Starting phenix.real_space_refine on Fri Sep 11 20:32:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wz9_21971/09_2026/6wz9_21971.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wz9_21971/09_2026/6wz9_21971.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6wz9_21971/09_2026/6wz9_21971.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wz9_21971/09_2026/6wz9_21971.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wz9_21971/09_2026/6wz9_21971.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wz9_21971/09_2026/6wz9_21971.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 296 5.49 5 S 12 5.16 5 C 6569 2.51 5 N 2233 2.21 5 O 2816 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11926 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "B" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 786 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "D" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 721 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 818 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "H" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 721 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 3050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 3050 Classifications: {'DNA': 148} Link IDs: {'rna3p': 147} Chain: "J" Number of atoms: 3018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 3018 Classifications: {'DNA': 148} Link IDs: {'rna3p': 147} Time building chain proxies: 2.37, per 1000 atoms: 0.20 Number of scatterers: 11926 At special positions: 0 Unit cell: (124.02, 95.4, 116.6, 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 12 16.00 P 296 15.00 O 2816 8.00 N 2233 7.00 C 6569 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: 0.72 Conformation dependent library (CDL) restraints added in 348.5 milliseconds 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1384 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 74.8% alpha, 3.3% beta 148 base pairs and 269 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.189A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) 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 removed outlier: 3.738A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 72 removed outlier: 4.265A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.920A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.580A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) 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: 3.764A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 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: 4.331A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 120 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.875A 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: 6.540A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.297A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.757A 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: 7.195A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (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 78 411 hydrogen bonds defined for protein. 1209 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 380 hydrogen bonds 760 hydrogen bond angles 0 basepair planarities 148 basepair parallelities 269 stacking parallelities Total time for adding SS restraints: 2.59 Time building geometry restraints manager: 1.07 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: 2091 1.33 - 1.45: 4337 1.45 - 1.57: 5701 1.57 - 1.69: 590 1.69 - 1.81: 22 Bond restraints: 12741 Sorted by residual: bond pdb=" C3' DG I -37 " pdb=" O3' DG I -37 " ideal model delta sigma weight residual 1.435 1.383 0.052 1.30e-02 5.92e+03 1.58e+01 bond pdb=" C3' DG I -6 " pdb=" O3' DG I -6 " ideal model delta sigma weight residual 1.435 1.386 0.049 1.30e-02 5.92e+03 1.44e+01 bond pdb=" C3' DG I -4 " pdb=" O3' DG I -4 " ideal model delta sigma weight residual 1.435 1.389 0.046 1.30e-02 5.92e+03 1.28e+01 bond pdb=" C3' DA J -67 " pdb=" C2' DA J -67 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.24e+01 bond pdb=" C3' DT J -16 " pdb=" O3' DT J -16 " ideal model delta sigma weight residual 1.435 1.390 0.045 1.30e-02 5.92e+03 1.22e+01 ... (remaining 12736 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 17801 2.23 - 4.47: 668 4.47 - 6.70: 11 6.70 - 8.93: 2 8.93 - 11.17: 2 Bond angle restraints: 18484 Sorted by residual: angle pdb=" O4' DA I 16 " pdb=" C1' DA I 16 " pdb=" N9 DA I 16 " ideal model delta sigma weight residual 108.00 111.41 -3.41 7.00e-01 2.04e+00 2.38e+01 angle pdb=" O4' DT I 33 " pdb=" C4' DT I 33 " pdb=" C3' DT I 33 " ideal model delta sigma weight residual 106.00 103.09 2.91 6.00e-01 2.78e+00 2.36e+01 angle pdb=" N3 DT J -72 " pdb=" C4 DT J -72 " pdb=" O4 DT J -72 " ideal model delta sigma weight residual 119.90 122.71 -2.81 6.00e-01 2.78e+00 2.19e+01 angle pdb=" O4' DA J 16 " pdb=" C1' DA J 16 " pdb=" N9 DA J 16 " ideal model delta sigma weight residual 108.00 111.24 -3.24 7.00e-01 2.04e+00 2.14e+01 angle pdb=" N3 DT J 30 " pdb=" C4 DT J 30 " pdb=" O4 DT J 30 " ideal model delta sigma weight residual 119.90 122.65 -2.75 6.00e-01 2.78e+00 2.11e+01 ... (remaining 18479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.12: 5262 33.12 - 66.24: 1589 66.24 - 99.36: 31 99.36 - 132.48: 0 132.48 - 165.60: 2 Dihedral angle restraints: 6884 sinusoidal: 4740 harmonic: 2144 Sorted by residual: dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DG I 21 " ideal model delta sinusoidal sigma weight residual 220.00 54.40 165.60 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DC I 52 " pdb=" C3' DC I 52 " pdb=" O3' DC I 52 " pdb=" P DC I 53 " ideal model delta sinusoidal sigma weight residual 220.00 80.53 139.47 1 3.50e+01 8.16e-04 1.38e+01 dihedral pdb=" CA PRO H 100 " pdb=" C PRO H 100 " pdb=" N GLY H 101 " pdb=" CA GLY H 101 " ideal model delta harmonic sigma weight residual 180.00 162.47 17.53 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 6881 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1111 0.034 - 0.069: 648 0.069 - 0.103: 260 0.103 - 0.138: 78 0.138 - 0.172: 13 Chirality restraints: 2110 Sorted by residual: chirality pdb=" CA LYS B 79 " pdb=" N LYS B 79 " pdb=" C LYS B 79 " pdb=" CB LYS B 79 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.42e-01 chirality pdb=" CA ILE D 86 " pdb=" N ILE D 86 " pdb=" C ILE D 86 " pdb=" CB ILE D 86 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.85e-01 chirality pdb=" C3' DC J 66 " pdb=" C4' DC J 66 " pdb=" O3' DC J 66 " pdb=" C2' DC J 66 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.77e-01 ... (remaining 2107 not shown) Planarity restraints: 1312 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 42 " -0.034 5.00e-02 4.00e+02 5.16e-02 4.26e+00 pdb=" N PRO A 43 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 43 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 43 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 47 " -0.029 2.00e-02 2.50e+03 1.22e-02 4.09e+00 pdb=" N9 DA I 47 " 0.023 2.00e-02 2.50e+03 pdb=" C8 DA I 47 " 0.008 2.00e-02 2.50e+03 pdb=" N7 DA I 47 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DA I 47 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA I 47 " -0.004 2.00e-02 2.50e+03 pdb=" N6 DA I 47 " -0.011 2.00e-02 2.50e+03 pdb=" N1 DA I 47 " 0.000 2.00e-02 2.50e+03 pdb=" C2 DA I 47 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DA I 47 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DA I 47 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG E 42 " 0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO E 43 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO E 43 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 43 " 0.027 5.00e-02 4.00e+02 ... (remaining 1309 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 71 2.59 - 3.17: 9062 3.17 - 3.75: 22466 3.75 - 4.32: 31511 4.32 - 4.90: 43549 Nonbonded interactions: 106659 Sorted by model distance: nonbonded pdb=" OG1 THR H 29 " pdb=" OP1 DT J 30 " model vdw 2.015 3.040 nonbonded pdb=" NZ LYS F 59 " pdb=" OE2 GLU F 63 " model vdw 2.151 3.120 nonbonded pdb=" NH2 ARG C 20 " pdb=" OP1 DG I -42 " model vdw 2.186 3.120 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.253 3.040 nonbonded pdb=" OE1 GLU A 105 " pdb=" NH2 ARG E 129 " model vdw 2.298 3.120 ... (remaining 106654 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' and resid 16 through 116) selection = (chain 'G' and resid 16 through 116) } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 12.750 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: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.570 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:9.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 12741 Z= 0.616 Angle : 0.895 11.165 18484 Z= 0.770 Chirality : 0.050 0.172 2110 Planarity : 0.005 0.052 1312 Dihedral : 28.895 165.603 5500 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.27 % Allowed : 4.55 % Favored : 93.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.28), residues: 722 helix: 0.56 (0.20), residues: 546 sheet: None (None), residues: 0 loop : -1.33 (0.38), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 83 TYR 0.019 0.002 TYR H 37 PHE 0.020 0.003 PHE H 67 HIS 0.013 0.003 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00724 / 0.62 (12741) covalent geometry : angle 0.89479 / 0.77 (18484) hydrogen bonds : bond 0.08981 / 6.07 ( 791) hydrogen bonds : angle 3.57803 / 2.62 ( 1969) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 154 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.5531 (mmm) cc_final: 0.5155 (mmm) REVERT: B 91 LYS cc_start: 0.7915 (ttmm) cc_final: 0.7649 (ttmt) REVERT: C 108 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7226 (mt) REVERT: D 31 LYS cc_start: 0.7140 (mmtt) cc_final: 0.6878 (tppt) REVERT: F 68 ASP cc_start: 0.7377 (m-30) cc_final: 0.6858 (m-30) REVERT: H 68 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7446 (mt-10) outliers start: 14 outliers final: 3 residues processed: 161 average time/residue: 0.7703 time to fit residues: 131.4952 Evaluate side-chains 107 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 102 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 113 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN C 24 GLN C 31 HIS C 38 ASN D 44 GLN D 81 ASN E 39 HIS E 108 ASN E 125 GLN F 93 GLN G 31 HIS G 89 ASN G 110 ASN H 44 GLN H 64 ASN H 81 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.128655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.112897 restraints weight = 23655.312| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 0.98 r_work: 0.3824 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3730 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12741 Z= 0.161 Angle : 0.707 8.950 18484 Z= 0.401 Chirality : 0.049 0.270 2110 Planarity : 0.005 0.051 1312 Dihedral : 31.913 166.096 4063 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 4.87 % Allowed : 12.99 % Favored : 82.14 % 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: 1.49 (0.29), residues: 722 helix: 1.59 (0.21), residues: 548 sheet: None (None), residues: 0 loop : -0.89 (0.39), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 29 TYR 0.013 0.002 TYR H 37 PHE 0.018 0.002 PHE B 100 HIS 0.007 0.002 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.16 (12741) covalent geometry : angle 0.70677 / 0.40 (18484) hydrogen bonds : bond 0.05125 / 3.43 ( 791) hydrogen bonds : angle 3.19933 / 2.32 ( 1969) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7231 (pm20) cc_final: 0.7019 (pm20) REVERT: A 90 MET cc_start: 0.6029 (mmm) cc_final: 0.5484 (mmm) REVERT: A 125 GLN cc_start: 0.7690 (mt0) cc_final: 0.7343 (mp10) REVERT: B 91 LYS cc_start: 0.7957 (ttmm) cc_final: 0.7698 (ttmt) REVERT: B 95 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7882 (mtt-85) REVERT: C 41 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7617 (mp0) REVERT: D 31 LYS cc_start: 0.7170 (mmtt) cc_final: 0.6802 (tppt) REVERT: F 68 ASP cc_start: 0.7820 (m-30) cc_final: 0.7364 (m-30) REVERT: H 90 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7159 (mp0) REVERT: H 113 LYS cc_start: 0.7264 (OUTLIER) cc_final: 0.6951 (tmtt) outliers start: 30 outliers final: 11 residues processed: 126 average time/residue: 0.7887 time to fit residues: 105.2274 Evaluate side-chains 115 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 113 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 97 optimal weight: 20.0000 chunk 78 optimal weight: 6.9990 chunk 7 optimal weight: 0.0170 chunk 54 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 67 optimal weight: 0.6980 chunk 71 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 70 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 113 HIS E 125 GLN H 44 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.129156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.113452 restraints weight = 23991.573| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 0.99 r_work: 0.3834 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3741 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12741 Z= 0.152 Angle : 0.658 8.397 18484 Z= 0.379 Chirality : 0.046 0.277 2110 Planarity : 0.005 0.048 1312 Dihedral : 31.741 165.955 4061 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 5.19 % Allowed : 15.26 % Favored : 79.55 % 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: 2.02 (0.29), residues: 722 helix: 1.99 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -0.66 (0.40), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 96 TYR 0.010 0.002 TYR H 118 PHE 0.022 0.002 PHE A 67 HIS 0.006 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.15 (12741) covalent geometry : angle 0.65763 / 0.38 (18484) hydrogen bonds : bond 0.04774 / 3.21 ( 791) hydrogen bonds : angle 3.04338 / 2.22 ( 1969) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 85 GLN cc_start: 0.7388 (OUTLIER) cc_final: 0.7147 (tm-30) REVERT: A 90 MET cc_start: 0.6013 (mmm) cc_final: 0.5415 (tmm) REVERT: A 125 GLN cc_start: 0.7721 (mt0) cc_final: 0.7357 (mp10) REVERT: B 74 GLU cc_start: 0.6984 (tp30) cc_final: 0.6779 (mm-30) REVERT: B 91 LYS cc_start: 0.7869 (ttmm) cc_final: 0.7609 (ttmt) REVERT: C 41 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7632 (mp0) REVERT: D 31 LYS cc_start: 0.7054 (mmtt) cc_final: 0.6650 (tppt) REVERT: F 68 ASP cc_start: 0.7809 (m-30) cc_final: 0.7352 (m-30) REVERT: H 90 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7245 (mp0) REVERT: H 113 LYS cc_start: 0.7194 (OUTLIER) cc_final: 0.6909 (tmtt) outliers start: 32 outliers final: 12 residues processed: 126 average time/residue: 0.7553 time to fit residues: 101.1009 Evaluate side-chains 113 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 113 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 0.2980 chunk 35 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 97 optimal weight: 20.0000 chunk 57 optimal weight: 0.6980 chunk 92 optimal weight: 7.9990 chunk 68 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 62 optimal weight: 0.3980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN E 125 GLN H 44 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.129211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.113572 restraints weight = 23890.975| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 0.98 r_work: 0.3837 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3744 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12741 Z= 0.146 Angle : 0.654 8.311 18484 Z= 0.376 Chirality : 0.045 0.282 2110 Planarity : 0.004 0.048 1312 Dihedral : 31.677 165.613 4061 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 4.87 % Allowed : 17.69 % Favored : 77.44 % 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: 2.20 (0.30), residues: 722 helix: 2.09 (0.21), residues: 548 sheet: None (None), residues: 0 loop : -0.58 (0.41), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 96 TYR 0.013 0.001 TYR G 50 PHE 0.022 0.002 PHE A 67 HIS 0.016 0.002 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.15 (12741) covalent geometry : angle 0.65446 / 0.38 (18484) hydrogen bonds : bond 0.04610 / 3.10 ( 791) hydrogen bonds : angle 2.99585 / 2.18 ( 1969) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.6050 (mmm) cc_final: 0.5498 (tmm) REVERT: A 125 GLN cc_start: 0.7614 (mt0) cc_final: 0.7121 (mp10) REVERT: C 29 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.6713 (ttm110) REVERT: D 31 LYS cc_start: 0.7207 (mmtt) cc_final: 0.6902 (mptm) REVERT: F 68 ASP cc_start: 0.7821 (m-30) cc_final: 0.7357 (m-30) REVERT: H 68 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7348 (mp0) REVERT: H 90 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7277 (mp0) REVERT: H 113 LYS cc_start: 0.7177 (OUTLIER) cc_final: 0.6904 (tmtt) outliers start: 30 outliers final: 11 residues processed: 124 average time/residue: 0.7132 time to fit residues: 94.1241 Evaluate side-chains 111 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 113 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 86 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 43 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 39 optimal weight: 0.6980 chunk 24 optimal weight: 0.1980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN B 27 GLN B 75 HIS E 125 GLN H 44 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.129183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.113544 restraints weight = 23849.437| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 0.98 r_work: 0.3836 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3742 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12741 Z= 0.148 Angle : 0.642 8.093 18484 Z= 0.371 Chirality : 0.045 0.284 2110 Planarity : 0.004 0.045 1312 Dihedral : 31.613 165.198 4060 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 5.36 % Allowed : 19.16 % Favored : 75.49 % 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: 2.23 (0.30), residues: 722 helix: 2.12 (0.21), residues: 548 sheet: None (None), residues: 0 loop : -0.60 (0.40), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 96 TYR 0.014 0.002 TYR G 50 PHE 0.024 0.002 PHE A 67 HIS 0.013 0.001 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.15 (12741) covalent geometry : angle 0.64187 / 0.37 (18484) hydrogen bonds : bond 0.04625 / 3.10 ( 791) hydrogen bonds : angle 3.00182 / 2.18 ( 1969) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 101 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: A 80 THR cc_start: 0.7996 (OUTLIER) cc_final: 0.7696 (t) REVERT: A 85 GLN cc_start: 0.7480 (OUTLIER) cc_final: 0.7128 (tt0) REVERT: A 90 MET cc_start: 0.6108 (mmm) cc_final: 0.5592 (tmm) REVERT: A 125 GLN cc_start: 0.7682 (mt0) cc_final: 0.7167 (mp10) REVERT: A 131 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.7879 (mtt180) REVERT: C 29 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.6656 (ttm110) REVERT: D 31 LYS cc_start: 0.7067 (mmtt) cc_final: 0.6762 (mptm) REVERT: E 120 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.7653 (mtm) REVERT: F 68 ASP cc_start: 0.7860 (m-30) cc_final: 0.7385 (m-30) REVERT: H 68 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7276 (mp0) REVERT: H 90 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7165 (mp0) REVERT: H 113 LYS cc_start: 0.7230 (OUTLIER) cc_final: 0.6962 (tmtt) outliers start: 33 outliers final: 12 residues processed: 117 average time/residue: 0.7471 time to fit residues: 92.8976 Evaluate side-chains 112 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 113 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 87 optimal weight: 9.9990 chunk 81 optimal weight: 9.9990 chunk 26 optimal weight: 0.8980 chunk 95 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 19 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 88 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 overall best weight: 4.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN D 81 ASN E 108 ASN E 125 GLN F 75 HIS G 38 ASN H 44 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.124168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.105986 restraints weight = 23895.213| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 1.23 r_work: 0.3658 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3555 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.153 12741 Z= 0.512 Angle : 1.113 10.047 18484 Z= 0.588 Chirality : 0.068 0.336 2110 Planarity : 0.011 0.114 1312 Dihedral : 32.219 159.486 4060 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 7.63 % Allowed : 17.37 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.28), residues: 722 helix: -0.17 (0.20), residues: 548 sheet: None (None), residues: 0 loop : -1.66 (0.41), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.002 ARG B 39 TYR 0.020 0.004 TYR D 37 PHE 0.029 0.005 PHE A 67 HIS 0.024 0.005 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.01095 / 0.51 (12741) covalent geometry : angle 1.11257 / 0.59 (18484) hydrogen bonds : bond 0.11599 / 7.96 ( 791) hydrogen bonds : angle 4.25738 / 3.07 ( 1969) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 99 time to evaluate : 0.318 Fit side-chains REVERT: A 63 ARG cc_start: 0.7459 (OUTLIER) cc_final: 0.7213 (mmt-90) REVERT: A 79 LYS cc_start: 0.6624 (tttt) cc_final: 0.6370 (tttt) REVERT: A 85 GLN cc_start: 0.7542 (OUTLIER) cc_final: 0.7060 (tt0) REVERT: A 90 MET cc_start: 0.6419 (mmm) cc_final: 0.5905 (mmm) REVERT: A 94 GLU cc_start: 0.7138 (mm-30) cc_final: 0.6697 (tm-30) REVERT: A 115 LYS cc_start: 0.7641 (mmtp) cc_final: 0.7021 (mtmm) REVERT: A 120 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.7248 (mtt) REVERT: A 131 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.8114 (mtt180) REVERT: B 78 ARG cc_start: 0.7417 (mtm180) cc_final: 0.7192 (mtp85) REVERT: B 95 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.7792 (mtp85) REVERT: C 29 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7314 (ttm110) REVERT: D 31 LYS cc_start: 0.7301 (mmtt) cc_final: 0.6792 (tppt) REVERT: E 131 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7945 (mtp85) REVERT: F 68 ASP cc_start: 0.8067 (m-30) cc_final: 0.7721 (m-30) REVERT: G 104 GLN cc_start: 0.6767 (OUTLIER) cc_final: 0.5963 (mp10) REVERT: H 69 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7577 (mtm180) REVERT: H 90 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7660 (mp0) outliers start: 47 outliers final: 19 residues processed: 127 average time/residue: 0.7571 time to fit residues: 102.0040 Evaluate side-chains 121 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 69 ARG Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 113 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 90 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 chunk 96 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 chunk 7 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN E 108 ASN E 125 GLN F 27 GLN H 44 GLN H 46 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.126322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.110610 restraints weight = 24063.989| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 0.99 r_work: 0.3787 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3694 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12741 Z= 0.172 Angle : 0.734 8.269 18484 Z= 0.411 Chirality : 0.049 0.286 2110 Planarity : 0.005 0.048 1312 Dihedral : 32.148 163.910 4060 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 6.01 % Allowed : 19.64 % Favored : 74.35 % 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: 0.75 (0.29), residues: 722 helix: 1.07 (0.21), residues: 548 sheet: None (None), residues: 0 loop : -1.21 (0.43), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 76 TYR 0.014 0.002 TYR D 37 PHE 0.029 0.002 PHE A 67 HIS 0.012 0.002 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.17 (12741) covalent geometry : angle 0.73359 / 0.41 (18484) hydrogen bonds : bond 0.05358 / 3.59 ( 791) hydrogen bonds : angle 3.41804 / 2.46 ( 1969) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 100 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: A 80 THR cc_start: 0.7963 (OUTLIER) cc_final: 0.7599 (t) REVERT: A 85 GLN cc_start: 0.7542 (OUTLIER) cc_final: 0.7326 (tm-30) REVERT: A 90 MET cc_start: 0.5973 (mmm) cc_final: 0.5593 (mmm) REVERT: A 115 LYS cc_start: 0.7479 (mmtp) cc_final: 0.7052 (mtmm) REVERT: A 131 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.7845 (mtt180) REVERT: B 78 ARG cc_start: 0.7249 (mtm180) cc_final: 0.7011 (mtp85) REVERT: C 29 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7001 (ttm110) REVERT: D 30 ARG cc_start: 0.6939 (OUTLIER) cc_final: 0.6736 (ttt180) REVERT: D 31 LYS cc_start: 0.7315 (mmtt) cc_final: 0.7045 (mptm) REVERT: E 131 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7448 (mtt180) REVERT: F 68 ASP cc_start: 0.7852 (m-30) cc_final: 0.7410 (m-30) REVERT: H 90 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7426 (mp0) REVERT: H 113 LYS cc_start: 0.7339 (OUTLIER) cc_final: 0.7048 (tmtt) outliers start: 37 outliers final: 21 residues processed: 122 average time/residue: 0.7044 time to fit residues: 91.2389 Evaluate side-chains 121 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 113 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 92 optimal weight: 7.9990 chunk 38 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 24 GLN E 125 GLN H 44 GLN H 46 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.127661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.111975 restraints weight = 24060.627| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 0.98 r_work: 0.3812 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3719 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12741 Z= 0.156 Angle : 0.676 9.679 18484 Z= 0.387 Chirality : 0.045 0.286 2110 Planarity : 0.005 0.049 1312 Dihedral : 31.838 166.086 4060 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 5.36 % Allowed : 21.10 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.30), residues: 722 helix: 1.67 (0.21), residues: 548 sheet: None (None), residues: 0 loop : -1.00 (0.43), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 35 TYR 0.014 0.001 TYR G 50 PHE 0.032 0.002 PHE A 67 HIS 0.006 0.001 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.16 (12741) covalent geometry : angle 0.67608 / 0.39 (18484) hydrogen bonds : bond 0.04904 / 3.30 ( 791) hydrogen bonds : angle 3.19158 / 2.31 ( 1969) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 101 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: A 80 THR cc_start: 0.7940 (OUTLIER) cc_final: 0.7638 (t) REVERT: A 90 MET cc_start: 0.5925 (mmm) cc_final: 0.5601 (tmm) REVERT: A 115 LYS cc_start: 0.7387 (mmtp) cc_final: 0.6963 (mtmm) REVERT: A 131 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.7769 (mtt180) REVERT: B 78 ARG cc_start: 0.7348 (mtm180) cc_final: 0.7067 (mtp85) REVERT: C 29 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.6881 (ttm110) REVERT: D 31 LYS cc_start: 0.7262 (mmtt) cc_final: 0.7002 (mptm) REVERT: F 68 ASP cc_start: 0.7862 (m-30) cc_final: 0.7422 (m-30) REVERT: H 68 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7358 (mp0) REVERT: H 90 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7379 (mp0) REVERT: H 113 LYS cc_start: 0.7266 (OUTLIER) cc_final: 0.7024 (tmtt) outliers start: 33 outliers final: 15 residues processed: 119 average time/residue: 0.7337 time to fit residues: 92.7726 Evaluate side-chains 117 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 113 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 57 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 81 optimal weight: 9.9990 chunk 32 optimal weight: 0.3980 chunk 65 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN B 27 GLN E 125 GLN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN H 46 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.127974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.112343 restraints weight = 24061.912| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 0.97 r_work: 0.3818 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3725 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12741 Z= 0.151 Angle : 0.659 7.696 18484 Z= 0.378 Chirality : 0.045 0.287 2110 Planarity : 0.005 0.050 1312 Dihedral : 31.760 166.053 4060 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 4.55 % Allowed : 22.24 % Favored : 73.21 % 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: 1.80 (0.30), residues: 722 helix: 1.83 (0.21), residues: 548 sheet: None (None), residues: 0 loop : -0.84 (0.43), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 35 TYR 0.018 0.002 TYR G 50 PHE 0.029 0.002 PHE A 67 HIS 0.006 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.15 (12741) covalent geometry : angle 0.65887 / 0.38 (18484) hydrogen bonds : bond 0.04731 / 3.17 ( 791) hydrogen bonds : angle 3.13606 / 2.27 ( 1969) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: A 80 THR cc_start: 0.7887 (OUTLIER) cc_final: 0.7586 (t) REVERT: A 85 GLN cc_start: 0.7641 (OUTLIER) cc_final: 0.7282 (tm130) REVERT: A 90 MET cc_start: 0.5915 (mmm) cc_final: 0.5538 (tmm) REVERT: A 115 LYS cc_start: 0.7375 (mmtp) cc_final: 0.7009 (mtmm) REVERT: A 125 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7654 (mt0) REVERT: A 131 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7780 (mtt180) REVERT: B 78 ARG cc_start: 0.7328 (mtm180) cc_final: 0.7034 (mtp85) REVERT: C 29 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.6893 (ttm110) REVERT: C 99 ARG cc_start: 0.7761 (mpt180) cc_final: 0.7424 (mpp-170) REVERT: D 31 LYS cc_start: 0.7230 (mmtt) cc_final: 0.6973 (mptm) REVERT: E 131 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7468 (mtt180) REVERT: F 68 ASP cc_start: 0.7845 (m-30) cc_final: 0.7423 (m-30) REVERT: H 68 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7272 (mp0) REVERT: H 90 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7312 (mp0) REVERT: H 113 LYS cc_start: 0.7254 (OUTLIER) cc_final: 0.7027 (tmtt) outliers start: 28 outliers final: 15 residues processed: 115 average time/residue: 0.7154 time to fit residues: 87.7191 Evaluate side-chains 121 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 113 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 81 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 74 optimal weight: 9.9990 chunk 32 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 77 optimal weight: 7.9990 chunk 69 optimal weight: 0.3980 chunk 1 optimal weight: 0.0020 chunk 38 optimal weight: 1.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 125 GLN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN H 46 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.128622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.113000 restraints weight = 24124.349| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 0.97 r_work: 0.3829 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3738 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12741 Z= 0.146 Angle : 0.660 7.520 18484 Z= 0.378 Chirality : 0.045 0.363 2110 Planarity : 0.004 0.050 1312 Dihedral : 31.709 165.992 4060 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 4.38 % Allowed : 22.89 % Favored : 72.73 % 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: 1.91 (0.30), residues: 722 helix: 1.90 (0.21), residues: 548 sheet: None (None), residues: 0 loop : -0.76 (0.43), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 35 TYR 0.025 0.002 TYR G 50 PHE 0.031 0.002 PHE A 67 HIS 0.005 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.15 (12741) covalent geometry : angle 0.65976 / 0.38 (18484) hydrogen bonds : bond 0.04595 / 3.08 ( 791) hydrogen bonds : angle 3.10962 / 2.24 ( 1969) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: A 80 THR cc_start: 0.7887 (OUTLIER) cc_final: 0.7619 (t) REVERT: A 85 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.7374 (tm130) REVERT: A 90 MET cc_start: 0.5890 (mmm) cc_final: 0.5561 (tmm) REVERT: A 115 LYS cc_start: 0.7366 (mmtp) cc_final: 0.7000 (mtmm) REVERT: A 120 MET cc_start: 0.7301 (OUTLIER) cc_final: 0.6797 (mtt) REVERT: A 125 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7624 (mt0) REVERT: A 131 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.7760 (mtt180) REVERT: B 78 ARG cc_start: 0.7322 (mtm180) cc_final: 0.7020 (mtp85) REVERT: C 29 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.6844 (ttm110) REVERT: C 99 ARG cc_start: 0.7788 (mpt180) cc_final: 0.7460 (mpp-170) REVERT: D 31 LYS cc_start: 0.7208 (mmtt) cc_final: 0.6957 (mptm) REVERT: E 131 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7425 (mtt180) REVERT: F 68 ASP cc_start: 0.7883 (m-30) cc_final: 0.7460 (m-30) REVERT: H 68 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7309 (mp0) REVERT: H 90 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7309 (mp0) REVERT: H 113 LYS cc_start: 0.7180 (OUTLIER) cc_final: 0.6974 (tmtt) outliers start: 27 outliers final: 14 residues processed: 117 average time/residue: 0.7614 time to fit residues: 94.4844 Evaluate side-chains 122 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 113 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 65 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 78 optimal weight: 6.9990 chunk 15 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN B 27 GLN E 125 GLN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN H 46 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.128034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.112382 restraints weight = 24027.670| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 0.98 r_work: 0.3819 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3727 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 12741 Z= 0.159 Angle : 0.662 8.322 18484 Z= 0.379 Chirality : 0.045 0.291 2110 Planarity : 0.005 0.050 1312 Dihedral : 31.683 165.581 4060 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.55 % Allowed : 22.73 % Favored : 72.73 % 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: 1.86 (0.30), residues: 722 helix: 1.87 (0.21), residues: 548 sheet: None (None), residues: 0 loop : -0.80 (0.43), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 35 TYR 0.022 0.002 TYR G 50 PHE 0.030 0.002 PHE A 67 HIS 0.006 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.16 (12741) covalent geometry : angle 0.66156 / 0.38 (18484) hydrogen bonds : bond 0.04842 / 3.25 ( 791) hydrogen bonds : angle 3.12251 / 2.25 ( 1969) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4304.23 seconds wall clock time: 73 minutes 51.65 seconds (4431.65 seconds total)