Starting phenix.real_space_refine on Fri Jul 3 02:01:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ohc_12900/07_2026/7ohc_12900.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ohc_12900/07_2026/7ohc_12900.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ohc_12900/07_2026/7ohc_12900.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ohc_12900/07_2026/7ohc_12900.map" model { file = "/net/cci-nas-00/data/ceres_data/7ohc_12900/07_2026/7ohc_12900.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ohc_12900/07_2026/7ohc_12900.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 289 5.49 5 S 12 5.16 5 C 6648 2.51 5 N 2262 2.21 5 O 2808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12019 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 843 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 767 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "E" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 818 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Time building chain proxies: 1.93, per 1000 atoms: 0.16 Number of scatterers: 12019 At special positions: 0 Unit cell: (74.55, 119.7, 115.5, 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 289 15.00 O 2808 8.00 N 2262 7.00 C 6648 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: 0.66 Conformation dependent library (CDL) restraints added in 167.4 milliseconds 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1432 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 72.3% alpha, 3.1% beta 144 base pairs and 274 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 4.244A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.340A 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 '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 100 through 121 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 23 through 29 removed outlier: 4.030A pdb=" N ILE F 26 " --> pdb=" O ARG F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.355A 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 91 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 100 through 122 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.917A 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: 6.461A 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: 7.407A 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: 6.754A 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: 7.182A 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 78 419 hydrogen bonds defined for protein. 1242 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 367 hydrogen bonds 730 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 274 stacking parallelities Total time for adding SS restraints: 1.99 Time building geometry restraints manager: 1.01 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: 1813 1.33 - 1.45: 4503 1.45 - 1.57: 5904 1.57 - 1.69: 580 1.69 - 1.81: 22 Bond restraints: 12822 Sorted by residual: bond pdb=" C5' DA I 50 " pdb=" C4' DA I 50 " ideal model delta sigma weight residual 1.512 1.548 -0.036 7.00e-03 2.04e+04 2.64e+01 bond pdb=" C3' DC I 49 " pdb=" O3' DC I 49 " ideal model delta sigma weight residual 1.435 1.494 -0.059 1.30e-02 5.92e+03 2.05e+01 bond pdb=" C3' DC I 49 " pdb=" C2' DC I 49 " ideal model delta sigma weight residual 1.516 1.551 -0.035 8.00e-03 1.56e+04 1.92e+01 bond pdb=" CB GLU H 110 " pdb=" CG GLU H 110 " ideal model delta sigma weight residual 1.520 1.407 0.113 3.00e-02 1.11e+03 1.41e+01 bond pdb=" C3' DC I -62 " pdb=" C2' DC I -62 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.30e+01 ... (remaining 12817 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 17511 2.09 - 4.17: 970 4.17 - 6.26: 45 6.26 - 8.34: 19 8.34 - 10.43: 11 Bond angle restraints: 18556 Sorted by residual: angle pdb=" O5' DA I 50 " pdb=" C5' DA I 50 " pdb=" C4' DA I 50 " ideal model delta sigma weight residual 109.40 115.42 -6.02 8.00e-01 1.56e+00 5.67e+01 angle pdb=" CA ASN C 73 " pdb=" CB ASN C 73 " pdb=" CG ASN C 73 " ideal model delta sigma weight residual 112.60 118.94 -6.34 1.00e+00 1.00e+00 4.03e+01 angle pdb=" O5' DA I -45 " pdb=" C5' DA I -45 " pdb=" C4' DA I -45 " ideal model delta sigma weight residual 109.40 113.91 -4.51 8.00e-01 1.56e+00 3.18e+01 angle pdb=" O4' DA J 16 " pdb=" C1' DA J 16 " pdb=" N9 DA J 16 " ideal model delta sigma weight residual 108.00 111.77 -3.77 7.00e-01 2.04e+00 2.91e+01 angle pdb=" O4' DG J 23 " pdb=" C1' DG J 23 " pdb=" N9 DG J 23 " ideal model delta sigma weight residual 108.00 111.61 -3.61 7.00e-01 2.04e+00 2.66e+01 ... (remaining 18551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.47: 4465 21.47 - 42.93: 1384 42.93 - 64.40: 1085 64.40 - 85.87: 47 85.87 - 107.34: 4 Dihedral angle restraints: 6985 sinusoidal: 4767 harmonic: 2218 Sorted by residual: 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 -161.60 -18.40 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA PRO D 100 " pdb=" C PRO D 100 " pdb=" N GLY D 101 " pdb=" CA GLY D 101 " ideal model delta harmonic sigma weight residual -180.00 -161.86 -18.14 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA PHE E 84 " pdb=" C PHE E 84 " pdb=" N GLN E 85 " pdb=" CA GLN E 85 " ideal model delta harmonic sigma weight residual 180.00 162.69 17.31 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 6982 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1922 0.082 - 0.165: 181 0.165 - 0.247: 7 0.247 - 0.330: 0 0.330 - 0.412: 1 Chirality restraints: 2111 Sorted by residual: chirality pdb=" CB THR D 116 " pdb=" CA THR D 116 " pdb=" OG1 THR D 116 " pdb=" CG2 THR D 116 " both_signs ideal model delta sigma weight residual False 2.55 2.14 0.41 2.00e-01 2.50e+01 4.24e+00 chirality pdb=" CB THR A 58 " pdb=" CA THR A 58 " pdb=" OG1 THR A 58 " pdb=" CG2 THR A 58 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CB THR H 112 " pdb=" CA THR H 112 " pdb=" OG1 THR H 112 " pdb=" CG2 THR H 112 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 2108 not shown) Planarity restraints: 1344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 73 " -0.018 2.00e-02 2.50e+03 3.58e-02 1.28e+01 pdb=" C ASN C 73 " 0.062 2.00e-02 2.50e+03 pdb=" O ASN C 73 " -0.024 2.00e-02 2.50e+03 pdb=" N LYS C 74 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 58 " -0.017 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C THR A 58 " 0.057 2.00e-02 2.50e+03 pdb=" O THR A 58 " -0.021 2.00e-02 2.50e+03 pdb=" N GLU A 59 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 69 " 0.036 2.00e-02 2.50e+03 2.11e-02 9.97e+00 pdb=" N1 DC I 69 " -0.049 2.00e-02 2.50e+03 pdb=" C2 DC I 69 " 0.010 2.00e-02 2.50e+03 pdb=" O2 DC I 69 " -0.008 2.00e-02 2.50e+03 pdb=" N3 DC I 69 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DC I 69 " 0.007 2.00e-02 2.50e+03 pdb=" N4 DC I 69 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DC I 69 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DC I 69 " -0.003 2.00e-02 2.50e+03 ... (remaining 1341 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 951 2.73 - 3.28: 10386 3.28 - 3.82: 24870 3.82 - 4.36: 30273 4.36 - 4.90: 41885 Nonbonded interactions: 108365 Sorted by model distance: nonbonded pdb=" O ASN C 73 " pdb=" ND2 ASN C 73 " model vdw 2.193 3.120 nonbonded pdb=" OG1 THR D 29 " pdb=" OP1 DT I 30 " model vdw 2.238 3.040 nonbonded pdb=" O2 DC I -23 " pdb=" N2 DG J 23 " model vdw 2.255 2.496 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.275 3.040 nonbonded pdb=" OD2 ASP D 65 " pdb=" OH TYR F 98 " model vdw 2.299 3.040 ... (remaining 108360 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' and resid 38 through 134) } ncs_group { reference = (chain 'B' and resid 23 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 13 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 28 through 122) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.470 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.580 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 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 0.113 12822 Z= 0.574 Angle : 0.973 10.429 18556 Z= 0.785 Chirality : 0.050 0.412 2111 Planarity : 0.006 0.052 1344 Dihedral : 29.622 107.336 5553 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.16 % Allowed : 15.70 % Favored : 84.14 % 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: 0.04 (0.27), residues: 748 helix: 0.44 (0.20), residues: 537 sheet: None (None), residues: 0 loop : -0.81 (0.35), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 72 TYR 0.051 0.003 TYR H 118 PHE 0.029 0.003 PHE G 25 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00682 / 0.57 (12822) covalent geometry : angle 0.97269 / 0.79 (18556) hydrogen bonds : bond 0.10696 / 7.04 ( 786) hydrogen bonds : angle 4.11912 / 2.95 ( 1972) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 205 time to evaluate : 0.230 Fit side-chains REVERT: A 42 ARG cc_start: 0.7818 (mmm160) cc_final: 0.7580 (mmm-85) REVERT: A 50 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7984 (mt-10) REVERT: C 90 ASP cc_start: 0.8094 (t70) cc_final: 0.7798 (t0) REVERT: D 31 LYS cc_start: 0.8728 (mptt) cc_final: 0.8420 (mmtm) REVERT: D 68 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7362 (tp30) REVERT: D 90 GLU cc_start: 0.8180 (mp0) cc_final: 0.7932 (mp0) REVERT: D 105 LYS cc_start: 0.8506 (ttmm) cc_final: 0.8266 (ttpp) REVERT: E 129 ARG cc_start: 0.8251 (tpt90) cc_final: 0.8010 (tpt90) REVERT: G 74 LYS cc_start: 0.8830 (ptpp) cc_final: 0.8400 (mtmm) REVERT: G 99 ARG cc_start: 0.7960 (mmm160) cc_final: 0.7691 (mmm-85) REVERT: H 65 ASP cc_start: 0.8752 (t70) cc_final: 0.8469 (t0) REVERT: H 76 ARG cc_start: 0.7811 (mtp180) cc_final: 0.7532 (mtm-85) outliers start: 1 outliers final: 1 residues processed: 205 average time/residue: 0.6993 time to fit residues: 151.7278 Evaluate side-chains 184 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 0.0980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.106751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.085369 restraints weight = 20339.694| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.37 r_work: 0.3168 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12822 Z= 0.146 Angle : 0.671 6.716 18556 Z= 0.389 Chirality : 0.048 0.232 2111 Planarity : 0.004 0.043 1344 Dihedral : 32.053 103.821 4030 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.14 % Allowed : 17.11 % Favored : 79.75 % 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: 1.60 (0.28), residues: 748 helix: 1.63 (0.21), residues: 547 sheet: None (None), residues: 0 loop : -0.45 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 30 TYR 0.012 0.001 TYR H 37 PHE 0.009 0.001 PHE A 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.15 (12822) covalent geometry : angle 0.67100 / 0.39 (18556) hydrogen bonds : bond 0.04969 / 3.39 ( 786) hydrogen bonds : angle 3.28896 / 2.35 ( 1972) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 193 time to evaluate : 0.210 Fit side-chains REVERT: A 42 ARG cc_start: 0.8008 (mmm160) cc_final: 0.7691 (mmm-85) REVERT: A 120 MET cc_start: 0.8751 (mmm) cc_final: 0.8465 (mmt) REVERT: B 79 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8818 (mttm) REVERT: C 73 ASN cc_start: 0.8942 (OUTLIER) cc_final: 0.8468 (t160) REVERT: D 31 LYS cc_start: 0.8866 (mptt) cc_final: 0.8664 (mptt) REVERT: D 68 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8179 (tp30) REVERT: D 90 GLU cc_start: 0.8688 (mp0) cc_final: 0.8450 (mp0) REVERT: E 68 GLN cc_start: 0.9190 (OUTLIER) cc_final: 0.8722 (tt0) REVERT: E 129 ARG cc_start: 0.8652 (tpt90) cc_final: 0.8227 (tpt90) REVERT: F 63 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8520 (mt-10) REVERT: G 99 ARG cc_start: 0.8447 (mmm160) cc_final: 0.8109 (mmm-85) REVERT: H 65 ASP cc_start: 0.9052 (t70) cc_final: 0.8787 (t0) REVERT: H 76 ARG cc_start: 0.8213 (mtp180) cc_final: 0.7883 (mtm-85) outliers start: 20 outliers final: 9 residues processed: 193 average time/residue: 0.6925 time to fit residues: 141.2949 Evaluate side-chains 191 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 178 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 113 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 76 optimal weight: 20.0000 chunk 43 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 98 optimal weight: 20.0000 chunk 94 optimal weight: 10.0000 chunk 89 optimal weight: 20.0000 chunk 95 optimal weight: 10.0000 chunk 87 optimal weight: 30.0000 chunk 79 optimal weight: 10.0000 overall best weight: 6.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS H 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.099946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.077714 restraints weight = 20539.386| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.49 r_work: 0.3015 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.082 12822 Z= 0.423 Angle : 0.828 8.425 18556 Z= 0.450 Chirality : 0.058 0.268 2111 Planarity : 0.006 0.056 1344 Dihedral : 32.282 117.511 4030 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.08 % Allowed : 17.74 % Favored : 78.18 % 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: 1.47 (0.29), residues: 748 helix: 1.52 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -0.43 (0.38), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 95 TYR 0.017 0.003 TYR E 54 PHE 0.036 0.003 PHE G 25 HIS 0.008 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00891 / 0.42 (12822) covalent geometry : angle 0.82761 / 0.45 (18556) hydrogen bonds : bond 0.08395 / 5.70 ( 786) hydrogen bonds : angle 3.35665 / 2.41 ( 1972) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 178 time to evaluate : 0.192 Fit side-chains REVERT: A 42 ARG cc_start: 0.8182 (mmm160) cc_final: 0.7638 (mmm-85) REVERT: B 68 ASP cc_start: 0.8798 (m-30) cc_final: 0.8516 (m-30) REVERT: B 92 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.8115 (ttp80) REVERT: C 64 GLU cc_start: 0.8612 (tt0) cc_final: 0.8233 (tp30) REVERT: C 73 ASN cc_start: 0.9030 (t160) cc_final: 0.8558 (t0) REVERT: D 90 GLU cc_start: 0.8820 (mp0) cc_final: 0.8527 (mp0) REVERT: E 68 GLN cc_start: 0.9219 (OUTLIER) cc_final: 0.8721 (tt0) REVERT: E 129 ARG cc_start: 0.8700 (tpt90) cc_final: 0.8190 (tpt90) REVERT: F 63 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8568 (mt-10) REVERT: G 113 SER cc_start: 0.9028 (m) cc_final: 0.8775 (p) outliers start: 26 outliers final: 11 residues processed: 184 average time/residue: 0.7347 time to fit residues: 143.0386 Evaluate side-chains 184 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 170 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 53 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 15 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 8 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 74 optimal weight: 20.0000 chunk 64 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.102727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.080917 restraints weight = 20106.738| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.37 r_work: 0.3082 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12822 Z= 0.142 Angle : 0.707 7.655 18556 Z= 0.396 Chirality : 0.051 0.268 2111 Planarity : 0.005 0.042 1344 Dihedral : 32.283 120.836 4028 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.83 % Allowed : 19.47 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.30), residues: 748 helix: 1.85 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.24 (0.39), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 72 TYR 0.028 0.002 TYR H 39 PHE 0.010 0.002 PHE G 25 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.14 (12822) covalent geometry : angle 0.70709 / 0.40 (18556) hydrogen bonds : bond 0.05025 / 3.46 ( 786) hydrogen bonds : angle 3.23604 / 2.33 ( 1972) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 190 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8386 (mt-10) REVERT: B 68 ASP cc_start: 0.8738 (m-30) cc_final: 0.8516 (m-30) REVERT: C 64 GLU cc_start: 0.8385 (tt0) cc_final: 0.8038 (tp30) REVERT: C 73 ASN cc_start: 0.8977 (t160) cc_final: 0.8499 (t0) REVERT: C 90 ASP cc_start: 0.8480 (t70) cc_final: 0.8143 (t70) REVERT: D 31 LYS cc_start: 0.8917 (mptt) cc_final: 0.8692 (mptt) REVERT: D 54 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8742 (mmtp) REVERT: E 68 GLN cc_start: 0.9171 (OUTLIER) cc_final: 0.8733 (tt0) REVERT: E 129 ARG cc_start: 0.8678 (tpt90) cc_final: 0.8240 (tpt90) REVERT: F 63 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8505 (mt-10) REVERT: G 113 SER cc_start: 0.8981 (m) cc_final: 0.8743 (p) REVERT: H 65 ASP cc_start: 0.9050 (t70) cc_final: 0.8793 (t0) REVERT: H 76 ARG cc_start: 0.8209 (mtp180) cc_final: 0.7911 (mtm-85) outliers start: 18 outliers final: 8 residues processed: 194 average time/residue: 0.7504 time to fit residues: 153.7204 Evaluate side-chains 194 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 183 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 53 SER 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 77 optimal weight: 20.0000 chunk 8 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 84 optimal weight: 20.0000 chunk 70 optimal weight: 0.8980 chunk 19 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 chunk 82 optimal weight: 20.0000 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.103175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.081474 restraints weight = 20129.303| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.37 r_work: 0.3091 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 12822 Z= 0.160 Angle : 0.645 7.031 18556 Z= 0.370 Chirality : 0.046 0.241 2111 Planarity : 0.004 0.048 1344 Dihedral : 31.895 127.149 4028 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.73 % Allowed : 21.51 % Favored : 76.77 % 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: 2.39 (0.30), residues: 748 helix: 2.21 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.13 (0.39), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 95 TYR 0.019 0.002 TYR H 39 PHE 0.010 0.002 PHE G 25 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.16 (12822) covalent geometry : angle 0.64510 / 0.37 (18556) hydrogen bonds : bond 0.04833 / 3.32 ( 786) hydrogen bonds : angle 3.05435 / 2.20 ( 1972) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 187 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: B 68 ASP cc_start: 0.8786 (m-30) cc_final: 0.8549 (m-30) REVERT: C 64 GLU cc_start: 0.8426 (tt0) cc_final: 0.8019 (tp30) REVERT: C 73 ASN cc_start: 0.9027 (t160) cc_final: 0.8540 (t0) REVERT: C 90 ASP cc_start: 0.8492 (t70) cc_final: 0.8201 (t70) REVERT: D 54 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8729 (mmtp) REVERT: D 90 GLU cc_start: 0.8811 (mp0) cc_final: 0.8567 (mp0) REVERT: E 68 GLN cc_start: 0.9146 (OUTLIER) cc_final: 0.8685 (tt0) REVERT: E 129 ARG cc_start: 0.8634 (tpt90) cc_final: 0.8179 (tpt90) REVERT: F 63 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8613 (mt-10) REVERT: H 39 TYR cc_start: 0.8327 (t80) cc_final: 0.8090 (t80) REVERT: H 65 ASP cc_start: 0.9016 (t70) cc_final: 0.8748 (t0) outliers start: 11 outliers final: 8 residues processed: 187 average time/residue: 0.8637 time to fit residues: 170.7191 Evaluate side-chains 194 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 183 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain H residue 53 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 85 optimal weight: 40.0000 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 84 optimal weight: 20.0000 chunk 8 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.103499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.081801 restraints weight = 20148.311| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.38 r_work: 0.3097 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12822 Z= 0.156 Angle : 0.634 6.930 18556 Z= 0.366 Chirality : 0.045 0.240 2111 Planarity : 0.004 0.044 1344 Dihedral : 31.730 131.630 4028 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.98 % Allowed : 21.19 % Favored : 75.82 % 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: 2.54 (0.30), residues: 748 helix: 2.28 (0.22), residues: 547 sheet: None (None), residues: 0 loop : 0.05 (0.39), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 83 TYR 0.011 0.002 TYR C 57 PHE 0.010 0.002 PHE F 100 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.16 (12822) covalent geometry : angle 0.63404 / 0.37 (18556) hydrogen bonds : bond 0.04606 / 3.16 ( 786) hydrogen bonds : angle 3.01204 / 2.16 ( 1972) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 190 time to evaluate : 0.194 Fit side-chains REVERT: A 42 ARG cc_start: 0.8390 (mmm160) cc_final: 0.8096 (mmm-85) REVERT: B 68 ASP cc_start: 0.8790 (m-30) cc_final: 0.8542 (m-30) REVERT: C 64 GLU cc_start: 0.8502 (tt0) cc_final: 0.8112 (tp30) REVERT: C 73 ASN cc_start: 0.8999 (OUTLIER) cc_final: 0.8537 (t0) REVERT: C 90 ASP cc_start: 0.8449 (t70) cc_final: 0.8156 (t70) REVERT: D 31 LYS cc_start: 0.8932 (mptt) cc_final: 0.8631 (mmtm) REVERT: D 90 GLU cc_start: 0.8846 (mp0) cc_final: 0.8592 (mp0) REVERT: E 68 GLN cc_start: 0.9210 (OUTLIER) cc_final: 0.8770 (tt0) REVERT: E 129 ARG cc_start: 0.8608 (tpt90) cc_final: 0.8178 (tpt90) REVERT: H 30 ARG cc_start: 0.6556 (mtp-110) cc_final: 0.6202 (mtt180) REVERT: H 39 TYR cc_start: 0.8257 (t80) cc_final: 0.7974 (t80) REVERT: H 65 ASP cc_start: 0.8986 (t70) cc_final: 0.8731 (t0) outliers start: 19 outliers final: 11 residues processed: 192 average time/residue: 0.8640 time to fit residues: 175.2644 Evaluate side-chains 196 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 183 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 53 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 11 optimal weight: 0.6980 chunk 79 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 76 optimal weight: 20.0000 chunk 99 optimal weight: 30.0000 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.101237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.079372 restraints weight = 20116.483| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.40 r_work: 0.3052 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 12822 Z= 0.259 Angle : 0.701 7.669 18556 Z= 0.392 Chirality : 0.049 0.257 2111 Planarity : 0.005 0.042 1344 Dihedral : 31.879 135.389 4028 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.67 % Allowed : 21.98 % Favored : 75.35 % 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: 2.40 (0.30), residues: 748 helix: 2.17 (0.22), residues: 547 sheet: None (None), residues: 0 loop : 0.02 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 83 TYR 0.013 0.002 TYR D 37 PHE 0.018 0.002 PHE G 25 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.26 (12822) covalent geometry : angle 0.70118 / 0.39 (18556) hydrogen bonds : bond 0.05975 / 4.08 ( 786) hydrogen bonds : angle 3.12440 / 2.25 ( 1972) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 182 time to evaluate : 0.331 Fit side-chains REVERT: A 42 ARG cc_start: 0.8342 (mmm160) cc_final: 0.8089 (mtp-110) REVERT: A 50 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8347 (mt-10) REVERT: B 68 ASP cc_start: 0.8809 (m-30) cc_final: 0.8553 (m-30) REVERT: C 73 ASN cc_start: 0.9011 (t160) cc_final: 0.8544 (t0) REVERT: C 90 ASP cc_start: 0.8483 (t70) cc_final: 0.8160 (t70) REVERT: D 54 LYS cc_start: 0.8985 (mmmt) cc_final: 0.8677 (mmtp) REVERT: E 68 GLN cc_start: 0.9191 (OUTLIER) cc_final: 0.8714 (tt0) REVERT: H 39 TYR cc_start: 0.8262 (t80) cc_final: 0.7910 (t80) REVERT: H 65 ASP cc_start: 0.9051 (t70) cc_final: 0.8773 (t0) outliers start: 17 outliers final: 11 residues processed: 186 average time/residue: 0.8392 time to fit residues: 165.0190 Evaluate side-chains 193 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 181 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 53 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 52 optimal weight: 0.7980 chunk 77 optimal weight: 10.0000 chunk 85 optimal weight: 40.0000 chunk 79 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 81 optimal weight: 20.0000 chunk 31 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN ** E 76 GLN ** 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 = 0.3642 r_free = 0.3642 target = 0.102511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.081327 restraints weight = 20316.052| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.32 r_work: 0.3096 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 12822 Z= 0.147 Angle : 0.676 7.630 18556 Z= 0.381 Chirality : 0.047 0.255 2111 Planarity : 0.004 0.041 1344 Dihedral : 31.902 136.048 4028 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.45 % Allowed : 21.66 % Favored : 74.88 % 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: 2.58 (0.30), residues: 748 helix: 2.30 (0.22), residues: 547 sheet: None (None), residues: 0 loop : 0.09 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 83 TYR 0.028 0.002 TYR G 57 PHE 0.013 0.002 PHE G 25 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.15 (12822) covalent geometry : angle 0.67575 / 0.38 (18556) hydrogen bonds : bond 0.05183 / 3.55 ( 786) hydrogen bonds : angle 3.11201 / 2.24 ( 1972) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 187 time to evaluate : 0.325 Fit side-chains REVERT: A 42 ARG cc_start: 0.8386 (mmm160) cc_final: 0.8143 (mtp-110) REVERT: B 68 ASP cc_start: 0.8782 (m-30) cc_final: 0.8546 (m-30) REVERT: C 64 GLU cc_start: 0.8654 (tm-30) cc_final: 0.8155 (tp30) REVERT: C 73 ASN cc_start: 0.8989 (OUTLIER) cc_final: 0.8521 (t0) REVERT: C 90 ASP cc_start: 0.8476 (t70) cc_final: 0.8171 (t70) REVERT: D 54 LYS cc_start: 0.8988 (mmmt) cc_final: 0.8619 (mmtp) REVERT: E 68 GLN cc_start: 0.9168 (OUTLIER) cc_final: 0.8681 (tt0) REVERT: E 129 ARG cc_start: 0.8603 (tpt90) cc_final: 0.8149 (tpt90) REVERT: F 93 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.7240 (mp10) REVERT: G 74 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8543 (mtmm) REVERT: H 30 ARG cc_start: 0.6653 (mtp-110) cc_final: 0.6384 (mtt180) REVERT: H 39 TYR cc_start: 0.8219 (t80) cc_final: 0.7842 (t80) REVERT: H 65 ASP cc_start: 0.9015 (t70) cc_final: 0.8783 (t0) REVERT: H 83 ARG cc_start: 0.8824 (mmt90) cc_final: 0.8475 (mmt180) outliers start: 22 outliers final: 10 residues processed: 191 average time/residue: 0.7724 time to fit residues: 156.0818 Evaluate side-chains 197 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 183 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 53 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 23 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 99 optimal weight: 30.0000 chunk 79 optimal weight: 20.0000 chunk 55 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 40 optimal weight: 0.0370 overall best weight: 1.7462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN H 46 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.102501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.081256 restraints weight = 20174.964| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.33 r_work: 0.3098 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 12822 Z= 0.177 Angle : 0.672 7.467 18556 Z= 0.379 Chirality : 0.047 0.252 2111 Planarity : 0.004 0.042 1344 Dihedral : 31.864 136.115 4028 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.83 % Allowed : 22.61 % Favored : 74.57 % 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: 2.57 (0.30), residues: 748 helix: 2.29 (0.22), residues: 547 sheet: None (None), residues: 0 loop : 0.09 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 83 TYR 0.022 0.002 TYR F 88 PHE 0.009 0.002 PHE A 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.18 (12822) covalent geometry : angle 0.67165 / 0.38 (18556) hydrogen bonds : bond 0.04968 / 3.41 ( 786) hydrogen bonds : angle 3.09369 / 2.23 ( 1972) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 182 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8385 (mt-10) REVERT: B 68 ASP cc_start: 0.8790 (m-30) cc_final: 0.8540 (m-30) REVERT: C 64 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8223 (tp30) REVERT: C 73 ASN cc_start: 0.9001 (OUTLIER) cc_final: 0.8534 (t0) REVERT: C 90 ASP cc_start: 0.8478 (t70) cc_final: 0.8176 (t70) REVERT: D 54 LYS cc_start: 0.8953 (mmmt) cc_final: 0.8621 (mmtp) REVERT: E 68 GLN cc_start: 0.9183 (OUTLIER) cc_final: 0.8715 (tt0) REVERT: E 129 ARG cc_start: 0.8598 (tpt90) cc_final: 0.8153 (tpt90) REVERT: F 68 ASP cc_start: 0.9196 (m-30) cc_final: 0.8937 (m-30) REVERT: F 84 MET cc_start: 0.9160 (OUTLIER) cc_final: 0.8942 (mmm) REVERT: F 93 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.7258 (mp10) REVERT: G 74 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8551 (mtmm) REVERT: H 30 ARG cc_start: 0.6653 (mtp-110) cc_final: 0.6388 (mtt180) REVERT: H 39 TYR cc_start: 0.8212 (t80) cc_final: 0.7827 (t80) REVERT: H 65 ASP cc_start: 0.9007 (t70) cc_final: 0.8774 (t0) REVERT: H 83 ARG cc_start: 0.8833 (mmt90) cc_final: 0.8487 (mmt180) outliers start: 18 outliers final: 10 residues processed: 186 average time/residue: 0.7258 time to fit residues: 142.8155 Evaluate side-chains 197 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 182 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 53 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 20 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 87 optimal weight: 30.0000 chunk 29 optimal weight: 1.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 46 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.102622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.081401 restraints weight = 20320.877| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.33 r_work: 0.3101 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 12822 Z= 0.187 Angle : 0.667 7.282 18556 Z= 0.378 Chirality : 0.046 0.248 2111 Planarity : 0.004 0.042 1344 Dihedral : 31.800 137.026 4028 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.67 % Allowed : 22.45 % Favored : 74.88 % 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: 2.57 (0.30), residues: 748 helix: 2.28 (0.22), residues: 547 sheet: None (None), residues: 0 loop : 0.10 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 83 TYR 0.030 0.002 TYR F 88 PHE 0.010 0.002 PHE G 25 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.19 (12822) covalent geometry : angle 0.66749 / 0.38 (18556) hydrogen bonds : bond 0.04893 / 3.35 ( 786) hydrogen bonds : angle 3.07655 / 2.22 ( 1972) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 183 time to evaluate : 0.278 Fit side-chains REVERT: A 42 ARG cc_start: 0.8379 (mmm160) cc_final: 0.8088 (mtp-110) REVERT: B 68 ASP cc_start: 0.8800 (m-30) cc_final: 0.8535 (m-30) REVERT: C 64 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8242 (tp30) REVERT: C 73 ASN cc_start: 0.9001 (OUTLIER) cc_final: 0.8519 (t0) REVERT: C 90 ASP cc_start: 0.8461 (t70) cc_final: 0.8188 (t70) REVERT: D 54 LYS cc_start: 0.8955 (mmmt) cc_final: 0.8618 (mmtp) REVERT: E 68 GLN cc_start: 0.9193 (OUTLIER) cc_final: 0.8723 (tt0) REVERT: F 68 ASP cc_start: 0.9196 (m-30) cc_final: 0.8938 (m-30) REVERT: F 93 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.7258 (mp10) REVERT: G 74 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8556 (mtmm) REVERT: H 30 ARG cc_start: 0.6669 (mtp-110) cc_final: 0.6404 (mtt180) REVERT: H 65 ASP cc_start: 0.9003 (t70) cc_final: 0.8756 (t0) REVERT: H 76 ARG cc_start: 0.8323 (mtp180) cc_final: 0.8036 (mtm-85) REVERT: H 83 ARG cc_start: 0.8840 (mmt90) cc_final: 0.8500 (mmt180) outliers start: 17 outliers final: 10 residues processed: 186 average time/residue: 0.7362 time to fit residues: 144.9341 Evaluate side-chains 197 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 183 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 53 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 94 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 89 optimal weight: 20.0000 chunk 58 optimal weight: 8.9990 chunk 41 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN H 46 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.103064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.081900 restraints weight = 20327.744| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.33 r_work: 0.3106 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 12822 Z= 0.152 Angle : 0.665 7.303 18556 Z= 0.377 Chirality : 0.046 0.247 2111 Planarity : 0.004 0.041 1344 Dihedral : 31.796 137.036 4028 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.51 % Allowed : 22.76 % Favored : 74.73 % 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: 2.62 (0.30), residues: 748 helix: 2.32 (0.22), residues: 547 sheet: None (None), residues: 0 loop : 0.12 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 83 TYR 0.037 0.002 TYR F 88 PHE 0.010 0.002 PHE A 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.15 (12822) covalent geometry : angle 0.66518 / 0.38 (18556) hydrogen bonds : bond 0.04800 / 3.29 ( 786) hydrogen bonds : angle 3.06673 / 2.21 ( 1972) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4944.58 seconds wall clock time: 84 minutes 29.66 seconds (5069.66 seconds total)