Starting phenix.real_space_refine on Fri Sep 11 20:39:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ohc_12900/09_2026/7ohc_12900.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ohc_12900/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7ohc_12900/09_2026/7ohc_12900.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ohc_12900/09_2026/7ohc_12900.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ohc_12900/09_2026/7ohc_12900.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ohc_12900/09_2026/7ohc_12900.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.54, per 1000 atoms: 0.21 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: 0.96 Conformation dependent library (CDL) restraints added in 399.2 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: 1.95 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: 2.40 Time building geometry restraints manager: 1.36 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: 17490 2.09 - 4.17: 991 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: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 13.170 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 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:8.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.050 ------------------------------------------------------------------------------- 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= 0.575 Angle : 0.982 10.429 18556 Z= 0.794 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 0.98173 / 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 : 0.203 Fit side-chains 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: 0.8183 time to fit residues: 177.5453 Evaluate side-chains 183 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 182 time to evaluate : 0.311 ------------------------------------------------------------------------------- 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: 10.0000 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 ** E 76 GLN ** 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 = 0.3695 r_free = 0.3695 target = 0.106262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.084835 restraints weight = 20290.134| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.38 r_work: 0.3161 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 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 0.036 12822 Z= 0.148 Angle : 0.693 7.186 18556 Z= 0.394 Chirality : 0.049 0.250 2111 Planarity : 0.004 0.045 1344 Dihedral : 31.971 102.748 4030 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.98 % Allowed : 17.11 % Favored : 79.91 % 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: 1.57 (0.28), residues: 748 helix: 1.61 (0.21), residues: 547 sheet: None (None), residues: 0 loop : -0.46 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 30 TYR 0.012 0.001 TYR H 37 PHE 0.009 0.001 PHE G 25 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.15 (12822) covalent geometry : angle 0.69278 / 0.39 (18556) hydrogen bonds : bond 0.05056 / 3.45 ( 786) hydrogen bonds : angle 3.29260 / 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 211 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 192 time to evaluate : 0.251 Fit side-chains REVERT: A 42 ARG cc_start: 0.7979 (mmm-85) cc_final: 0.7383 (mmm-85) REVERT: A 120 MET cc_start: 0.8774 (mmm) cc_final: 0.8484 (mmt) REVERT: B 79 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8826 (mttm) REVERT: C 73 ASN cc_start: 0.8975 (OUTLIER) cc_final: 0.8519 (t160) REVERT: C 90 ASP cc_start: 0.8518 (t70) cc_final: 0.8059 (t0) REVERT: D 31 LYS cc_start: 0.8866 (mptt) cc_final: 0.8662 (mptt) REVERT: D 68 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8177 (tp30) REVERT: E 68 GLN cc_start: 0.9196 (OUTLIER) cc_final: 0.8730 (tt0) REVERT: E 129 ARG cc_start: 0.8652 (tpt90) cc_final: 0.8232 (tpt90) REVERT: F 63 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8520 (mt-10) REVERT: G 99 ARG cc_start: 0.8453 (mmm160) cc_final: 0.8115 (mmm-85) REVERT: H 39 TYR cc_start: 0.8147 (t80) cc_final: 0.7940 (t80) REVERT: H 65 ASP cc_start: 0.9050 (t70) cc_final: 0.8785 (t0) REVERT: H 76 ARG cc_start: 0.8225 (mtp180) cc_final: 0.7893 (mtm-85) outliers start: 19 outliers final: 8 residues processed: 192 average time/residue: 0.8075 time to fit residues: 163.9903 Evaluate side-chains 191 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 179 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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 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: 4.9990 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: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN H 46 HIS H 81 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.099668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.077519 restraints weight = 20527.674| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.42 r_work: 0.3013 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1923 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= 0.437 Angle : 0.868 8.404 18556 Z= 0.463 Chirality : 0.060 0.266 2111 Planarity : 0.006 0.057 1344 Dihedral : 32.174 115.504 4030 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.55 % Allowed : 16.80 % Favored : 78.65 % 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: 1.37 (0.29), residues: 748 helix: 1.45 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -0.44 (0.38), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 39 TYR 0.017 0.003 TYR E 54 PHE 0.037 0.003 PHE G 25 HIS 0.009 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00927 / 0.44 (12822) covalent geometry : angle 0.86849 / 0.46 (18556) hydrogen bonds : bond 0.08509 / 5.77 ( 786) hydrogen bonds : angle 3.36840 / 2.42 ( 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 208 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 179 time to evaluate : 0.323 Fit side-chains REVERT: B 68 ASP cc_start: 0.8828 (m-30) cc_final: 0.8573 (m-30) REVERT: B 79 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8851 (mttm) REVERT: B 92 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.8116 (ttp80) REVERT: C 64 GLU cc_start: 0.8616 (tt0) cc_final: 0.8239 (tp30) REVERT: C 73 ASN cc_start: 0.9032 (t160) cc_final: 0.8551 (t0) REVERT: D 90 GLU cc_start: 0.8909 (mp0) cc_final: 0.8543 (mp0) REVERT: E 68 GLN cc_start: 0.9220 (OUTLIER) cc_final: 0.8784 (tt0) REVERT: E 129 ARG cc_start: 0.8706 (tpt90) cc_final: 0.8198 (tpt90) REVERT: F 63 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8570 (mt-10) REVERT: G 113 SER cc_start: 0.9032 (m) cc_final: 0.8779 (p) REVERT: H 39 TYR cc_start: 0.8365 (t80) cc_final: 0.8030 (t80) REVERT: H 65 ASP cc_start: 0.9096 (t70) cc_final: 0.8872 (t0) outliers start: 29 outliers final: 11 residues processed: 186 average time/residue: 0.8422 time to fit residues: 165.3316 Evaluate side-chains 186 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 171 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 79 LYS 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: 3.9990 chunk 41 optimal weight: 0.8980 chunk 8 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 74 optimal weight: 20.0000 chunk 64 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** 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 = 0.3628 r_free = 0.3628 target = 0.102473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.080658 restraints weight = 20163.201| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.37 r_work: 0.3078 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12822 Z= 0.145 Angle : 0.738 7.393 18556 Z= 0.406 Chirality : 0.052 0.274 2111 Planarity : 0.005 0.044 1344 Dihedral : 32.184 118.897 4028 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 3.45 % Allowed : 18.52 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.30), residues: 748 helix: 1.81 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.28 (0.38), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 76 TYR 0.015 0.002 TYR G 57 PHE 0.011 0.002 PHE F 100 HIS 0.002 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.14 (12822) covalent geometry : angle 0.73814 / 0.41 (18556) hydrogen bonds : bond 0.05187 / 3.57 ( 786) hydrogen bonds : angle 3.25037 / 2.34 ( 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 210 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 0.264 Fit side-chains REVERT: A 42 ARG cc_start: 0.8190 (mmm-85) cc_final: 0.7654 (mmm-85) REVERT: A 50 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8416 (mt-10) REVERT: B 68 ASP cc_start: 0.8748 (m-30) cc_final: 0.8514 (m-30) REVERT: C 64 GLU cc_start: 0.8389 (tt0) cc_final: 0.8053 (tp30) REVERT: C 73 ASN cc_start: 0.8994 (t160) cc_final: 0.8526 (t0) REVERT: C 90 ASP cc_start: 0.8451 (t70) cc_final: 0.8126 (t70) REVERT: D 31 LYS cc_start: 0.8920 (mptt) cc_final: 0.8691 (mptt) REVERT: D 90 GLU cc_start: 0.8865 (mp0) cc_final: 0.8661 (mp0) REVERT: E 129 ARG cc_start: 0.8674 (tpt90) cc_final: 0.8242 (tpt90) REVERT: F 63 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8502 (mt-10) REVERT: G 113 SER cc_start: 0.8997 (m) cc_final: 0.8756 (p) REVERT: H 39 TYR cc_start: 0.8302 (t80) cc_final: 0.7842 (t80) REVERT: H 65 ASP cc_start: 0.9065 (t70) cc_final: 0.8797 (t0) REVERT: H 68 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8241 (pt0) outliers start: 22 outliers final: 10 residues processed: 191 average time/residue: 0.8115 time to fit residues: 164.2880 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 : 0.325 ------------------------------------------------------------------------------- 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 C residue 101 THR Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 88 SER 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 52 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 68 GLU 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: 0.7980 chunk 16 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 84 optimal weight: 20.0000 chunk 70 optimal weight: 3.9990 chunk 19 optimal weight: 0.0870 chunk 18 optimal weight: 2.9990 chunk 82 optimal weight: 20.0000 overall best weight: 1.1360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.102739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.080949 restraints weight = 20145.764| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.37 r_work: 0.3078 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12822 Z= 0.167 Angle : 0.703 7.247 18556 Z= 0.390 Chirality : 0.048 0.258 2111 Planarity : 0.004 0.053 1344 Dihedral : 31.998 120.648 4028 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.67 % Allowed : 20.25 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.30), residues: 748 helix: 2.10 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.22 (0.39), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 83 TYR 0.015 0.002 TYR G 57 PHE 0.011 0.002 PHE F 100 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.17 (12822) covalent geometry : angle 0.70302 / 0.39 (18556) hydrogen bonds : bond 0.04871 / 3.34 ( 786) hydrogen bonds : angle 3.12685 / 2.26 ( 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 205 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 188 time to evaluate : 0.219 Fit side-chains REVERT: A 50 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8382 (mt-10) REVERT: B 68 ASP cc_start: 0.8775 (m-30) cc_final: 0.8543 (m-30) REVERT: C 64 GLU cc_start: 0.8483 (tt0) cc_final: 0.8115 (tp30) REVERT: C 73 ASN cc_start: 0.9008 (t160) cc_final: 0.8548 (t0) REVERT: C 90 ASP cc_start: 0.8484 (t70) cc_final: 0.8150 (t70) REVERT: D 31 LYS cc_start: 0.8932 (mptt) cc_final: 0.8644 (mptt) REVERT: E 68 GLN cc_start: 0.9112 (OUTLIER) cc_final: 0.8426 (tt0) REVERT: E 120 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.7899 (mtt) REVERT: E 129 ARG cc_start: 0.8687 (tpt90) cc_final: 0.8242 (tpt90) REVERT: F 63 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8499 (mt-10) REVERT: G 113 SER cc_start: 0.8958 (m) cc_final: 0.8741 (p) REVERT: H 39 TYR cc_start: 0.8295 (t80) cc_final: 0.7812 (t80) REVERT: H 65 ASP cc_start: 0.9028 (t70) cc_final: 0.8752 (t0) outliers start: 17 outliers final: 10 residues processed: 190 average time/residue: 0.8554 time to fit residues: 171.6047 Evaluate side-chains 197 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 184 time to evaluate : 0.252 ------------------------------------------------------------------------------- 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 E residue 120 MET Chi-restraints excluded: chain E residue 122 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 85 optimal weight: 40.0000 chunk 14 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 84 optimal weight: 20.0000 chunk 8 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN ** E 68 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 = 0.3646 r_free = 0.3646 target = 0.103351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.081741 restraints weight = 20219.751| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.37 r_work: 0.3100 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12822 Z= 0.160 Angle : 0.655 6.683 18556 Z= 0.373 Chirality : 0.046 0.239 2111 Planarity : 0.005 0.066 1344 Dihedral : 31.668 126.917 4028 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.83 % Allowed : 20.57 % Favored : 76.61 % 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: 2.53 (0.30), residues: 748 helix: 2.31 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.08 (0.39), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 95 TYR 0.016 0.002 TYR G 57 PHE 0.009 0.002 PHE G 25 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.16 (12822) covalent geometry : angle 0.65457 / 0.37 (18556) hydrogen bonds : bond 0.04731 / 3.25 ( 786) hydrogen bonds : angle 3.03235 / 2.19 ( 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 208 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 190 time to evaluate : 0.295 Fit side-chains REVERT: B 68 ASP cc_start: 0.8776 (m-30) cc_final: 0.8539 (m-30) REVERT: C 64 GLU cc_start: 0.8449 (tt0) cc_final: 0.8084 (tp30) REVERT: C 73 ASN cc_start: 0.9034 (t160) cc_final: 0.8549 (t0) REVERT: C 90 ASP cc_start: 0.8453 (t70) cc_final: 0.8167 (t70) REVERT: E 68 GLN cc_start: 0.9145 (OUTLIER) cc_final: 0.8573 (tt0) REVERT: E 129 ARG cc_start: 0.8612 (tpt90) cc_final: 0.8161 (tpt90) REVERT: G 74 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8600 (ptpp) REVERT: G 113 SER cc_start: 0.8929 (m) cc_final: 0.8719 (p) REVERT: H 39 TYR cc_start: 0.8255 (t80) cc_final: 0.7741 (t80) REVERT: H 65 ASP cc_start: 0.9004 (t70) cc_final: 0.8778 (t0) outliers start: 18 outliers final: 10 residues processed: 191 average time/residue: 0.8404 time to fit residues: 169.7724 Evaluate side-chains 195 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 183 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 101 THR Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 74 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: 0.7980 chunk 79 optimal weight: 20.0000 chunk 60 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 76 optimal weight: 20.0000 chunk 99 optimal weight: 30.0000 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 68 GLN ** 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 = 0.3654 r_free = 0.3654 target = 0.103783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.082124 restraints weight = 20212.684| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.37 r_work: 0.3104 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12822 Z= 0.151 Angle : 0.654 6.724 18556 Z= 0.372 Chirality : 0.046 0.239 2111 Planarity : 0.004 0.052 1344 Dihedral : 31.629 128.832 4028 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.83 % Allowed : 21.19 % Favored : 75.98 % 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: 2.64 (0.30), residues: 748 helix: 2.37 (0.22), residues: 547 sheet: None (None), residues: 0 loop : 0.02 (0.39), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 42 TYR 0.013 0.001 TYR G 57 PHE 0.008 0.001 PHE A 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.15 (12822) covalent geometry : angle 0.65368 / 0.37 (18556) hydrogen bonds : bond 0.04578 / 3.14 ( 786) hydrogen bonds : angle 3.02823 / 2.18 ( 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 205 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 187 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: B 68 ASP cc_start: 0.8781 (m-30) cc_final: 0.8529 (m-30) REVERT: B 92 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.7978 (ttp80) REVERT: C 64 GLU cc_start: 0.8433 (tt0) cc_final: 0.8049 (tp30) REVERT: C 73 ASN cc_start: 0.9018 (OUTLIER) cc_final: 0.8539 (t0) REVERT: C 90 ASP cc_start: 0.8446 (t70) cc_final: 0.8138 (t70) REVERT: D 54 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8709 (mmtp) REVERT: E 68 GLN cc_start: 0.9147 (OUTLIER) cc_final: 0.8609 (tt0) REVERT: E 129 ARG cc_start: 0.8617 (tpt90) cc_final: 0.8192 (tpt90) REVERT: G 74 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8616 (ptpp) REVERT: G 113 SER cc_start: 0.8935 (m) cc_final: 0.8724 (p) REVERT: H 30 ARG cc_start: 0.6569 (mtp-110) cc_final: 0.6230 (mtt180) REVERT: H 39 TYR cc_start: 0.8251 (t80) cc_final: 0.7741 (t80) REVERT: H 65 ASP cc_start: 0.9000 (t70) cc_final: 0.8793 (t0) outliers start: 18 outliers final: 9 residues processed: 190 average time/residue: 0.8205 time to fit residues: 164.9635 Evaluate side-chains 199 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 185 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 73 ASN 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 49 LEU Chi-restraints excluded: chain F residue 77 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 52 optimal weight: 4.9990 chunk 77 optimal weight: 20.0000 chunk 85 optimal weight: 40.0000 chunk 79 optimal weight: 20.0000 chunk 56 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 81 optimal weight: 20.0000 chunk 31 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN ** E 68 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 = 0.3666 r_free = 0.3666 target = 0.103900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.082411 restraints weight = 20289.084| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.37 r_work: 0.3134 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12822 Z= 0.150 Angle : 0.643 6.597 18556 Z= 0.368 Chirality : 0.045 0.236 2111 Planarity : 0.004 0.043 1344 Dihedral : 31.516 132.224 4028 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.83 % Allowed : 21.51 % Favored : 75.67 % 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 (0.30), residues: 748 helix: 2.39 (0.21), residues: 547 sheet: None (None), residues: 0 loop : 0.10 (0.39), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 42 TYR 0.011 0.001 TYR C 57 PHE 0.008 0.001 PHE A 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.15 (12822) covalent geometry : angle 0.64272 / 0.37 (18556) hydrogen bonds : bond 0.04519 / 3.10 ( 786) hydrogen bonds : angle 2.99137 / 2.15 ( 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 205 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 187 time to evaluate : 0.318 Fit side-chains REVERT: A 42 ARG cc_start: 0.8237 (mmm-85) cc_final: 0.7682 (mtp85) REVERT: B 68 ASP cc_start: 0.8786 (m-30) cc_final: 0.8539 (m-30) REVERT: C 73 ASN cc_start: 0.9045 (OUTLIER) cc_final: 0.8579 (t0) REVERT: C 90 ASP cc_start: 0.8438 (t70) cc_final: 0.8140 (t70) REVERT: D 31 LYS cc_start: 0.8883 (mptt) cc_final: 0.8637 (mmtm) REVERT: E 68 GLN cc_start: 0.9096 (OUTLIER) cc_final: 0.8895 (tt0) REVERT: E 120 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.8287 (mtp) REVERT: E 129 ARG cc_start: 0.8586 (tpt90) cc_final: 0.8164 (tpt90) REVERT: F 93 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.7208 (mp10) REVERT: G 74 LYS cc_start: 0.8993 (ptpp) cc_final: 0.8477 (mtmm) REVERT: G 113 SER cc_start: 0.8928 (m) cc_final: 0.8722 (p) REVERT: H 30 ARG cc_start: 0.6539 (mtp-110) cc_final: 0.6222 (mtt180) REVERT: H 39 TYR cc_start: 0.8301 (t80) cc_final: 0.7809 (t80) REVERT: H 65 ASP cc_start: 0.8954 (t70) cc_final: 0.8741 (t0) REVERT: H 110 GLU cc_start: 0.7713 (pt0) cc_final: 0.7445 (pt0) REVERT: H 113 LYS cc_start: 0.8930 (ttpt) cc_final: 0.8700 (pttm) outliers start: 18 outliers final: 8 residues processed: 193 average time/residue: 0.8563 time to fit residues: 174.9689 Evaluate side-chains 194 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 182 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 87 SER 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 E residue 120 MET Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 109 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: 1.9990 chunk 18 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 99 optimal weight: 30.0000 chunk 79 optimal weight: 20.0000 chunk 55 optimal weight: 6.9990 chunk 62 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 68 GLN ** 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 = 0.3676 r_free = 0.3676 target = 0.104364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.083261 restraints weight = 20270.413| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.33 r_work: 0.3140 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 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 0.047 12822 Z= 0.151 Angle : 0.641 6.667 18556 Z= 0.366 Chirality : 0.045 0.236 2111 Planarity : 0.004 0.043 1344 Dihedral : 31.474 134.144 4028 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.04 % Allowed : 23.08 % 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: 2.72 (0.30), residues: 748 helix: 2.39 (0.21), residues: 547 sheet: None (None), residues: 0 loop : 0.17 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 95 TYR 0.010 0.001 TYR C 57 PHE 0.008 0.001 PHE A 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.15 (12822) covalent geometry : angle 0.64145 / 0.37 (18556) hydrogen bonds : bond 0.04505 / 3.09 ( 786) hydrogen bonds : angle 2.98196 / 2.13 ( 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 196 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 183 time to evaluate : 0.324 Fit side-chains REVERT: A 42 ARG cc_start: 0.8192 (mmm-85) cc_final: 0.7721 (mtp85) REVERT: B 68 ASP cc_start: 0.8784 (m-30) cc_final: 0.8536 (m-30) REVERT: C 73 ASN cc_start: 0.9040 (OUTLIER) cc_final: 0.8574 (t0) REVERT: C 90 ASP cc_start: 0.8436 (t70) cc_final: 0.8136 (t70) REVERT: D 31 LYS cc_start: 0.8830 (mptt) cc_final: 0.8555 (mmtm) REVERT: E 120 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8283 (mtp) REVERT: E 129 ARG cc_start: 0.8561 (tpt90) cc_final: 0.8138 (tpt90) REVERT: F 93 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.7186 (mp10) REVERT: G 74 LYS cc_start: 0.8980 (ptpp) cc_final: 0.8494 (mtmm) REVERT: H 30 ARG cc_start: 0.6614 (mtp-110) cc_final: 0.6298 (mtt180) REVERT: H 39 TYR cc_start: 0.8282 (t80) cc_final: 0.7780 (t80) REVERT: H 65 ASP cc_start: 0.8944 (t70) cc_final: 0.8719 (t0) REVERT: H 76 ARG cc_start: 0.8304 (mtp180) cc_final: 0.8008 (mtm-85) outliers start: 13 outliers final: 7 residues processed: 186 average time/residue: 0.8507 time to fit residues: 167.2202 Evaluate side-chains 190 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 180 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 87 SER 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 120 MET Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 93 GLN 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: 0.7980 chunk 78 optimal weight: 9.9990 chunk 67 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 97 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 6 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 87 optimal weight: 30.0000 chunk 29 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.104731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.083617 restraints weight = 20384.277| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.33 r_work: 0.3147 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 12822 Z= 0.140 Angle : 0.650 9.127 18556 Z= 0.369 Chirality : 0.044 0.235 2111 Planarity : 0.004 0.043 1344 Dihedral : 31.471 134.295 4028 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.73 % Allowed : 23.70 % 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: 2.77 (0.30), residues: 748 helix: 2.43 (0.22), residues: 547 sheet: None (None), residues: 0 loop : 0.18 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 83 TYR 0.027 0.002 TYR F 88 PHE 0.009 0.001 PHE A 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.14 (12822) covalent geometry : angle 0.64982 / 0.37 (18556) hydrogen bonds : bond 0.04435 / 3.05 ( 786) hydrogen bonds : angle 2.97643 / 2.12 ( 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 190 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 179 time to evaluate : 0.349 Fit side-chains REVERT: A 42 ARG cc_start: 0.8194 (mmm-85) cc_final: 0.7729 (mtp85) REVERT: C 73 ASN cc_start: 0.9042 (OUTLIER) cc_final: 0.8575 (t0) REVERT: C 90 ASP cc_start: 0.8428 (t70) cc_final: 0.8130 (t70) REVERT: D 54 LYS cc_start: 0.8994 (mmmt) cc_final: 0.8663 (mmtp) REVERT: E 120 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.8263 (mtp) REVERT: E 129 ARG cc_start: 0.8564 (tpt90) cc_final: 0.8139 (tpt90) REVERT: F 93 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.7169 (mp10) REVERT: G 74 LYS cc_start: 0.8973 (ptpp) cc_final: 0.8489 (mtmm) REVERT: H 30 ARG cc_start: 0.6619 (mtp-110) cc_final: 0.6319 (mtt180) REVERT: H 39 TYR cc_start: 0.8264 (t80) cc_final: 0.7759 (t80) REVERT: H 76 ARG cc_start: 0.8298 (mtp180) cc_final: 0.8004 (mtm-85) outliers start: 11 outliers final: 7 residues processed: 182 average time/residue: 0.8716 time to fit residues: 167.5758 Evaluate side-chains 189 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 179 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 87 SER 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 120 MET Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 93 GLN 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: 2.9990 chunk 53 optimal weight: 8.9990 chunk 14 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 89 optimal weight: 20.0000 chunk 58 optimal weight: 9.9990 chunk 41 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN ** E 68 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 = 0.3685 r_free = 0.3685 target = 0.104896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.083775 restraints weight = 20409.538| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.35 r_work: 0.3149 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 12822 Z= 0.138 Angle : 0.650 8.987 18556 Z= 0.369 Chirality : 0.044 0.235 2111 Planarity : 0.004 0.043 1344 Dihedral : 31.464 134.357 4028 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.88 % Allowed : 23.70 % Favored : 74.41 % 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: 2.79 (0.30), residues: 748 helix: 2.45 (0.22), residues: 547 sheet: None (None), residues: 0 loop : 0.19 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 83 TYR 0.024 0.002 TYR F 88 PHE 0.009 0.001 PHE A 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.14 (12822) covalent geometry : angle 0.64963 / 0.37 (18556) hydrogen bonds : bond 0.04397 / 3.02 ( 786) hydrogen bonds : angle 2.97035 / 2.12 ( 1972) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5380.42 seconds wall clock time: 91 minutes 56.77 seconds (5516.77 seconds total)