.50 ( 860) hydrogen bonds : angle 4.10372 / 2.98 ( 2146) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2189.70 seconds wall clock time: 38 minutes 49.25 seconds (2329.25 seconds total)