Starting phenix.real_space_refine on Wed Aug 5 22:40:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10yc_75524/08_2026/10yc_75524.cif Found real_map, /net/cci-nas-00/data/ceres_data/10yc_75524/08_2026/10yc_75524.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/10yc_75524/08_2026/10yc_75524.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10yc_75524/08_2026/10yc_75524.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/10yc_75524/08_2026/10yc_75524.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10yc_75524/08_2026/10yc_75524.map" } resolution = 2.7 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= 0.005 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 294 5.49 5 S 10 5.16 5 C 6625 2.51 5 N 2250 2.21 5 O 2819 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11998 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 832 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 720 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "K" Number of atoms: 2312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 2312 Classifications: {'DNA': 112} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 111} Time building chain proxies: 2.62, per 1000 atoms: 0.22 Number of scatterers: 11998 At special positions: 0 Unit cell: (74.328, 123.88, 116.708, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 294 15.00 O 2819 8.00 N 2250 7.00 C 6625 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 271.9 milliseconds 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1406 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 9 sheets defined 72.5% alpha, 2.7% beta 146 base pairs and 252 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 50 through 55 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 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: 3.586A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.657A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.349A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.507A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.778A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.575A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.390A 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 removed outlier: 3.575A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 124 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.163A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.292A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.986A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.276A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 401 hydrogen bonds defined for protein. 1191 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 374 hydrogen bonds 748 hydrogen bond angles 0 basepair planarities 146 basepair parallelities 252 stacking parallelities Total time for adding SS restraints: 2.25 Time building geometry restraints manager: 1.37 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: 2098 1.33 - 1.45: 4255 1.45 - 1.57: 5852 1.57 - 1.69: 585 1.69 - 1.80: 20 Bond restraints: 12810 Sorted by residual: bond pdb=" C3' DG K 52 " pdb=" C2' DG K 52 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C5' DA I 120 " pdb=" C4' DA I 120 " ideal model delta sigma weight residual 1.512 1.534 -0.022 7.00e-03 2.04e+04 1.01e+01 bond pdb=" C3' DT J 15 " pdb=" C2' DT J 15 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.83e+00 bond pdb=" C3' DG I 55 " pdb=" C2' DG I 55 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.76e+00 bond pdb=" C5' DG I 121 " pdb=" C4' DG I 121 " ideal model delta sigma weight residual 1.512 1.534 -0.022 7.00e-03 2.04e+04 9.61e+00 ... (remaining 12805 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 16749 1.31 - 2.62: 1620 2.62 - 3.93: 169 3.93 - 5.24: 14 5.24 - 6.54: 7 Bond angle restraints: 18559 Sorted by residual: angle pdb=" N3 DT K 50 " pdb=" C4 DT K 50 " pdb=" O4 DT K 50 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.01e+01 angle pdb=" N3 DT I 32 " pdb=" C4 DT I 32 " pdb=" O4 DT I 32 " 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 31 " pdb=" C4 DT I 31 " pdb=" O4 DT I 31 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT I 35 " pdb=" C4 DT I 35 " pdb=" O4 DT I 35 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" N3 DT I 75 " pdb=" C4 DT I 75 " pdb=" O4 DT I 75 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.87e+01 ... (remaining 18554 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.62: 5072 28.62 - 57.24: 1730 57.24 - 85.87: 135 85.87 - 114.49: 4 114.49 - 143.11: 3 Dihedral angle restraints: 6944 sinusoidal: 4763 harmonic: 2181 Sorted by residual: dihedral pdb=" CA GLU A 50 " pdb=" C GLU A 50 " pdb=" N ILE A 51 " pdb=" CA ILE A 51 " ideal model delta harmonic sigma weight residual 180.00 159.76 20.24 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA LEU A 48 " pdb=" C LEU A 48 " pdb=" N ARG A 49 " pdb=" CA ARG A 49 " ideal model delta harmonic sigma weight residual 180.00 160.52 19.48 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" C4' DT J 15 " pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DC J 16 " ideal model delta sinusoidal sigma weight residual 220.00 76.89 143.11 1 3.50e+01 8.16e-04 1.41e+01 ... (remaining 6941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1260 0.035 - 0.071: 615 0.071 - 0.106: 177 0.106 - 0.141: 58 0.141 - 0.177: 3 Chirality restraints: 2113 Sorted by residual: chirality pdb=" C3' DC K 126 " pdb=" C4' DC K 126 " pdb=" O3' DC K 126 " pdb=" C2' DC K 126 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 7.80e-01 chirality pdb=" CA GLN H 47 " pdb=" N GLN H 47 " pdb=" C GLN H 47 " pdb=" CB GLN H 47 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.23e-01 chirality pdb=" CA GLN E 68 " pdb=" N GLN E 68 " pdb=" C GLN E 68 " pdb=" CB GLN E 68 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.66e-01 ... (remaining 2110 not shown) Planarity restraints: 1328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP F 24 " 0.014 2.00e-02 2.50e+03 2.93e-02 8.57e+00 pdb=" CG ASP F 24 " -0.051 2.00e-02 2.50e+03 pdb=" OD1 ASP F 24 " 0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP F 24 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU F 63 " 0.011 2.00e-02 2.50e+03 2.11e-02 4.46e+00 pdb=" C GLU F 63 " -0.037 2.00e-02 2.50e+03 pdb=" O GLU F 63 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN F 64 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 59 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.30e+00 pdb=" C LYS F 59 " -0.036 2.00e-02 2.50e+03 pdb=" O LYS F 59 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL F 60 " 0.012 2.00e-02 2.50e+03 ... (remaining 1325 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 5158 2.98 - 3.46: 11154 3.46 - 3.94: 24924 3.94 - 4.42: 27588 4.42 - 4.90: 36137 Nonbonded interactions: 104961 Sorted by model distance: nonbonded pdb=" O5' DA I 124 " pdb=" O4' DA I 124 " model vdw 2.505 2.432 nonbonded pdb=" O ASP F 24 " pdb=" OD1 ASP F 24 " model vdw 2.569 3.040 nonbonded pdb=" N ILE G 79 " pdb=" O ILE G 79 " model vdw 2.576 2.496 nonbonded pdb=" N ILE C 79 " pdb=" O ILE C 79 " model vdw 2.584 2.496 nonbonded pdb=" N1 DG K 67 " pdb=" C4 DG K 67 " model vdw 2.594 2.672 ... (remaining 104956 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 11 through 117) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 34 through 124) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.410 Find NCS groups from input model: 0.130 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: 0.010 Load rotamer database and sin/cos tables:7.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 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 0.034 12810 Z= 0.529 Angle : 0.780 6.544 18559 Z= 0.695 Chirality : 0.045 0.177 2113 Planarity : 0.005 0.043 1328 Dihedral : 28.350 143.110 5538 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.16 % Allowed : 20.48 % Favored : 79.36 % 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: 1.47 (0.30), residues: 737 helix: 1.58 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -0.67 (0.39), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 42 TYR 0.017 0.002 TYR F 88 PHE 0.008 0.002 PHE C 25 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00592 / 0.53 (12810) covalent geometry : angle 0.77980 / 0.70 (18559) hydrogen bonds : bond 0.10899 / 6.95 ( 775) hydrogen bonds : angle 4.33173 / 3.00 ( 1939) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 162 time to evaluate : 0.323 Fit side-chains REVERT: A 57 SER cc_start: 0.9056 (t) cc_final: 0.8814 (t) REVERT: A 59 GLU cc_start: 0.8084 (pt0) cc_final: 0.7828 (pm20) REVERT: C 73 ASN cc_start: 0.8694 (t0) cc_final: 0.8138 (t0) REVERT: D 108 LYS cc_start: 0.9005 (mtmt) cc_final: 0.8734 (mtpm) REVERT: E 59 GLU cc_start: 0.8710 (pm20) cc_final: 0.8142 (pm20) REVERT: G 73 ASN cc_start: 0.8482 (t160) cc_final: 0.8107 (t160) REVERT: G 90 ASP cc_start: 0.8830 (t70) cc_final: 0.8483 (t0) REVERT: H 108 LYS cc_start: 0.8644 (mtmm) cc_final: 0.8444 (mtpm) outliers start: 1 outliers final: 1 residues processed: 162 average time/residue: 0.8954 time to fit residues: 153.1336 Evaluate side-chains 158 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN E 108 ASN F 25 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.106507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.067950 restraints weight = 20116.650| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 1.54 r_work: 0.2728 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2582 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.0536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12810 Z= 0.181 Angle : 0.629 6.717 18559 Z= 0.377 Chirality : 0.045 0.208 2113 Planarity : 0.004 0.049 1328 Dihedral : 30.731 145.687 4051 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.76 % Allowed : 18.56 % Favored : 79.68 % 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: 2.21 (0.30), residues: 737 helix: 2.17 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.69 (0.41), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 42 TYR 0.011 0.001 TYR H 40 PHE 0.007 0.001 PHE E 84 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.18 (12810) covalent geometry : angle 0.62861 / 0.38 (18559) hydrogen bonds : bond 0.04865 / 3.31 ( 775) hydrogen bonds : angle 3.30484 / 2.27 ( 1939) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 157 time to evaluate : 0.326 Fit side-chains REVERT: A 57 SER cc_start: 0.9106 (t) cc_final: 0.8820 (t) REVERT: A 59 GLU cc_start: 0.8097 (pt0) cc_final: 0.7879 (pm20) REVERT: C 73 ASN cc_start: 0.8702 (t0) cc_final: 0.8155 (t0) REVERT: D 108 LYS cc_start: 0.8827 (mtmt) cc_final: 0.8593 (mtpm) REVERT: E 59 GLU cc_start: 0.8634 (pm20) cc_final: 0.7977 (pm20) REVERT: G 73 ASN cc_start: 0.8440 (t0) cc_final: 0.7999 (t160) REVERT: G 90 ASP cc_start: 0.8561 (t70) cc_final: 0.8207 (t0) outliers start: 11 outliers final: 8 residues processed: 160 average time/residue: 0.8689 time to fit residues: 146.9183 Evaluate side-chains 163 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 155 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 22 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 85 optimal weight: 40.0000 chunk 46 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN E 68 GLN E 85 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.105979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.067098 restraints weight = 20382.876| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.56 r_work: 0.2738 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2594 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.0719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12810 Z= 0.192 Angle : 0.630 6.664 18559 Z= 0.373 Chirality : 0.045 0.231 2113 Planarity : 0.004 0.044 1328 Dihedral : 30.901 145.549 4051 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.72 % Allowed : 17.44 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.48 (0.31), residues: 737 helix: 2.38 (0.22), residues: 551 sheet: None (None), residues: 0 loop : -0.66 (0.41), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 129 TYR 0.011 0.001 TYR H 42 PHE 0.009 0.002 PHE C 25 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.19 (12810) covalent geometry : angle 0.62967 / 0.37 (18559) hydrogen bonds : bond 0.04443 / 3.05 ( 775) hydrogen bonds : angle 3.08912 / 2.12 ( 1939) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 0.333 Fit side-chains REVERT: A 56 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8794 (ttpp) REVERT: A 57 SER cc_start: 0.9088 (t) cc_final: 0.8758 (t) REVERT: A 59 GLU cc_start: 0.8021 (pt0) cc_final: 0.7796 (pm20) REVERT: C 73 ASN cc_start: 0.8680 (t0) cc_final: 0.8133 (t0) REVERT: D 108 LYS cc_start: 0.8735 (mtmt) cc_final: 0.8519 (mtpm) REVERT: E 59 GLU cc_start: 0.8620 (pm20) cc_final: 0.7926 (pm20) REVERT: G 73 ASN cc_start: 0.8438 (OUTLIER) cc_final: 0.7981 (t160) REVERT: G 90 ASP cc_start: 0.8543 (t70) cc_final: 0.8275 (t0) REVERT: H 93 GLU cc_start: 0.9124 (mp0) cc_final: 0.8882 (mp0) outliers start: 17 outliers final: 12 residues processed: 161 average time/residue: 0.8936 time to fit residues: 151.9707 Evaluate side-chains 163 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 39 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 53 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 84 optimal weight: 20.0000 chunk 87 optimal weight: 30.0000 chunk 20 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.105837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.066866 restraints weight = 20117.233| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 1.56 r_work: 0.2701 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2556 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.0845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12810 Z= 0.185 Angle : 0.619 6.720 18559 Z= 0.366 Chirality : 0.044 0.225 2113 Planarity : 0.004 0.046 1328 Dihedral : 31.008 145.943 4051 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.56 % Allowed : 18.40 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.61 (0.31), residues: 737 helix: 2.46 (0.22), residues: 553 sheet: None (None), residues: 0 loop : -0.58 (0.41), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 42 TYR 0.010 0.002 TYR F 88 PHE 0.010 0.002 PHE A 67 HIS 0.003 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.18 (12810) covalent geometry : angle 0.61908 / 0.37 (18559) hydrogen bonds : bond 0.04335 / 2.99 ( 775) hydrogen bonds : angle 3.02637 / 2.08 ( 1939) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.347 Fit side-chains REVERT: A 56 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8812 (ttpp) REVERT: A 57 SER cc_start: 0.9063 (t) cc_final: 0.8738 (t) REVERT: A 59 GLU cc_start: 0.8105 (pt0) cc_final: 0.7901 (pm20) REVERT: C 73 ASN cc_start: 0.8702 (t0) cc_final: 0.8154 (t0) REVERT: D 108 LYS cc_start: 0.8794 (mtmt) cc_final: 0.8574 (mtpm) REVERT: E 59 GLU cc_start: 0.8637 (pm20) cc_final: 0.7956 (pm20) REVERT: G 73 ASN cc_start: 0.8466 (OUTLIER) cc_final: 0.8014 (t160) REVERT: G 90 ASP cc_start: 0.8509 (t70) cc_final: 0.8272 (t0) outliers start: 16 outliers final: 10 residues processed: 154 average time/residue: 0.9123 time to fit residues: 148.1325 Evaluate side-chains 158 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 39 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 87 optimal weight: 30.0000 chunk 4 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 98 optimal weight: 20.0000 chunk 32 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.105342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.066193 restraints weight = 20111.942| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 1.55 r_work: 0.2689 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2542 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12810 Z= 0.197 Angle : 0.630 7.187 18559 Z= 0.367 Chirality : 0.045 0.245 2113 Planarity : 0.004 0.045 1328 Dihedral : 31.198 145.887 4051 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.40 % Allowed : 18.24 % Favored : 79.36 % 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: 2.69 (0.31), residues: 737 helix: 2.54 (0.22), residues: 551 sheet: None (None), residues: 0 loop : -0.60 (0.41), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 42 TYR 0.011 0.002 TYR C 57 PHE 0.010 0.002 PHE A 67 HIS 0.003 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.20 (12810) covalent geometry : angle 0.63018 / 0.37 (18559) hydrogen bonds : bond 0.04347 / 2.99 ( 775) hydrogen bonds : angle 2.95265 / 2.04 ( 1939) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.268 Fit side-chains REVERT: A 57 SER cc_start: 0.9032 (t) cc_final: 0.8703 (t) REVERT: C 73 ASN cc_start: 0.8687 (t0) cc_final: 0.8142 (t0) REVERT: D 108 LYS cc_start: 0.8792 (mtmt) cc_final: 0.8580 (mtpm) REVERT: E 59 GLU cc_start: 0.8657 (pm20) cc_final: 0.7977 (pm20) REVERT: G 73 ASN cc_start: 0.8491 (OUTLIER) cc_final: 0.8016 (t160) REVERT: G 90 ASP cc_start: 0.8482 (t70) cc_final: 0.8255 (t0) REVERT: H 93 GLU cc_start: 0.9191 (mp0) cc_final: 0.8946 (mp0) outliers start: 15 outliers final: 12 residues processed: 155 average time/residue: 0.8741 time to fit residues: 143.0102 Evaluate side-chains 158 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 39 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 74 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.105813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.066833 restraints weight = 20094.369| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 1.55 r_work: 0.2708 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2563 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12810 Z= 0.142 Angle : 0.615 7.204 18559 Z= 0.361 Chirality : 0.044 0.240 2113 Planarity : 0.004 0.043 1328 Dihedral : 31.200 145.862 4049 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.36 % Allowed : 18.40 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.88 (0.31), residues: 737 helix: 2.67 (0.22), residues: 551 sheet: None (None), residues: 0 loop : -0.52 (0.42), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 79 TYR 0.012 0.001 TYR H 42 PHE 0.011 0.001 PHE A 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.14 (12810) covalent geometry : angle 0.61507 / 0.36 (18559) hydrogen bonds : bond 0.04074 / 2.81 ( 775) hydrogen bonds : angle 2.93351 / 2.02 ( 1939) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.313 Fit side-chains REVERT: A 57 SER cc_start: 0.8930 (t) cc_final: 0.8693 (t) REVERT: A 59 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.8002 (pm20) REVERT: A 120 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.8259 (mtt) REVERT: B 92 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.8231 (ttp80) REVERT: C 73 ASN cc_start: 0.8690 (t0) cc_final: 0.8141 (t0) REVERT: D 108 LYS cc_start: 0.8763 (mtmt) cc_final: 0.8555 (mtpm) REVERT: E 59 GLU cc_start: 0.8620 (pm20) cc_final: 0.7951 (pm20) REVERT: G 73 ASN cc_start: 0.8488 (OUTLIER) cc_final: 0.8000 (t160) REVERT: G 90 ASP cc_start: 0.8465 (t70) cc_final: 0.8230 (t0) outliers start: 21 outliers final: 13 residues processed: 153 average time/residue: 0.8341 time to fit residues: 134.6093 Evaluate side-chains 164 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 39 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 48 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.105721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.066745 restraints weight = 20010.172| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 1.54 r_work: 0.2706 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2562 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12810 Z= 0.159 Angle : 0.611 7.193 18559 Z= 0.359 Chirality : 0.044 0.247 2113 Planarity : 0.004 0.043 1328 Dihedral : 31.193 145.830 4049 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.88 % Allowed : 18.40 % Favored : 78.72 % 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: 2.84 (0.31), residues: 737 helix: 2.64 (0.22), residues: 551 sheet: None (None), residues: 0 loop : -0.54 (0.42), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 77 TYR 0.011 0.001 TYR H 42 PHE 0.009 0.001 PHE A 67 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.16 (12810) covalent geometry : angle 0.61076 / 0.36 (18559) hydrogen bonds : bond 0.04014 / 2.77 ( 775) hydrogen bonds : angle 2.91179 / 2.00 ( 1939) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 0.331 Fit side-chains REVERT: A 57 SER cc_start: 0.8929 (t) cc_final: 0.8665 (t) REVERT: A 59 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.8037 (pm20) REVERT: B 92 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8236 (ttp80) REVERT: C 73 ASN cc_start: 0.8690 (t0) cc_final: 0.8142 (t0) REVERT: D 108 LYS cc_start: 0.8760 (mtmt) cc_final: 0.8551 (mtpm) REVERT: E 59 GLU cc_start: 0.8617 (pm20) cc_final: 0.7946 (pm20) REVERT: G 73 ASN cc_start: 0.8493 (OUTLIER) cc_final: 0.8011 (t160) REVERT: G 90 ASP cc_start: 0.8456 (t70) cc_final: 0.8222 (t0) outliers start: 18 outliers final: 12 residues processed: 155 average time/residue: 0.8884 time to fit residues: 145.2703 Evaluate side-chains 163 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 63 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 96 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 99 optimal weight: 20.0000 chunk 68 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 7 optimal weight: 0.5980 overall best weight: 5.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN E 68 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.101832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.062631 restraints weight = 20007.059| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 1.55 r_work: 0.2603 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2457 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.079 12810 Z= 0.438 Angle : 0.802 7.929 18559 Z= 0.432 Chirality : 0.057 0.252 2113 Planarity : 0.006 0.056 1328 Dihedral : 31.854 153.891 4049 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.72 % Allowed : 19.04 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.30), residues: 737 helix: 2.12 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -1.07 (0.38), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 55 TYR 0.021 0.002 TYR A 54 PHE 0.016 0.003 PHE C 25 HIS 0.005 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00970 / 0.44 (12810) covalent geometry : angle 0.80248 / 0.43 (18559) hydrogen bonds : bond 0.07045 / 4.81 ( 775) hydrogen bonds : angle 3.20150 / 2.24 ( 1939) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.342 Fit side-chains REVERT: A 57 SER cc_start: 0.8929 (t) cc_final: 0.8660 (t) REVERT: A 59 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8426 (pm20) REVERT: C 73 ASN cc_start: 0.8692 (t0) cc_final: 0.8164 (t0) REVERT: D 108 LYS cc_start: 0.8836 (mtmt) cc_final: 0.8618 (mtpm) REVERT: E 59 GLU cc_start: 0.8780 (pm20) cc_final: 0.8093 (pm20) REVERT: F 91 LYS cc_start: 0.9073 (ttmt) cc_final: 0.8758 (ttpp) REVERT: G 73 ASN cc_start: 0.8610 (OUTLIER) cc_final: 0.8122 (t160) REVERT: G 90 ASP cc_start: 0.8571 (t70) cc_final: 0.8178 (t0) outliers start: 17 outliers final: 13 residues processed: 149 average time/residue: 0.9165 time to fit residues: 143.7201 Evaluate side-chains 155 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 63 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 23 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 83 optimal weight: 10.0000 chunk 31 optimal weight: 0.7980 chunk 96 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.104632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.065864 restraints weight = 19985.648| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 1.52 r_work: 0.2676 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2531 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12810 Z= 0.169 Angle : 0.655 7.314 18559 Z= 0.371 Chirality : 0.046 0.271 2113 Planarity : 0.004 0.049 1328 Dihedral : 31.669 148.280 4049 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.08 % Allowed : 19.52 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.61 (0.30), residues: 737 helix: 2.57 (0.22), residues: 539 sheet: None (None), residues: 0 loop : -0.72 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 42 TYR 0.012 0.001 TYR H 42 PHE 0.010 0.001 PHE A 67 HIS 0.003 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.17 (12810) covalent geometry : angle 0.65470 / 0.37 (18559) hydrogen bonds : bond 0.03995 / 2.77 ( 775) hydrogen bonds : angle 2.94499 / 2.03 ( 1939) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 0.337 Fit side-chains REVERT: A 57 SER cc_start: 0.8906 (t) cc_final: 0.8611 (t) REVERT: A 59 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8160 (pm20) REVERT: B 92 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.8205 (ttp80) REVERT: C 73 ASN cc_start: 0.8674 (t0) cc_final: 0.8152 (t0) REVERT: D 108 LYS cc_start: 0.8739 (mtmt) cc_final: 0.8525 (mtpm) REVERT: E 59 GLU cc_start: 0.8712 (pm20) cc_final: 0.8027 (pm20) REVERT: G 73 ASN cc_start: 0.8528 (OUTLIER) cc_final: 0.8172 (t160) REVERT: G 90 ASP cc_start: 0.8484 (t70) cc_final: 0.8245 (t0) REVERT: H 93 GLU cc_start: 0.9215 (mp0) cc_final: 0.8984 (mp0) REVERT: H 99 ARG cc_start: 0.8949 (mtm110) cc_final: 0.8309 (mtt-85) outliers start: 13 outliers final: 8 residues processed: 151 average time/residue: 0.8889 time to fit residues: 141.4740 Evaluate side-chains 155 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 63 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 69 optimal weight: 0.7980 chunk 92 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 72 optimal weight: 30.0000 chunk 30 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN E 68 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.106158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.067342 restraints weight = 20135.137| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 1.55 r_work: 0.2712 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2568 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12810 Z= 0.147 Angle : 0.604 6.813 18559 Z= 0.354 Chirality : 0.043 0.282 2113 Planarity : 0.004 0.052 1328 Dihedral : 31.379 145.969 4049 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.92 % Allowed : 19.84 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.81 (0.31), residues: 737 helix: 2.62 (0.22), residues: 551 sheet: None (None), residues: 0 loop : -0.55 (0.42), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 86 TYR 0.013 0.001 TYR H 42 PHE 0.010 0.001 PHE A 67 HIS 0.002 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.15 (12810) covalent geometry : angle 0.60417 / 0.35 (18559) hydrogen bonds : bond 0.03740 / 2.58 ( 775) hydrogen bonds : angle 2.83540 / 1.94 ( 1939) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 150 time to evaluate : 0.320 Fit side-chains REVERT: B 92 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8175 (ttp80) REVERT: C 73 ASN cc_start: 0.8677 (t0) cc_final: 0.8158 (t0) REVERT: D 108 LYS cc_start: 0.8676 (mtmt) cc_final: 0.8468 (mtpm) REVERT: E 59 GLU cc_start: 0.8598 (pm20) cc_final: 0.7931 (pm20) REVERT: G 73 ASN cc_start: 0.8509 (OUTLIER) cc_final: 0.8047 (t160) REVERT: G 90 ASP cc_start: 0.8426 (t70) cc_final: 0.8225 (t0) REVERT: H 63 ASN cc_start: 0.8884 (OUTLIER) cc_final: 0.8514 (m-40) REVERT: H 93 GLU cc_start: 0.9211 (mp0) cc_final: 0.8981 (mp0) outliers start: 12 outliers final: 8 residues processed: 156 average time/residue: 0.8187 time to fit residues: 134.7362 Evaluate side-chains 157 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 146 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 63 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 75 optimal weight: 10.0000 chunk 51 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 19 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 0.2980 chunk 26 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN E 68 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.106356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.067487 restraints weight = 20169.522| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 1.55 r_work: 0.2728 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2585 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12810 Z= 0.133 Angle : 0.600 7.017 18559 Z= 0.354 Chirality : 0.043 0.282 2113 Planarity : 0.004 0.050 1328 Dihedral : 31.361 145.895 4049 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.92 % Allowed : 20.32 % Favored : 77.76 % 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: 2.90 (0.31), residues: 737 helix: 2.68 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.50 (0.42), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 79 TYR 0.013 0.001 TYR F 88 PHE 0.011 0.001 PHE A 67 HIS 0.002 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.13 (12810) covalent geometry : angle 0.59993 / 0.35 (18559) hydrogen bonds : bond 0.03586 / 2.48 ( 775) hydrogen bonds : angle 2.80486 / 1.92 ( 1939) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4865.77 seconds wall clock time: 83 minutes 19.79 seconds (4999.79 seconds total)