Starting phenix.real_space_refine on Fri Jul 3 03:53:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k46_62048/07_2026/9k46_62048.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k46_62048/07_2026/9k46_62048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k46_62048/07_2026/9k46_62048.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k46_62048/07_2026/9k46_62048.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k46_62048/07_2026/9k46_62048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k46_62048/07_2026/9k46_62048.map" } resolution = 2.85 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= -0.004 sd= 0.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 289 5.49 5 S 14 5.16 5 C 6597 2.51 5 N 2172 2.21 5 O 2772 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s 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: 11844 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 644 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 785 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "E" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 644 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 785 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "I" Number of atoms: 2950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2950 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2992 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Time building chain proxies: 2.81, per 1000 atoms: 0.24 Number of scatterers: 11844 At special positions: 0 Unit cell: (123.28, 80.4, 115.776, 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 289 15.00 O 2772 8.00 N 2172 7.00 C 6597 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 236.8 milliseconds 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1388 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 72.4% alpha, 3.2% beta 144 base pairs and 255 stacking pairs defined. Time for finding SS restraints: 2.00 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 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 131 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.590A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 25 through 30 Processing helix chain 'C' and resid 35 through 46 Processing helix chain 'C' and resid 55 through 82 Processing helix chain 'C' and resid 88 through 98 Processing helix chain 'C' and resid 99 through 106 Processing helix chain 'D' and resid 60 through 72 Processing helix chain 'D' and resid 78 through 107 Processing helix chain 'D' and resid 113 through 125 Processing helix chain 'D' and resid 127 through 147 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.587A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'G' and resid 25 through 31 Processing helix chain 'G' and resid 35 through 46 Processing helix chain 'G' and resid 55 through 82 Processing helix chain 'G' and resid 88 through 98 Processing helix chain 'G' and resid 99 through 106 Processing helix chain 'H' and resid 60 through 72 Processing helix chain 'H' and resid 78 through 107 Processing helix chain 'H' and resid 113 through 125 Processing helix chain 'H' and resid 127 through 147 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.090A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.824A pdb=" N THR B 96 " --> pdb=" O THR G 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 51 through 52 removed outlier: 7.224A pdb=" N ARG C 51 " --> pdb=" O ILE D 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 86 through 87 Processing sheet with id=AA6, first strand: chain 'C' and resid 109 through 111 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.149A 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 51 through 52 removed outlier: 7.123A pdb=" N ARG G 51 " --> pdb=" O ILE H 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 86 through 87 408 hydrogen bonds defined for protein. 1206 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 346 hydrogen bonds 692 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 255 stacking parallelities Total time for adding SS restraints: 2.37 Time building geometry restraints manager: 1.29 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: 2001 1.33 - 1.45: 4263 1.45 - 1.57: 5784 1.57 - 1.69: 577 1.69 - 1.81: 26 Bond restraints: 12651 Sorted by residual: bond pdb=" O3' DG I -26 " pdb=" P DT I -25 " ideal model delta sigma weight residual 1.607 1.668 -0.061 1.50e-02 4.44e+03 1.64e+01 bond pdb=" O3' DT J -36 " pdb=" P DG J -35 " ideal model delta sigma weight residual 1.607 1.658 -0.051 1.50e-02 4.44e+03 1.18e+01 bond pdb=" C3' DA I -20 " pdb=" C2' DA I -20 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 bond pdb=" O3' DC J -24 " pdb=" P DC J -23 " ideal model delta sigma weight residual 1.607 1.655 -0.048 1.50e-02 4.44e+03 1.04e+01 bond pdb=" C3' DG I -40 " pdb=" C2' DG I -40 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 ... (remaining 12646 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 15958 1.03 - 2.07: 1670 2.07 - 3.10: 644 3.10 - 4.14: 43 4.14 - 5.17: 10 Bond angle restraints: 18325 Sorted by residual: angle pdb=" N3 DT I -11 " pdb=" C4 DT I -11 " pdb=" O4 DT I -11 " ideal model delta sigma weight residual 119.90 122.61 -2.71 6.00e-01 2.78e+00 2.05e+01 angle pdb=" N3 DT I 22 " pdb=" C4 DT I 22 " pdb=" O4 DT I 22 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.02e+01 angle pdb=" N3 DT I -53 " pdb=" C4 DT I -53 " pdb=" O4 DT I -53 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.00e+01 angle pdb=" N3 DT I -33 " pdb=" C4 DT I -33 " pdb=" O4 DT I -33 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 2.00e+01 angle pdb=" N3 DT I -69 " pdb=" C4 DT I -69 " pdb=" O4 DT I -69 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.98e+01 ... (remaining 18320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.36: 4612 23.36 - 46.72: 1515 46.72 - 70.08: 789 70.08 - 93.44: 26 93.44 - 116.80: 1 Dihedral angle restraints: 6943 sinusoidal: 4791 harmonic: 2152 Sorted by residual: dihedral pdb=" C4' DG J -17 " pdb=" C3' DG J -17 " pdb=" O3' DG J -17 " pdb=" P DC J -16 " ideal model delta sinusoidal sigma weight residual -140.00 -23.20 -116.80 1 3.50e+01 8.16e-04 1.14e+01 dihedral pdb=" CG ARG E 49 " pdb=" CD ARG E 49 " pdb=" NE ARG E 49 " pdb=" CZ ARG E 49 " ideal model delta sinusoidal sigma weight residual 180.00 137.26 42.74 2 1.50e+01 4.44e-03 9.83e+00 dihedral pdb=" CG ARG G 97 " pdb=" CD ARG G 97 " pdb=" NE ARG G 97 " pdb=" CZ ARG G 97 " ideal model delta sinusoidal sigma weight residual -180.00 -137.43 -42.57 2 1.50e+01 4.44e-03 9.76e+00 ... (remaining 6940 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1129 0.031 - 0.061: 616 0.061 - 0.092: 218 0.092 - 0.122: 114 0.122 - 0.153: 12 Chirality restraints: 2089 Sorted by residual: chirality pdb=" P DC J 44 " pdb=" OP1 DC J 44 " pdb=" OP2 DC J 44 " pdb=" O5' DC J 44 " both_signs ideal model delta sigma weight residual True 2.34 -2.49 -0.15 2.00e-01 2.50e+01 5.85e-01 chirality pdb=" P DA I -8 " pdb=" OP1 DA I -8 " pdb=" OP2 DA I -8 " pdb=" O5' DA I -8 " both_signs ideal model delta sigma weight residual True 2.34 -2.49 -0.15 2.00e-01 2.50e+01 5.79e-01 chirality pdb=" P DT I 13 " pdb=" OP1 DT I 13 " pdb=" OP2 DT I 13 " pdb=" O5' DT I 13 " both_signs ideal model delta sigma weight residual True 2.34 -2.48 -0.15 2.00e-01 2.50e+01 5.33e-01 ... (remaining 2086 not shown) Planarity restraints: 1306 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 59 " -0.008 2.00e-02 2.50e+03 1.63e-02 2.65e+00 pdb=" C LYS B 59 " 0.028 2.00e-02 2.50e+03 pdb=" O LYS B 59 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE B 60 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 59 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.55e+00 pdb=" C LYS F 59 " -0.028 2.00e-02 2.50e+03 pdb=" O LYS F 59 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE F 60 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU F 52 " -0.007 2.00e-02 2.50e+03 1.46e-02 2.14e+00 pdb=" CD GLU F 52 " 0.025 2.00e-02 2.50e+03 pdb=" OE1 GLU F 52 " -0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU F 52 " -0.009 2.00e-02 2.50e+03 ... (remaining 1303 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 910 2.74 - 3.28: 10492 3.28 - 3.82: 23150 3.82 - 4.36: 28452 4.36 - 4.90: 40346 Nonbonded interactions: 103350 Sorted by model distance: nonbonded pdb=" NH2 ARG C 41 " pdb=" OE1 GLU D 58 " model vdw 2.198 3.120 nonbonded pdb=" O ASN G 82 " pdb=" ND2 ASN G 82 " model vdw 2.201 3.120 nonbonded pdb=" O ASN C 82 " pdb=" ND2 ASN C 82 " model vdw 2.203 3.120 nonbonded pdb=" OH TYR C 48 " pdb=" OE2 GLU D 94 " model vdw 2.216 3.040 nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.250 3.040 ... (remaining 103345 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=0.00 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: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.380 Find NCS groups from input model: 0.110 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:6.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 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 0.061 12651 Z= 0.503 Angle : 0.745 5.173 18325 Z= 0.680 Chirality : 0.045 0.153 2089 Planarity : 0.004 0.034 1306 Dihedral : 29.027 116.802 5555 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.80 % Allowed : 20.67 % Favored : 78.53 % 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: 1.40 (0.30), residues: 730 helix: 1.32 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.06 (0.40), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 41 TYR 0.016 0.001 TYR H 63 PHE 0.006 0.001 PHE G 34 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.50 (12651) covalent geometry : angle 0.74524 / 0.68 (18325) hydrogen bonds : bond 0.12183 / 8.32 ( 754) hydrogen bonds : angle 5.19157 / 3.75 ( 1898) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 178 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8470 (tt0) cc_final: 0.7793 (tt0) REVERT: C 121 ASN cc_start: 0.9122 (t0) cc_final: 0.8887 (t0) REVERT: D 56 ASN cc_start: 0.9292 (m-40) cc_final: 0.8927 (m-40) REVERT: D 91 ASP cc_start: 0.8784 (t0) cc_final: 0.8551 (t0) REVERT: E 73 GLU cc_start: 0.8338 (tt0) cc_final: 0.7702 (tt0) REVERT: F 27 GLN cc_start: 0.9224 (tp40) cc_final: 0.9007 (mp10) REVERT: G 121 ASN cc_start: 0.9198 (t0) cc_final: 0.8962 (t0) REVERT: H 56 ASN cc_start: 0.8899 (m-40) cc_final: 0.8516 (m-40) REVERT: H 91 ASP cc_start: 0.8689 (t0) cc_final: 0.8483 (t0) outliers start: 5 outliers final: 4 residues processed: 181 average time/residue: 0.7784 time to fit residues: 149.3330 Evaluate side-chains 147 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 143 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 49 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.2980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN C 82 ASN D 107 ASN D 132 HIS G 82 ASN H 107 ASN H 132 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.066091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.044123 restraints weight = 40107.487| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 1.91 r_work: 0.2625 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12651 Z= 0.184 Angle : 0.657 8.155 18325 Z= 0.387 Chirality : 0.045 0.216 2089 Planarity : 0.005 0.039 1306 Dihedral : 31.734 124.814 4082 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.88 % Allowed : 23.40 % Favored : 73.72 % 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: 2.41 (0.30), residues: 730 helix: 2.13 (0.22), residues: 554 sheet: None (None), residues: 0 loop : -0.08 (0.42), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 80 TYR 0.016 0.002 TYR B 51 PHE 0.008 0.001 PHE A 67 HIS 0.003 0.001 HIS H 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.18 (12651) covalent geometry : angle 0.65652 / 0.39 (18325) hydrogen bonds : bond 0.05615 / 3.79 ( 754) hydrogen bonds : angle 3.26030 / 2.35 ( 1898) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 149 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8558 (pm20) cc_final: 0.8091 (pm20) REVERT: A 73 GLU cc_start: 0.8685 (tt0) cc_final: 0.8274 (tt0) REVERT: A 94 GLU cc_start: 0.8889 (tp30) cc_final: 0.8650 (tt0) REVERT: C 80 ARG cc_start: 0.9179 (ttm-80) cc_final: 0.8965 (ttp80) REVERT: C 82 ASN cc_start: 0.8994 (t0) cc_final: 0.8763 (t160) REVERT: C 104 LYS cc_start: 0.9570 (ttpt) cc_final: 0.9335 (ttmm) REVERT: C 121 ASN cc_start: 0.8862 (t0) cc_final: 0.8433 (t0) REVERT: D 56 ASN cc_start: 0.8974 (m-40) cc_final: 0.8581 (m-40) REVERT: D 91 ASP cc_start: 0.9245 (t0) cc_final: 0.8882 (t0) REVERT: E 73 GLU cc_start: 0.8653 (tt0) cc_final: 0.8372 (tt0) REVERT: F 27 GLN cc_start: 0.9477 (tp40) cc_final: 0.9110 (mp10) REVERT: G 99 ASP cc_start: 0.8771 (t0) cc_final: 0.8144 (t0) REVERT: G 121 ASN cc_start: 0.8918 (t0) cc_final: 0.8579 (t0) REVERT: H 56 ASN cc_start: 0.8709 (m-40) cc_final: 0.8366 (m-40) REVERT: H 128 GLU cc_start: 0.8524 (tp30) cc_final: 0.8276 (mm-30) outliers start: 18 outliers final: 4 residues processed: 158 average time/residue: 0.8009 time to fit residues: 133.8850 Evaluate side-chains 148 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 144 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain H residue 85 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 18 optimal weight: 1.9990 chunk 85 optimal weight: 40.0000 chunk 28 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 36 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 98 optimal weight: 20.0000 chunk 9 optimal weight: 0.0870 chunk 76 optimal weight: 20.0000 overall best weight: 1.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.065274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.043320 restraints weight = 41005.569| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 1.95 r_work: 0.2620 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12651 Z= 0.165 Angle : 0.614 7.742 18325 Z= 0.367 Chirality : 0.043 0.209 2089 Planarity : 0.004 0.043 1306 Dihedral : 31.771 129.016 4075 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.40 % Allowed : 23.88 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.00 (0.30), residues: 730 helix: 2.56 (0.21), residues: 556 sheet: None (None), residues: 0 loop : 0.06 (0.44), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 80 TYR 0.012 0.002 TYR H 63 PHE 0.010 0.001 PHE E 67 HIS 0.002 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.16 (12651) covalent geometry : angle 0.61362 / 0.37 (18325) hydrogen bonds : bond 0.04810 / 3.27 ( 754) hydrogen bonds : angle 2.89230 / 2.09 ( 1898) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8723 (pm20) cc_final: 0.7796 (pm20) REVERT: A 73 GLU cc_start: 0.8733 (tt0) cc_final: 0.8327 (tt0) REVERT: B 27 GLN cc_start: 0.9230 (OUTLIER) cc_final: 0.8974 (mp10) REVERT: C 28 MET cc_start: 0.9311 (tmm) cc_final: 0.9093 (tmm) REVERT: C 80 ARG cc_start: 0.9172 (ttm-80) cc_final: 0.8939 (ttp80) REVERT: C 99 ASP cc_start: 0.8794 (t0) cc_final: 0.8048 (t0) REVERT: C 104 LYS cc_start: 0.9583 (ttpt) cc_final: 0.9355 (ttmm) REVERT: C 121 ASN cc_start: 0.8861 (t0) cc_final: 0.8490 (t0) REVERT: D 56 ASN cc_start: 0.9047 (m-40) cc_final: 0.8623 (m-40) REVERT: D 91 ASP cc_start: 0.9303 (t0) cc_final: 0.8903 (t0) REVERT: E 59 GLU cc_start: 0.8620 (pm20) cc_final: 0.8257 (pm20) REVERT: E 73 GLU cc_start: 0.8780 (tt0) cc_final: 0.8281 (tt0) REVERT: F 27 GLN cc_start: 0.9455 (tp40) cc_final: 0.9119 (mp10) REVERT: G 28 MET cc_start: 0.9116 (tmm) cc_final: 0.8868 (tmm) REVERT: G 65 GLU cc_start: 0.9288 (tt0) cc_final: 0.9069 (tt0) REVERT: G 80 ARG cc_start: 0.9206 (ttm-80) cc_final: 0.8954 (ttp80) REVERT: G 82 ASN cc_start: 0.8809 (t0) cc_final: 0.8594 (t160) REVERT: G 99 ASP cc_start: 0.8677 (t0) cc_final: 0.8002 (t0) REVERT: G 104 LYS cc_start: 0.9560 (ttpt) cc_final: 0.9312 (ttmm) REVERT: G 121 ASN cc_start: 0.8872 (t0) cc_final: 0.8529 (t0) REVERT: H 56 ASN cc_start: 0.8695 (m-40) cc_final: 0.8373 (m-40) REVERT: H 109 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8637 (tttm) REVERT: H 128 GLU cc_start: 0.8660 (tp30) cc_final: 0.8401 (mm-30) outliers start: 15 outliers final: 4 residues processed: 164 average time/residue: 0.7810 time to fit residues: 135.5561 Evaluate side-chains 155 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 149 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 109 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 86 optimal weight: 30.0000 chunk 75 optimal weight: 20.0000 chunk 77 optimal weight: 20.0000 chunk 20 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 81 optimal weight: 20.0000 chunk 44 optimal weight: 0.0970 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 11 optimal weight: 0.3980 overall best weight: 1.2580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.064596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.043051 restraints weight = 41441.371| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 1.97 r_work: 0.2614 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 12651 Z= 0.141 Angle : 0.596 7.607 18325 Z= 0.356 Chirality : 0.043 0.200 2089 Planarity : 0.004 0.041 1306 Dihedral : 31.725 131.229 4075 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.24 % Allowed : 24.84 % Favored : 72.92 % 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: 3.32 (0.30), residues: 730 helix: 2.81 (0.21), residues: 556 sheet: None (None), residues: 0 loop : 0.10 (0.44), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 105 TYR 0.012 0.001 TYR H 63 PHE 0.010 0.001 PHE A 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.14 (12651) covalent geometry : angle 0.59604 / 0.36 (18325) hydrogen bonds : bond 0.04262 / 2.93 ( 754) hydrogen bonds : angle 2.73317 / 1.98 ( 1898) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8651 (pm20) cc_final: 0.8295 (pm20) REVERT: A 73 GLU cc_start: 0.8800 (tt0) cc_final: 0.8399 (tt0) REVERT: A 94 GLU cc_start: 0.8756 (tp30) cc_final: 0.8512 (tt0) REVERT: B 85 ASP cc_start: 0.9342 (m-30) cc_final: 0.9129 (m-30) REVERT: C 28 MET cc_start: 0.9268 (tmm) cc_final: 0.9052 (tmm) REVERT: C 99 ASP cc_start: 0.8719 (t0) cc_final: 0.7898 (t0) REVERT: C 104 LYS cc_start: 0.9581 (ttpt) cc_final: 0.9357 (ttmm) REVERT: C 121 ASN cc_start: 0.8843 (t0) cc_final: 0.8576 (t0) REVERT: D 56 ASN cc_start: 0.8986 (m-40) cc_final: 0.8638 (m-40) REVERT: D 91 ASP cc_start: 0.9307 (t0) cc_final: 0.8894 (t0) REVERT: E 59 GLU cc_start: 0.8530 (pm20) cc_final: 0.8178 (pm20) REVERT: E 73 GLU cc_start: 0.8808 (tt0) cc_final: 0.8363 (tt0) REVERT: F 27 GLN cc_start: 0.9445 (OUTLIER) cc_final: 0.9053 (mp10) REVERT: G 28 MET cc_start: 0.9219 (tmm) cc_final: 0.8962 (tmm) REVERT: G 29 LYS cc_start: 0.9372 (OUTLIER) cc_final: 0.9152 (tttt) REVERT: G 99 ASP cc_start: 0.8676 (t0) cc_final: 0.7980 (t0) REVERT: G 104 LYS cc_start: 0.9558 (ttpt) cc_final: 0.9326 (ttmm) REVERT: H 56 ASN cc_start: 0.8682 (m-40) cc_final: 0.8361 (m-40) REVERT: H 109 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8501 (tttm) REVERT: H 128 GLU cc_start: 0.8602 (tp30) cc_final: 0.8354 (mm-30) outliers start: 14 outliers final: 4 residues processed: 168 average time/residue: 0.7794 time to fit residues: 138.4800 Evaluate side-chains 156 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 149 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 109 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 81 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 86 optimal weight: 30.0000 chunk 90 optimal weight: 20.0000 chunk 2 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 87 optimal weight: 30.0000 chunk 51 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.064805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.043302 restraints weight = 41333.237| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 1.96 r_work: 0.2625 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12651 Z= 0.132 Angle : 0.591 7.974 18325 Z= 0.354 Chirality : 0.042 0.199 2089 Planarity : 0.004 0.045 1306 Dihedral : 31.689 132.426 4073 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.24 % Allowed : 25.80 % Favored : 71.96 % 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: 3.48 (0.30), residues: 730 helix: 2.93 (0.21), residues: 556 sheet: None (None), residues: 0 loop : 0.16 (0.44), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 80 TYR 0.012 0.001 TYR H 63 PHE 0.010 0.001 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.13 (12651) covalent geometry : angle 0.59076 / 0.35 (18325) hydrogen bonds : bond 0.04073 / 2.80 ( 754) hydrogen bonds : angle 2.64452 / 1.91 ( 1898) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 154 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8634 (pm20) cc_final: 0.8203 (pm20) REVERT: A 94 GLU cc_start: 0.8788 (tp30) cc_final: 0.8579 (tt0) REVERT: B 85 ASP cc_start: 0.9344 (m-30) cc_final: 0.9133 (m-30) REVERT: C 28 MET cc_start: 0.9281 (tmm) cc_final: 0.9052 (tmm) REVERT: C 80 ARG cc_start: 0.9173 (ttm-80) cc_final: 0.8963 (ttp80) REVERT: C 99 ASP cc_start: 0.8699 (t0) cc_final: 0.7899 (t0) REVERT: C 104 LYS cc_start: 0.9589 (ttpt) cc_final: 0.9368 (ttmm) REVERT: C 121 ASN cc_start: 0.8815 (t0) cc_final: 0.8514 (t0) REVERT: D 56 ASN cc_start: 0.8978 (m-40) cc_final: 0.8670 (m-40) REVERT: D 91 ASP cc_start: 0.9301 (t0) cc_final: 0.8877 (t0) REVERT: E 59 GLU cc_start: 0.8536 (pm20) cc_final: 0.8173 (pm20) REVERT: E 73 GLU cc_start: 0.8815 (tt0) cc_final: 0.8414 (tt0) REVERT: F 27 GLN cc_start: 0.9419 (OUTLIER) cc_final: 0.9060 (mp10) REVERT: F 85 ASP cc_start: 0.9377 (m-30) cc_final: 0.9173 (m-30) REVERT: G 29 LYS cc_start: 0.9392 (OUTLIER) cc_final: 0.9171 (tttt) REVERT: G 99 ASP cc_start: 0.8619 (t0) cc_final: 0.7913 (t0) REVERT: G 104 LYS cc_start: 0.9564 (ttpt) cc_final: 0.9326 (ttmm) REVERT: H 56 ASN cc_start: 0.8690 (m-40) cc_final: 0.8394 (m-40) REVERT: H 109 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8353 (tttp) REVERT: H 128 GLU cc_start: 0.8566 (tp30) cc_final: 0.8361 (mm-30) outliers start: 14 outliers final: 5 residues processed: 162 average time/residue: 0.7784 time to fit residues: 133.5844 Evaluate side-chains 157 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 149 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 109 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 47 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 88 optimal weight: 20.0000 chunk 72 optimal weight: 30.0000 chunk 32 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 85 optimal weight: 30.0000 chunk 22 optimal weight: 0.9980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN C 82 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.063920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.042636 restraints weight = 41695.054| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 1.97 r_work: 0.2598 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12651 Z= 0.161 Angle : 0.609 7.796 18325 Z= 0.360 Chirality : 0.042 0.201 2089 Planarity : 0.004 0.040 1306 Dihedral : 31.752 133.137 4073 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.08 % Allowed : 26.12 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.55 (0.30), residues: 730 helix: 2.98 (0.21), residues: 556 sheet: None (None), residues: 0 loop : 0.16 (0.44), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 80 TYR 0.011 0.002 TYR H 63 PHE 0.009 0.001 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.16 (12651) covalent geometry : angle 0.60880 / 0.36 (18325) hydrogen bonds : bond 0.04508 / 3.10 ( 754) hydrogen bonds : angle 2.70239 / 1.96 ( 1898) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8247 (pm20) REVERT: A 94 GLU cc_start: 0.8833 (tp30) cc_final: 0.8608 (tt0) REVERT: C 28 MET cc_start: 0.9329 (tmm) cc_final: 0.8989 (tmm) REVERT: C 80 ARG cc_start: 0.9197 (ttm-80) cc_final: 0.8950 (ttp80) REVERT: C 99 ASP cc_start: 0.8739 (t0) cc_final: 0.7910 (t0) REVERT: C 104 LYS cc_start: 0.9602 (ttpt) cc_final: 0.9376 (ttmm) REVERT: C 121 ASN cc_start: 0.8824 (t0) cc_final: 0.8569 (t0) REVERT: D 56 ASN cc_start: 0.8959 (m-40) cc_final: 0.8618 (m-40) REVERT: D 91 ASP cc_start: 0.9308 (t0) cc_final: 0.8885 (t0) REVERT: E 59 GLU cc_start: 0.8562 (pm20) cc_final: 0.8152 (pm20) REVERT: E 73 GLU cc_start: 0.8848 (tt0) cc_final: 0.8448 (tt0) REVERT: F 27 GLN cc_start: 0.9412 (OUTLIER) cc_final: 0.9090 (mp10) REVERT: G 28 MET cc_start: 0.9185 (tmm) cc_final: 0.8954 (tmm) REVERT: G 99 ASP cc_start: 0.8673 (t0) cc_final: 0.7939 (t0) REVERT: G 104 LYS cc_start: 0.9570 (ttpt) cc_final: 0.9329 (ttmm) REVERT: H 56 ASN cc_start: 0.8731 (m-40) cc_final: 0.8445 (m-40) REVERT: H 109 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8382 (tttp) REVERT: H 128 GLU cc_start: 0.8610 (tp30) cc_final: 0.8371 (mm-30) outliers start: 13 outliers final: 6 residues processed: 150 average time/residue: 0.7631 time to fit residues: 121.1072 Evaluate side-chains 149 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 140 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 109 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 18 optimal weight: 2.9990 chunk 73 optimal weight: 30.0000 chunk 39 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 83 optimal weight: 20.0000 chunk 38 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 97 optimal weight: 20.0000 chunk 51 optimal weight: 5.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.063604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.042347 restraints weight = 41562.503| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 1.97 r_work: 0.2592 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12651 Z= 0.160 Angle : 0.605 7.674 18325 Z= 0.357 Chirality : 0.042 0.199 2089 Planarity : 0.004 0.039 1306 Dihedral : 31.749 133.987 4073 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.08 % Allowed : 26.60 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.54 (0.30), residues: 730 helix: 2.99 (0.21), residues: 556 sheet: None (None), residues: 0 loop : 0.09 (0.44), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 80 TYR 0.011 0.002 TYR H 63 PHE 0.010 0.001 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.16 (12651) covalent geometry : angle 0.60451 / 0.36 (18325) hydrogen bonds : bond 0.04295 / 2.96 ( 754) hydrogen bonds : angle 2.69178 / 1.95 ( 1898) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8299 (pm20) REVERT: C 28 MET cc_start: 0.9352 (tmm) cc_final: 0.9053 (tmm) REVERT: C 99 ASP cc_start: 0.8744 (t0) cc_final: 0.7944 (t0) REVERT: C 104 LYS cc_start: 0.9594 (ttpt) cc_final: 0.9364 (ttmm) REVERT: C 121 ASN cc_start: 0.8846 (t0) cc_final: 0.8589 (t0) REVERT: D 56 ASN cc_start: 0.8995 (m-40) cc_final: 0.8677 (m-40) REVERT: D 91 ASP cc_start: 0.9334 (t0) cc_final: 0.8920 (t0) REVERT: E 59 GLU cc_start: 0.8571 (pm20) cc_final: 0.8159 (pm20) REVERT: E 73 GLU cc_start: 0.8855 (tt0) cc_final: 0.8283 (tt0) REVERT: F 23 ARG cc_start: 0.7849 (mmm160) cc_final: 0.7455 (mmm160) REVERT: F 27 GLN cc_start: 0.9427 (OUTLIER) cc_final: 0.9092 (mp10) REVERT: G 99 ASP cc_start: 0.8684 (t0) cc_final: 0.7932 (t0) REVERT: G 104 LYS cc_start: 0.9571 (ttpt) cc_final: 0.9341 (ttmm) REVERT: H 109 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8393 (tttp) REVERT: H 128 GLU cc_start: 0.8624 (tp30) cc_final: 0.8357 (mm-30) outliers start: 13 outliers final: 8 residues processed: 152 average time/residue: 0.7139 time to fit residues: 114.9251 Evaluate side-chains 149 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 138 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 109 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 83 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 chunk 97 optimal weight: 20.0000 chunk 3 optimal weight: 3.9990 chunk 90 optimal weight: 20.0000 chunk 56 optimal weight: 0.7980 chunk 95 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 85 GLN H 56 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.063334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.042161 restraints weight = 41736.399| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 1.96 r_work: 0.2594 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12651 Z= 0.160 Angle : 0.619 11.717 18325 Z= 0.361 Chirality : 0.042 0.199 2089 Planarity : 0.004 0.045 1306 Dihedral : 31.749 134.579 4073 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.08 % Allowed : 27.56 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.52 (0.30), residues: 730 helix: 2.99 (0.21), residues: 556 sheet: None (None), residues: 0 loop : 0.05 (0.44), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 80 TYR 0.011 0.002 TYR F 88 PHE 0.010 0.001 PHE E 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.16 (12651) covalent geometry : angle 0.61878 / 0.36 (18325) hydrogen bonds : bond 0.04336 / 2.98 ( 754) hydrogen bonds : angle 2.69160 / 1.95 ( 1898) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 147 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8264 (pm20) REVERT: A 73 GLU cc_start: 0.9019 (tt0) cc_final: 0.8307 (tt0) REVERT: C 28 MET cc_start: 0.9358 (tmm) cc_final: 0.9072 (tmm) REVERT: C 99 ASP cc_start: 0.8830 (t0) cc_final: 0.8000 (t0) REVERT: C 104 LYS cc_start: 0.9588 (ttpt) cc_final: 0.9352 (ttmm) REVERT: C 121 ASN cc_start: 0.8858 (t0) cc_final: 0.8391 (t0) REVERT: D 56 ASN cc_start: 0.9029 (m-40) cc_final: 0.8723 (m-40) REVERT: D 91 ASP cc_start: 0.9322 (t0) cc_final: 0.8902 (t0) REVERT: E 59 GLU cc_start: 0.8589 (pm20) cc_final: 0.7949 (pm20) REVERT: E 73 GLU cc_start: 0.8888 (tt0) cc_final: 0.8433 (tt0) REVERT: F 27 GLN cc_start: 0.9438 (OUTLIER) cc_final: 0.9088 (mp10) REVERT: G 82 ASN cc_start: 0.8923 (t0) cc_final: 0.8656 (t160) REVERT: G 99 ASP cc_start: 0.8689 (t0) cc_final: 0.7934 (t0) REVERT: G 104 LYS cc_start: 0.9562 (ttpt) cc_final: 0.9339 (ttmm) REVERT: H 109 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8373 (tttp) outliers start: 13 outliers final: 9 residues processed: 154 average time/residue: 0.7173 time to fit residues: 117.3344 Evaluate side-chains 151 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 109 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 78 optimal weight: 10.0000 chunk 66 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 26 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 87 optimal weight: 30.0000 chunk 41 optimal weight: 0.9980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.063757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.042418 restraints weight = 41131.406| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 1.97 r_work: 0.2609 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 12651 Z= 0.140 Angle : 0.611 14.654 18325 Z= 0.359 Chirality : 0.042 0.199 2089 Planarity : 0.004 0.041 1306 Dihedral : 31.678 135.068 4073 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.08 % Allowed : 28.04 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.49 (0.30), residues: 730 helix: 2.99 (0.21), residues: 554 sheet: None (None), residues: 0 loop : 0.02 (0.44), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 38 TYR 0.015 0.002 TYR H 106 PHE 0.011 0.001 PHE A 67 HIS 0.005 0.001 HIS H 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.14 (12651) covalent geometry : angle 0.61115 / 0.36 (18325) hydrogen bonds : bond 0.04008 / 2.76 ( 754) hydrogen bonds : angle 2.64314 / 1.92 ( 1898) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8284 (pm20) REVERT: A 73 GLU cc_start: 0.8936 (tt0) cc_final: 0.8639 (tt0) REVERT: C 28 MET cc_start: 0.9365 (tmm) cc_final: 0.9048 (tmm) REVERT: C 82 ASN cc_start: 0.8954 (t0) cc_final: 0.8694 (t160) REVERT: C 99 ASP cc_start: 0.8731 (t0) cc_final: 0.7919 (t0) REVERT: C 104 LYS cc_start: 0.9586 (ttpt) cc_final: 0.9345 (ttmm) REVERT: C 121 ASN cc_start: 0.8850 (t0) cc_final: 0.8375 (t0) REVERT: D 56 ASN cc_start: 0.9012 (m-40) cc_final: 0.8579 (m-40) REVERT: D 91 ASP cc_start: 0.9314 (t0) cc_final: 0.8865 (t0) REVERT: E 59 GLU cc_start: 0.8598 (pm20) cc_final: 0.8118 (pm20) REVERT: F 27 GLN cc_start: 0.9436 (OUTLIER) cc_final: 0.9069 (mp10) REVERT: G 82 ASN cc_start: 0.8936 (t0) cc_final: 0.8668 (t160) REVERT: G 99 ASP cc_start: 0.8668 (t0) cc_final: 0.7955 (t0) REVERT: G 104 LYS cc_start: 0.9573 (ttpt) cc_final: 0.9349 (ttmm) REVERT: H 109 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8355 (tttp) outliers start: 13 outliers final: 9 residues processed: 151 average time/residue: 0.6917 time to fit residues: 110.9024 Evaluate side-chains 153 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 109 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 58 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 74 optimal weight: 20.0000 chunk 36 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 76 optimal weight: 20.0000 chunk 94 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.062639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.041480 restraints weight = 42024.099| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 1.99 r_work: 0.2572 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12651 Z= 0.183 Angle : 0.653 14.750 18325 Z= 0.372 Chirality : 0.043 0.202 2089 Planarity : 0.004 0.038 1306 Dihedral : 31.756 134.863 4073 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.76 % Allowed : 28.85 % Favored : 69.39 % 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: 3.57 (0.30), residues: 730 helix: 3.11 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -0.01 (0.43), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 80 TYR 0.013 0.002 TYR B 88 PHE 0.010 0.001 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.18 (12651) covalent geometry : angle 0.65295 / 0.37 (18325) hydrogen bonds : bond 0.04793 / 3.28 ( 754) hydrogen bonds : angle 2.76373 / 2.00 ( 1898) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 140 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8616 (pm20) cc_final: 0.8269 (pm20) REVERT: A 73 GLU cc_start: 0.9018 (tt0) cc_final: 0.8250 (tt0) REVERT: C 28 MET cc_start: 0.9376 (tmm) cc_final: 0.9054 (tmm) REVERT: C 82 ASN cc_start: 0.9021 (t0) cc_final: 0.8726 (t160) REVERT: C 99 ASP cc_start: 0.8863 (t0) cc_final: 0.8053 (t0) REVERT: C 104 LYS cc_start: 0.9595 (ttpt) cc_final: 0.9360 (ttmm) REVERT: C 121 ASN cc_start: 0.8901 (t0) cc_final: 0.8434 (t0) REVERT: D 56 ASN cc_start: 0.9050 (m-40) cc_final: 0.8590 (m-40) REVERT: D 91 ASP cc_start: 0.9354 (t0) cc_final: 0.8928 (t0) REVERT: E 59 GLU cc_start: 0.8626 (pm20) cc_final: 0.8147 (pm20) REVERT: F 27 GLN cc_start: 0.9439 (OUTLIER) cc_final: 0.9165 (mp10) REVERT: G 82 ASN cc_start: 0.9013 (t0) cc_final: 0.8713 (t160) REVERT: G 99 ASP cc_start: 0.8721 (t0) cc_final: 0.7912 (t0) REVERT: G 104 LYS cc_start: 0.9575 (ttpt) cc_final: 0.9344 (ttmm) REVERT: H 99 GLU cc_start: 0.9195 (tp30) cc_final: 0.8907 (tp30) REVERT: H 109 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8437 (tttm) outliers start: 11 outliers final: 9 residues processed: 146 average time/residue: 0.6869 time to fit residues: 106.3234 Evaluate side-chains 151 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 140 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 109 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 4.9990 chunk 73 optimal weight: 30.0000 chunk 15 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 74 optimal weight: 20.0000 chunk 10 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 88 optimal weight: 20.0000 chunk 59 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.062433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.041304 restraints weight = 41918.781| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 2.01 r_work: 0.2573 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12651 Z= 0.176 Angle : 0.644 15.131 18325 Z= 0.369 Chirality : 0.043 0.205 2089 Planarity : 0.004 0.041 1306 Dihedral : 31.780 135.365 4073 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.24 % Allowed : 28.69 % Favored : 69.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.36 (0.30), residues: 730 helix: 2.90 (0.21), residues: 556 sheet: None (None), residues: 0 loop : -0.11 (0.44), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 80 TYR 0.015 0.002 TYR H 106 PHE 0.012 0.001 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.18 (12651) covalent geometry : angle 0.64390 / 0.37 (18325) hydrogen bonds : bond 0.04335 / 2.97 ( 754) hydrogen bonds : angle 2.75683 / 1.99 ( 1898) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3517.92 seconds wall clock time: 60 minutes 32.69 seconds (3632.69 seconds total)