Starting phenix.real_space_refine on Thu Jul 2 23:58:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d3p_46543/07_2026/9d3p_46543.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d3p_46543/07_2026/9d3p_46543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9d3p_46543/07_2026/9d3p_46543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d3p_46543/07_2026/9d3p_46543.map" model { file = "/net/cci-nas-00/data/ceres_data/9d3p_46543/07_2026/9d3p_46543.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d3p_46543/07_2026/9d3p_46543.cif" } resolution = 2.5 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= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 246 5.49 5 S 14 5.16 5 C 6180 2.51 5 N 2083 2.21 5 O 2540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11063 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 652 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 735 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 811 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 100} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 2530 Classifications: {'DNA': 123} Link IDs: {'rna3p': 122} Chain: "J" Number of atoms: 2513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 2513 Classifications: {'DNA': 123} Link IDs: {'rna3p': 122} Time building chain proxies: 2.04, per 1000 atoms: 0.18 Number of scatterers: 11063 At special positions: 0 Unit cell: (116.875, 76.67, 117.81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 246 15.00 O 2540 8.00 N 2083 7.00 C 6180 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: 0.99 Conformation dependent library (CDL) restraints added in 156.7 milliseconds 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1420 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 72.6% alpha, 3.1% beta 120 base pairs and 226 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.369A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE C 62 " --> pdb=" O LEU C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.524A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.125A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.653A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.558A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (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: 4.411A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.617A pdb=" N LEU G 116 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.905A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (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 103 through 123 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.937A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.983A 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 removed outlier: 6.578A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.607A 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: 7.107A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 407 hydrogen bonds defined for protein. 1200 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 314 hydrogen bonds 628 hydrogen bond angles 0 basepair planarities 120 basepair parallelities 226 stacking parallelities Total time for adding SS restraints: 1.55 Time building geometry restraints manager: 1.22 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: 2588 1.34 - 1.46: 3416 1.46 - 1.57: 5236 1.57 - 1.69: 490 1.69 - 1.81: 26 Bond restraints: 11756 Sorted by residual: bond pdb=" C3' DG J 21 " pdb=" C2' DG J 21 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DC I 43 " pdb=" C2' DC I 43 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DG I 19 " pdb=" C2' DG I 19 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 bond pdb=" C3' DA I -30 " pdb=" C2' DA I -30 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.36e+00 bond pdb=" C3' DG J 63 " pdb=" C2' DG J 63 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.30e+00 ... (remaining 11751 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 16160 1.80 - 3.60: 733 3.60 - 5.40: 22 5.40 - 7.20: 5 7.20 - 9.00: 2 Bond angle restraints: 16922 Sorted by residual: angle pdb=" N VAL A 117 " pdb=" CA VAL A 117 " pdb=" C VAL A 117 " ideal model delta sigma weight residual 113.53 108.37 5.16 9.80e-01 1.04e+00 2.77e+01 angle pdb=" O4' DC J 69 " pdb=" C4' DC J 69 " pdb=" C3' DC J 69 " ideal model delta sigma weight residual 106.00 103.12 2.88 6.00e-01 2.78e+00 2.31e+01 angle pdb=" N3 DT J 39 " pdb=" C4 DT J 39 " pdb=" O4 DT J 39 " ideal model delta sigma weight residual 119.90 122.61 -2.71 6.00e-01 2.78e+00 2.04e+01 angle pdb=" N3 DT J 30 " pdb=" C4 DT J 30 " pdb=" O4 DT J 30 " ideal model delta sigma weight residual 119.90 122.61 -2.71 6.00e-01 2.78e+00 2.04e+01 angle pdb=" N3 DT I -67 " pdb=" C4 DT I -67 " pdb=" O4 DT I -67 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.96e+01 ... (remaining 16917 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.14: 5009 34.14 - 68.28: 1398 68.28 - 102.41: 23 102.41 - 136.55: 1 136.55 - 170.69: 1 Dihedral angle restraints: 6432 sinusoidal: 4228 harmonic: 2204 Sorted by residual: dihedral pdb=" C4' DA J -17 " pdb=" C3' DA J -17 " pdb=" O3' DA J -17 " pdb=" P DG J -16 " ideal model delta sinusoidal sigma weight residual -140.00 30.69 -170.69 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 91.51 128.49 1 3.50e+01 8.16e-04 1.27e+01 dihedral pdb=" CG ARG A 131 " pdb=" CD ARG A 131 " pdb=" NE ARG A 131 " pdb=" CZ ARG A 131 " ideal model delta sinusoidal sigma weight residual -90.00 -134.76 44.76 2 1.50e+01 4.44e-03 1.06e+01 ... (remaining 6429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 985 0.029 - 0.057: 597 0.057 - 0.086: 218 0.086 - 0.114: 104 0.114 - 0.143: 22 Chirality restraints: 1926 Sorted by residual: chirality pdb=" C3' DC J 7 " pdb=" C4' DC J 7 " pdb=" O3' DC J 7 " pdb=" C2' DC J 7 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" C3' DT I -67 " pdb=" C4' DT I -67 " pdb=" O3' DT I -67 " pdb=" C2' DT I -67 " both_signs ideal model delta sigma weight residual False -2.73 -2.60 -0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" C4' DT I 17 " pdb=" C5' DT I 17 " pdb=" O4' DT I 17 " pdb=" C3' DT I 17 " both_signs ideal model delta sigma weight residual False -2.53 -2.40 -0.13 2.00e-01 2.50e+01 4.19e-01 ... (remaining 1923 not shown) Planarity restraints: 1291 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET E 120 " 0.033 5.00e-02 4.00e+02 5.07e-02 4.11e+00 pdb=" N PRO E 121 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO E 121 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 121 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " -0.032 5.00e-02 4.00e+02 4.85e-02 3.76e+00 pdb=" N PRO G 80 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 17 " 0.023 2.00e-02 2.50e+03 1.19e-02 3.52e+00 pdb=" N1 DT I 17 " -0.024 2.00e-02 2.50e+03 pdb=" C2 DT I 17 " -0.004 2.00e-02 2.50e+03 pdb=" O2 DT I 17 " -0.006 2.00e-02 2.50e+03 pdb=" N3 DT I 17 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DT I 17 " 0.006 2.00e-02 2.50e+03 pdb=" O4 DT I 17 " 0.010 2.00e-02 2.50e+03 pdb=" C5 DT I 17 " -0.001 2.00e-02 2.50e+03 pdb=" C7 DT I 17 " -0.008 2.00e-02 2.50e+03 pdb=" C6 DT I 17 " 0.004 2.00e-02 2.50e+03 ... (remaining 1288 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1923 2.78 - 3.31: 9470 3.31 - 3.84: 22144 3.84 - 4.37: 26644 4.37 - 4.90: 37664 Nonbonded interactions: 97845 Sorted by model distance: nonbonded pdb=" OG SER D 36 " pdb=" OG SER D 38 " model vdw 2.246 3.040 nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.264 3.040 nonbonded pdb=" NE2 GLN C 84 " pdb=" O GLY C 106 " model vdw 2.273 3.120 nonbonded pdb=" NH1 ARG G 29 " pdb=" O SER H 36 " model vdw 2.354 3.120 nonbonded pdb=" NH1 ARG A 129 " pdb=" OD1 ASP E 106 " model vdw 2.363 3.120 ... (remaining 97840 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' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O )))) } ncs_group { reference = (chain 'C' and ((resid 13 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 118)) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 33 through 124) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.510 Find NCS groups from input model: 0.070 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:5.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 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 0.041 11756 Z= 0.505 Angle : 0.756 8.995 16922 Z= 0.658 Chirality : 0.044 0.143 1926 Planarity : 0.005 0.051 1291 Dihedral : 28.649 170.689 5012 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.06 % Allowed : 24.92 % Favored : 73.02 % 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: 0.90 (0.29), residues: 746 helix: 1.22 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.96 (0.36), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 86 TYR 0.014 0.002 TYR A 54 PHE 0.011 0.002 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.50 (11756) covalent geometry : angle 0.75590 / 0.66 (16922) hydrogen bonds : bond 0.10501 / 7.10 ( 721) hydrogen bonds : angle 4.42258 / 3.12 ( 1828) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.241 Fit side-chains outliers start: 13 outliers final: 13 residues processed: 136 average time/residue: 0.8860 time to fit residues: 126.0342 Evaluate side-chains 134 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 111 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 30.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN E 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.193230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.145205 restraints weight = 10050.406| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 1.07 r_work: 0.3551 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.0453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11756 Z= 0.154 Angle : 0.644 8.443 16922 Z= 0.376 Chirality : 0.047 0.219 1926 Planarity : 0.005 0.049 1291 Dihedral : 30.789 166.580 3533 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 4.13 % Allowed : 22.06 % Favored : 73.81 % 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: 1.73 (0.30), residues: 746 helix: 1.85 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.79 (0.38), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 35 TYR 0.011 0.002 TYR H 40 PHE 0.012 0.002 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.15 (11756) covalent geometry : angle 0.64383 / 0.38 (16922) hydrogen bonds : bond 0.04909 / 3.30 ( 721) hydrogen bonds : angle 3.16342 / 2.24 ( 1828) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.302 Fit side-chains REVERT: C 91 GLU cc_start: 0.7249 (tt0) cc_final: 0.7048 (mp0) REVERT: D 86 ARG cc_start: 0.8256 (mmt90) cc_final: 0.7849 (mmt90) REVERT: E 87 SER cc_start: 0.8744 (OUTLIER) cc_final: 0.8488 (p) REVERT: F 77 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8382 (mtmt) REVERT: F 92 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.7536 (ttp80) REVERT: H 116 LYS cc_start: 0.7993 (ttmt) cc_final: 0.7685 (ttmt) outliers start: 26 outliers final: 15 residues processed: 139 average time/residue: 0.9688 time to fit residues: 140.7954 Evaluate side-chains 136 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 19 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 95 optimal weight: 50.0000 chunk 15 optimal weight: 0.9980 chunk 64 optimal weight: 8.9990 chunk 23 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN E 68 GLN E 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.194120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.146183 restraints weight = 10151.540| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 1.07 r_work: 0.3559 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.0578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11756 Z= 0.137 Angle : 0.623 8.092 16922 Z= 0.366 Chirality : 0.046 0.215 1926 Planarity : 0.004 0.047 1291 Dihedral : 30.812 167.190 3524 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.81 % Allowed : 21.90 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.30), residues: 746 helix: 2.14 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.70 (0.38), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 35 TYR 0.012 0.001 TYR A 54 PHE 0.013 0.002 PHE E 67 HIS 0.003 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.14 (11756) covalent geometry : angle 0.62350 / 0.37 (16922) hydrogen bonds : bond 0.04521 / 3.06 ( 721) hydrogen bonds : angle 3.11780 / 2.21 ( 1828) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.227 Fit side-chains REVERT: A 80 THR cc_start: 0.8588 (p) cc_final: 0.8376 (t) REVERT: E 87 SER cc_start: 0.8714 (OUTLIER) cc_final: 0.8472 (p) REVERT: F 77 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8360 (mtmt) outliers start: 24 outliers final: 15 residues processed: 132 average time/residue: 0.8679 time to fit residues: 119.7430 Evaluate side-chains 133 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 91 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 45 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 36 optimal weight: 20.0000 chunk 91 optimal weight: 20.0000 chunk 20 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 73 optimal weight: 40.0000 chunk 14 optimal weight: 0.7980 chunk 27 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN E 68 GLN G 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.191547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.143475 restraints weight = 10088.271| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 1.07 r_work: 0.3528 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.0755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11756 Z= 0.174 Angle : 0.645 7.688 16922 Z= 0.372 Chirality : 0.047 0.225 1926 Planarity : 0.005 0.047 1291 Dihedral : 30.970 166.160 3524 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 4.44 % Allowed : 20.16 % Favored : 75.40 % 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: 2.04 (0.30), residues: 746 helix: 2.11 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -0.78 (0.38), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 35 TYR 0.012 0.002 TYR C 57 PHE 0.013 0.002 PHE E 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.17 (11756) covalent geometry : angle 0.64482 / 0.37 (16922) hydrogen bonds : bond 0.05315 / 3.58 ( 721) hydrogen bonds : angle 3.06965 / 2.18 ( 1828) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 124 time to evaluate : 0.389 Fit side-chains REVERT: A 80 THR cc_start: 0.8609 (p) cc_final: 0.8388 (t) REVERT: C 73 ASN cc_start: 0.7013 (t0) cc_final: 0.6623 (t0) REVERT: D 33 ARG cc_start: 0.5869 (OUTLIER) cc_final: 0.4733 (mtp180) REVERT: D 86 ARG cc_start: 0.8248 (mmt90) cc_final: 0.8031 (mmt90) REVERT: F 77 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8450 (mtmt) REVERT: H 55 SER cc_start: 0.8631 (m) cc_final: 0.8324 (t) REVERT: H 91 SER cc_start: 0.8788 (OUTLIER) cc_final: 0.8506 (m) REVERT: H 116 LYS cc_start: 0.7966 (ttmt) cc_final: 0.7646 (ttmt) outliers start: 28 outliers final: 12 residues processed: 142 average time/residue: 0.8556 time to fit residues: 127.1529 Evaluate side-chains 137 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 91 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 5 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 81 optimal weight: 20.0000 chunk 84 optimal weight: 40.0000 chunk 79 optimal weight: 20.0000 chunk 61 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 77 optimal weight: 20.0000 chunk 15 optimal weight: 0.8980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 93 GLN G 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.192287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.144414 restraints weight = 10013.267| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 1.06 r_work: 0.3538 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.0762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11756 Z= 0.145 Angle : 0.628 7.732 16922 Z= 0.364 Chirality : 0.046 0.224 1926 Planarity : 0.004 0.046 1291 Dihedral : 30.996 166.334 3521 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.49 % Allowed : 21.11 % Favored : 75.40 % 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: 2.13 (0.30), residues: 746 helix: 2.16 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.72 (0.38), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 35 TYR 0.012 0.002 TYR H 40 PHE 0.013 0.002 PHE E 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.14 (11756) covalent geometry : angle 0.62836 / 0.36 (16922) hydrogen bonds : bond 0.04913 / 3.32 ( 721) hydrogen bonds : angle 3.06005 / 2.17 ( 1828) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.338 Fit side-chains REVERT: A 80 THR cc_start: 0.8606 (p) cc_final: 0.8391 (t) REVERT: C 73 ASN cc_start: 0.6938 (t0) cc_final: 0.6526 (t0) REVERT: F 77 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8395 (mtmt) REVERT: F 95 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7930 (mtt-85) REVERT: H 55 SER cc_start: 0.8612 (m) cc_final: 0.8311 (t) REVERT: H 91 SER cc_start: 0.8736 (OUTLIER) cc_final: 0.8467 (m) outliers start: 22 outliers final: 15 residues processed: 135 average time/residue: 0.9310 time to fit residues: 131.5845 Evaluate side-chains 135 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 91 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 38 optimal weight: 4.9990 chunk 74 optimal weight: 30.0000 chunk 6 optimal weight: 4.9990 chunk 84 optimal weight: 40.0000 chunk 32 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 88 optimal weight: 20.0000 chunk 54 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN E 68 GLN G 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.189647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.141298 restraints weight = 10133.712| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 1.08 r_work: 0.3501 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.0887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11756 Z= 0.215 Angle : 0.686 8.440 16922 Z= 0.387 Chirality : 0.050 0.234 1926 Planarity : 0.005 0.046 1291 Dihedral : 31.150 163.314 3521 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 4.13 % Allowed : 20.16 % Favored : 75.71 % 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: 1.73 (0.29), residues: 746 helix: 1.87 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -0.86 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 86 TYR 0.015 0.002 TYR C 57 PHE 0.014 0.002 PHE E 67 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.21 (11756) covalent geometry : angle 0.68573 / 0.39 (16922) hydrogen bonds : bond 0.06063 / 4.08 ( 721) hydrogen bonds : angle 3.16056 / 2.25 ( 1828) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.307 Fit side-chains REVERT: A 80 THR cc_start: 0.8665 (p) cc_final: 0.8363 (t) REVERT: C 73 ASN cc_start: 0.7194 (t0) cc_final: 0.6666 (t0) REVERT: D 33 ARG cc_start: 0.5870 (OUTLIER) cc_final: 0.4727 (mtp180) REVERT: F 77 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8503 (mtmt) REVERT: F 95 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.7580 (mtp-110) REVERT: H 91 SER cc_start: 0.8825 (OUTLIER) cc_final: 0.8556 (m) REVERT: H 116 LYS cc_start: 0.8000 (ttmt) cc_final: 0.7682 (ttmt) outliers start: 26 outliers final: 14 residues processed: 139 average time/residue: 0.9338 time to fit residues: 135.5973 Evaluate side-chains 138 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 91 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 53 optimal weight: 10.0000 chunk 47 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 73 optimal weight: 40.0000 chunk 77 optimal weight: 20.0000 chunk 78 optimal weight: 20.0000 chunk 19 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN G 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.190188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.141993 restraints weight = 9982.865| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 1.07 r_work: 0.3504 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11756 Z= 0.170 Angle : 0.667 8.693 16922 Z= 0.379 Chirality : 0.048 0.234 1926 Planarity : 0.005 0.047 1291 Dihedral : 31.155 163.089 3521 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.33 % Allowed : 21.75 % Favored : 74.92 % 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: 1.75 (0.29), residues: 746 helix: 1.89 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -0.87 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 35 TYR 0.014 0.002 TYR C 57 PHE 0.015 0.002 PHE E 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.17 (11756) covalent geometry : angle 0.66740 / 0.38 (16922) hydrogen bonds : bond 0.05773 / 3.89 ( 721) hydrogen bonds : angle 3.14706 / 2.24 ( 1828) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.241 Fit side-chains REVERT: A 80 THR cc_start: 0.8635 (p) cc_final: 0.8362 (t) REVERT: C 73 ASN cc_start: 0.7176 (t0) cc_final: 0.6646 (t0) REVERT: D 33 ARG cc_start: 0.5856 (OUTLIER) cc_final: 0.4721 (mtp180) REVERT: G 92 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7290 (mt-10) REVERT: H 91 SER cc_start: 0.8800 (OUTLIER) cc_final: 0.8555 (m) REVERT: H 116 LYS cc_start: 0.7992 (ttmt) cc_final: 0.7674 (ttmt) outliers start: 21 outliers final: 16 residues processed: 136 average time/residue: 0.8632 time to fit residues: 122.7695 Evaluate side-chains 139 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 111 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 92 optimal weight: 30.0000 chunk 7 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 40 optimal weight: 0.0050 chunk 5 optimal weight: 1.9990 chunk 76 optimal weight: 20.0000 chunk 39 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN G 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.192253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.144509 restraints weight = 10003.923| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 1.06 r_work: 0.3538 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.0890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11756 Z= 0.131 Angle : 0.638 8.067 16922 Z= 0.364 Chirality : 0.047 0.223 1926 Planarity : 0.005 0.062 1291 Dihedral : 31.166 163.879 3521 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.70 % Allowed : 21.75 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.30), residues: 746 helix: 2.18 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.73 (0.38), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 86 TYR 0.012 0.001 TYR C 57 PHE 0.015 0.002 PHE E 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.13 (11756) covalent geometry : angle 0.63763 / 0.36 (16922) hydrogen bonds : bond 0.04703 / 3.17 ( 721) hydrogen bonds : angle 3.08143 / 2.19 ( 1828) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.291 Fit side-chains REVERT: A 80 THR cc_start: 0.8642 (p) cc_final: 0.8407 (t) REVERT: C 73 ASN cc_start: 0.7180 (t0) cc_final: 0.6625 (t0) REVERT: D 33 ARG cc_start: 0.5896 (OUTLIER) cc_final: 0.4768 (mtp180) REVERT: G 84 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7448 (tm-30) outliers start: 17 outliers final: 11 residues processed: 137 average time/residue: 0.9183 time to fit residues: 131.8285 Evaluate side-chains 133 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 84 GLN Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 71 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 46 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 85 optimal weight: 30.0000 chunk 35 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 81 optimal weight: 20.0000 chunk 43 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN E 68 GLN G 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.192495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.144689 restraints weight = 9953.250| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 1.06 r_work: 0.3543 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.0901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11756 Z= 0.143 Angle : 0.632 7.535 16922 Z= 0.362 Chirality : 0.046 0.219 1926 Planarity : 0.005 0.051 1291 Dihedral : 31.147 164.109 3520 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.22 % Allowed : 22.06 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.30), residues: 746 helix: 2.24 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.66 (0.38), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 35 TYR 0.012 0.001 TYR C 57 PHE 0.014 0.002 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.14 (11756) covalent geometry : angle 0.63226 / 0.36 (16922) hydrogen bonds : bond 0.04611 / 3.11 ( 721) hydrogen bonds : angle 3.02326 / 2.15 ( 1828) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.308 Fit side-chains REVERT: A 80 THR cc_start: 0.8631 (p) cc_final: 0.8406 (t) REVERT: C 73 ASN cc_start: 0.7164 (t0) cc_final: 0.6578 (t0) REVERT: D 33 ARG cc_start: 0.5909 (OUTLIER) cc_final: 0.4762 (mtp180) REVERT: G 92 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7236 (mt-10) outliers start: 14 outliers final: 10 residues processed: 133 average time/residue: 0.9483 time to fit residues: 131.8933 Evaluate side-chains 133 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 71 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 36 optimal weight: 20.0000 chunk 94 optimal weight: 20.0000 chunk 73 optimal weight: 40.0000 chunk 81 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN E 68 GLN E 93 GLN G 73 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.190662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.142530 restraints weight = 10088.862| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 1.08 r_work: 0.3520 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11756 Z= 0.188 Angle : 0.658 7.917 16922 Z= 0.374 Chirality : 0.048 0.225 1926 Planarity : 0.005 0.053 1291 Dihedral : 31.153 162.955 3520 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.38 % Allowed : 21.90 % Favored : 75.71 % 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: 1.99 (0.30), residues: 746 helix: 2.05 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -0.75 (0.38), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 35 TYR 0.014 0.002 TYR C 57 PHE 0.012 0.002 PHE E 67 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.19 (11756) covalent geometry : angle 0.65766 / 0.37 (16922) hydrogen bonds : bond 0.05443 / 3.67 ( 721) hydrogen bonds : angle 3.09831 / 2.21 ( 1828) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.274 Fit side-chains REVERT: A 80 THR cc_start: 0.8673 (p) cc_final: 0.8455 (t) REVERT: A 129 ARG cc_start: 0.8035 (tmt170) cc_final: 0.7781 (tpt90) REVERT: C 73 ASN cc_start: 0.7295 (t0) cc_final: 0.6712 (t0) REVERT: D 33 ARG cc_start: 0.5933 (OUTLIER) cc_final: 0.4778 (mtp180) REVERT: H 116 LYS cc_start: 0.8013 (ttmt) cc_final: 0.7701 (ttmt) outliers start: 15 outliers final: 12 residues processed: 132 average time/residue: 0.9281 time to fit residues: 128.0192 Evaluate side-chains 135 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 111 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 88 optimal weight: 20.0000 chunk 65 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 63 optimal weight: 7.9990 chunk 90 optimal weight: 20.0000 chunk 95 optimal weight: 50.0000 chunk 52 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 85 optimal weight: 30.0000 chunk 46 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN E 68 GLN G 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.191260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.143213 restraints weight = 10054.193| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 1.07 r_work: 0.3522 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11756 Z= 0.146 Angle : 0.643 8.129 16922 Z= 0.368 Chirality : 0.046 0.226 1926 Planarity : 0.005 0.052 1291 Dihedral : 31.154 162.926 3520 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.90 % Allowed : 22.86 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.30), residues: 746 helix: 2.10 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -0.73 (0.38), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 35 TYR 0.013 0.001 TYR C 57 PHE 0.014 0.002 PHE E 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.15 (11756) covalent geometry : angle 0.64333 / 0.37 (16922) hydrogen bonds : bond 0.05218 / 3.52 ( 721) hydrogen bonds : angle 3.08766 / 2.20 ( 1828) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4158.17 seconds wall clock time: 71 minutes 15.17 seconds (4275.17 seconds total)