Starting phenix.real_space_refine on Wed Aug 5 21:01:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8guk_34275/08_2026/8guk_34275.cif Found real_map, /net/cci-nas-00/data/ceres_data/8guk_34275/08_2026/8guk_34275.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8guk_34275/08_2026/8guk_34275.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8guk_34275/08_2026/8guk_34275.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8guk_34275/08_2026/8guk_34275.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8guk_34275/08_2026/8guk_34275.map" } resolution = 2.51 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= -0.005 sd= 0.055 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 294 5.49 5 S 14 5.16 5 C 6686 2.51 5 N 2277 2.21 5 O 2827 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12098 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 846 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "F" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 851 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 105} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Time building chain proxies: 2.41, per 1000 atoms: 0.20 Number of scatterers: 12098 At special positions: 0 Unit cell: (72.45, 113.4, 119.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 294 15.00 O 2827 8.00 N 2277 7.00 C 6686 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: 0.88 Conformation dependent library (CDL) restraints added in 273.3 milliseconds 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1430 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 73.7% alpha, 2.9% beta 146 base pairs and 260 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.552A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.373A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.593A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 4.096A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.576A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.228A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 124 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.643A 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 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.120A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.724A 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: 7.137A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (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 78 424 hydrogen bonds defined for protein. 1242 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 375 hydrogen bonds 750 hydrogen bond angles 0 basepair planarities 146 basepair parallelities 260 stacking parallelities Total time for adding SS restraints: 2.01 Time building geometry restraints manager: 1.17 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: 2168 1.33 - 1.45: 4244 1.45 - 1.57: 5889 1.57 - 1.69: 586 1.69 - 1.80: 24 Bond restraints: 12911 Sorted by residual: bond pdb=" C3' DG J 52 " pdb=" C2' DG J 52 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DG I 13 " pdb=" C2' DG I 13 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DA I 52 " pdb=" C2' DA I 52 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DC I 116 " pdb=" C2' DC I 116 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DC I 54 " pdb=" C2' DC I 54 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.78e+00 ... (remaining 12906 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 17773 1.80 - 3.60: 872 3.60 - 5.40: 39 5.40 - 7.20: 5 7.20 - 9.00: 1 Bond angle restraints: 18690 Sorted by residual: angle pdb=" O4' DG I 121 " pdb=" C4' DG I 121 " pdb=" C3' DG I 121 " ideal model delta sigma weight residual 106.00 103.30 2.70 6.00e-01 2.78e+00 2.02e+01 angle pdb=" O4' DG J 25 " pdb=" C4' DG J 25 " pdb=" C3' DG J 25 " ideal model delta sigma weight residual 106.00 103.32 2.68 6.00e-01 2.78e+00 1.99e+01 angle pdb=" N3 DT I 15 " pdb=" C4 DT I 15 " pdb=" O4 DT I 15 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.98e+01 angle pdb=" O4' DT I 48 " pdb=" C4' DT I 48 " pdb=" C3' DT I 48 " ideal model delta sigma weight residual 106.00 103.34 2.66 6.00e-01 2.78e+00 1.97e+01 angle pdb=" N3 DT I 32 " pdb=" C4 DT I 32 " pdb=" O4 DT I 32 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 ... (remaining 18685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.01: 5451 35.01 - 70.02: 1530 70.02 - 105.03: 28 105.03 - 140.04: 1 140.04 - 175.04: 7 Dihedral angle restraints: 7017 sinusoidal: 4800 harmonic: 2217 Sorted by residual: dihedral pdb=" C4' DT I 32 " pdb=" C3' DT I 32 " pdb=" O3' DT I 32 " pdb=" P DG I 33 " ideal model delta sinusoidal sigma weight residual 220.00 44.96 175.04 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DG J 4 " pdb=" C3' DG J 4 " pdb=" O3' DG J 4 " pdb=" P DG J 5 " ideal model delta sinusoidal sigma weight residual -140.00 33.09 -173.09 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DT I 77 " pdb=" C3' DT I 77 " pdb=" O3' DT I 77 " pdb=" P DC I 78 " ideal model delta sinusoidal sigma weight residual -140.00 29.87 -169.87 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 7014 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1412 0.040 - 0.080: 530 0.080 - 0.121: 163 0.121 - 0.161: 16 0.161 - 0.201: 4 Chirality restraints: 2125 Sorted by residual: chirality pdb=" C3' DA I 41 " pdb=" C4' DA I 41 " pdb=" O3' DA I 41 " pdb=" C2' DA I 41 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" C3' DT I 32 " pdb=" C4' DT I 32 " pdb=" O3' DT I 32 " pdb=" C2' DT I 32 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.38e-01 chirality pdb=" C3' DA I 131 " pdb=" C4' DA I 131 " pdb=" O3' DA I 131 " pdb=" C2' DA I 131 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.53e-01 ... (remaining 2122 not shown) Planarity restraints: 1345 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN G 73 " 0.010 2.00e-02 2.50e+03 1.93e-02 3.71e+00 pdb=" C ASN G 73 " -0.033 2.00e-02 2.50e+03 pdb=" O ASN G 73 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS G 74 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS E 37 " -0.030 5.00e-02 4.00e+02 4.67e-02 3.48e+00 pdb=" N PRO E 38 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO E 38 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 38 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU H 71 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.05e+00 pdb=" CD GLU H 71 " -0.030 2.00e-02 2.50e+03 pdb=" OE1 GLU H 71 " 0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU H 71 " 0.011 2.00e-02 2.50e+03 ... (remaining 1342 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1260 2.74 - 3.28: 10901 3.28 - 3.82: 25697 3.82 - 4.36: 29975 4.36 - 4.90: 42058 Nonbonded interactions: 109891 Sorted by model distance: nonbonded pdb=" N GLN C 104 " pdb=" OE2 GLU E 94 " model vdw 2.202 3.120 nonbonded pdb=" O HIS F 75 " pdb=" NH2 ARG H 92 " model vdw 2.237 3.120 nonbonded pdb=" OE1 GLU D 76 " pdb=" NH2 ARG D 79 " model vdw 2.238 3.120 nonbonded pdb=" OE1 GLU E 73 " pdb=" ND2 ASN F 25 " model vdw 2.245 3.120 nonbonded pdb=" O HIS B 75 " pdb=" NH1 ARG D 92 " model vdw 2.247 3.120 ... (remaining 109886 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 10 through 119) } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.270 Find NCS groups from input model: 0.110 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:5.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 12911 Z= 0.522 Angle : 0.770 9.002 18690 Z= 0.671 Chirality : 0.045 0.201 2125 Planarity : 0.005 0.060 1345 Dihedral : 29.885 175.045 5587 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.15 % Allowed : 31.23 % Favored : 65.62 % 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: 2.28 (0.30), residues: 749 helix: 2.15 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.28 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG H 99 TYR 0.019 0.001 TYR H 83 PHE 0.009 0.001 PHE E 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00593 / 0.52 (12911) covalent geometry : angle 0.76980 / 0.67 (18690) hydrogen bonds : bond 0.09278 / 6.10 ( 799) hydrogen bonds : angle 3.78834 / 2.80 ( 1992) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 181 time to evaluate : 0.237 Fit side-chains REVERT: D 92 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.7898 (ttm-80) REVERT: H 63 ASN cc_start: 0.8792 (t0) cc_final: 0.8397 (m-40) outliers start: 20 outliers final: 13 residues processed: 196 average time/residue: 0.6790 time to fit residues: 140.8761 Evaluate side-chains 192 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 178 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 106 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 9.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 108 ASN B 25 ASN E 108 ASN F 27 GLN G 73 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.104210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.083044 restraints weight = 19390.832| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.26 r_work: 0.3086 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.0673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12911 Z= 0.162 Angle : 0.673 8.499 18690 Z= 0.391 Chirality : 0.048 0.359 2125 Planarity : 0.005 0.039 1345 Dihedral : 32.233 175.235 4087 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 5.68 % Allowed : 26.50 % Favored : 67.82 % 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: 2.31 (0.30), residues: 749 helix: 2.15 (0.22), residues: 554 sheet: None (None), residues: 0 loop : -0.24 (0.40), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 99 TYR 0.015 0.001 TYR H 83 PHE 0.009 0.001 PHE E 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.16 (12911) covalent geometry : angle 0.67345 / 0.39 (18690) hydrogen bonds : bond 0.04367 / 2.95 ( 799) hydrogen bonds : angle 3.29471 / 2.40 ( 1992) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 201 time to evaluate : 0.287 Fit side-chains REVERT: A 120 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8105 (mtt) REVERT: B 95 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.7736 (mmm160) REVERT: C 77 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.7610 (ttp-170) REVERT: D 34 LYS cc_start: 0.8759 (mmmm) cc_final: 0.8504 (mppt) REVERT: D 93 GLU cc_start: 0.8210 (mp0) cc_final: 0.7961 (mp0) REVERT: H 63 ASN cc_start: 0.8690 (t0) cc_final: 0.8427 (m-40) outliers start: 36 outliers final: 16 residues processed: 215 average time/residue: 0.6712 time to fit residues: 153.4764 Evaluate side-chains 209 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 190 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 23 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 15 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 chunk 94 optimal weight: 8.9990 chunk 71 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN D 95 GLN E 108 ASN F 25 ASN F 27 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.100019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.078292 restraints weight = 19203.425| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.23 r_work: 0.2987 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 12911 Z= 0.276 Angle : 0.747 10.887 18690 Z= 0.415 Chirality : 0.053 0.398 2125 Planarity : 0.005 0.036 1345 Dihedral : 32.558 170.084 4075 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 5.36 % Allowed : 26.66 % Favored : 67.98 % 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: 2.03 (0.30), residues: 749 helix: 1.96 (0.22), residues: 555 sheet: None (None), residues: 0 loop : -0.40 (0.39), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 99 TYR 0.021 0.002 TYR H 83 PHE 0.011 0.002 PHE A 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.28 (12911) covalent geometry : angle 0.74738 / 0.41 (18690) hydrogen bonds : bond 0.06298 / 4.33 ( 799) hydrogen bonds : angle 3.35510 / 2.46 ( 1992) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 177 time to evaluate : 0.230 Fit side-chains REVERT: A 120 MET cc_start: 0.8860 (mtt) cc_final: 0.8191 (mtt) REVERT: B 77 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8950 (mtmp) REVERT: C 77 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.7512 (ttp-170) REVERT: D 34 LYS cc_start: 0.8744 (mmmm) cc_final: 0.8451 (mppt) REVERT: E 59 GLU cc_start: 0.8978 (pm20) cc_final: 0.8727 (pm20) REVERT: F 95 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8344 (mtp85) REVERT: G 16 THR cc_start: 0.9261 (OUTLIER) cc_final: 0.9033 (p) REVERT: G 73 ASN cc_start: 0.8649 (t160) cc_final: 0.8167 (t0) REVERT: G 104 GLN cc_start: 0.8639 (mm-40) cc_final: 0.8377 (mm110) outliers start: 34 outliers final: 20 residues processed: 194 average time/residue: 0.7455 time to fit residues: 153.4543 Evaluate side-chains 196 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 172 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 34 optimal weight: 0.4980 chunk 37 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 63 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 99 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 94 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN D 95 GLN F 27 GLN G 24 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.101665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.080129 restraints weight = 18862.484| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.23 r_work: 0.3012 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12911 Z= 0.190 Angle : 0.710 10.122 18690 Z= 0.398 Chirality : 0.050 0.390 2125 Planarity : 0.005 0.038 1345 Dihedral : 32.596 172.159 4071 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.73 % Allowed : 27.44 % Favored : 67.82 % 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: 2.06 (0.30), residues: 749 helix: 1.98 (0.22), residues: 555 sheet: None (None), residues: 0 loop : -0.42 (0.39), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 35 TYR 0.016 0.002 TYR H 83 PHE 0.011 0.002 PHE E 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.19 (12911) covalent geometry : angle 0.70968 / 0.40 (18690) hydrogen bonds : bond 0.04960 / 3.40 ( 799) hydrogen bonds : angle 3.29194 / 2.40 ( 1992) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 186 time to evaluate : 0.257 Fit side-chains REVERT: A 53 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.7880 (ttp-110) REVERT: A 120 MET cc_start: 0.8819 (mtt) cc_final: 0.8164 (mtt) REVERT: B 77 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8956 (mtmp) REVERT: C 77 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.7489 (ttp-170) REVERT: D 34 LYS cc_start: 0.8719 (mmmm) cc_final: 0.8495 (mppt) REVERT: E 49 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.8174 (ptp90) REVERT: E 59 GLU cc_start: 0.8991 (pm20) cc_final: 0.8742 (pm20) REVERT: G 73 ASN cc_start: 0.8630 (t160) cc_final: 0.8094 (t0) REVERT: G 104 GLN cc_start: 0.8608 (mm-40) cc_final: 0.8365 (mm110) REVERT: H 63 ASN cc_start: 0.8849 (t0) cc_final: 0.8362 (m-40) outliers start: 30 outliers final: 20 residues processed: 201 average time/residue: 0.6533 time to fit residues: 139.4364 Evaluate side-chains 206 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 182 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 92 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 56 optimal weight: 0.5980 chunk 97 optimal weight: 8.9990 chunk 8 optimal weight: 0.0570 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN D 63 ASN D 95 GLN F 27 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.102412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.080958 restraints weight = 18944.644| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.24 r_work: 0.3034 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12911 Z= 0.161 Angle : 0.697 9.854 18690 Z= 0.394 Chirality : 0.049 0.388 2125 Planarity : 0.005 0.039 1345 Dihedral : 32.580 172.948 4071 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 4.10 % Allowed : 28.86 % Favored : 67.03 % 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: 2.14 (0.30), residues: 749 helix: 2.04 (0.21), residues: 555 sheet: None (None), residues: 0 loop : -0.40 (0.39), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 86 TYR 0.014 0.001 TYR F 51 PHE 0.012 0.002 PHE E 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.16 (12911) covalent geometry : angle 0.69700 / 0.39 (18690) hydrogen bonds : bond 0.04454 / 3.04 ( 799) hydrogen bonds : angle 3.24503 / 2.37 ( 1992) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 189 time to evaluate : 0.341 Fit side-chains REVERT: C 77 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7481 (ttp-170) REVERT: D 34 LYS cc_start: 0.8719 (mmmm) cc_final: 0.8483 (mppt) REVERT: D 76 GLU cc_start: 0.8883 (tp30) cc_final: 0.8619 (tp30) REVERT: E 49 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.8156 (ptp90) REVERT: E 59 GLU cc_start: 0.9014 (pm20) cc_final: 0.8715 (pm20) REVERT: G 73 ASN cc_start: 0.8614 (t160) cc_final: 0.8091 (t0) REVERT: G 104 GLN cc_start: 0.8572 (mm-40) cc_final: 0.8348 (mm110) REVERT: H 63 ASN cc_start: 0.8870 (t0) cc_final: 0.8411 (m-40) outliers start: 26 outliers final: 18 residues processed: 203 average time/residue: 0.6935 time to fit residues: 149.4275 Evaluate side-chains 204 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 184 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 17 optimal weight: 7.9990 chunk 38 optimal weight: 0.8980 chunk 8 optimal weight: 0.4980 chunk 83 optimal weight: 9.9990 chunk 94 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 57 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN F 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.101824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.080202 restraints weight = 19135.483| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.23 r_work: 0.3033 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12911 Z= 0.189 Angle : 0.683 7.923 18690 Z= 0.388 Chirality : 0.049 0.388 2125 Planarity : 0.005 0.051 1345 Dihedral : 32.483 173.711 4071 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.26 % Allowed : 27.92 % Favored : 67.82 % 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: 2.21 (0.30), residues: 749 helix: 2.10 (0.22), residues: 555 sheet: None (None), residues: 0 loop : -0.38 (0.39), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 99 TYR 0.011 0.001 TYR H 83 PHE 0.012 0.002 PHE E 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.19 (12911) covalent geometry : angle 0.68315 / 0.39 (18690) hydrogen bonds : bond 0.04458 / 3.04 ( 799) hydrogen bonds : angle 3.18955 / 2.33 ( 1992) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 187 time to evaluate : 0.335 Fit side-chains REVERT: A 53 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.7857 (ttp-110) REVERT: A 120 MET cc_start: 0.8794 (mtt) cc_final: 0.8099 (mtt) REVERT: B 77 LYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8955 (mtmp) REVERT: C 77 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7484 (ttp-170) REVERT: E 49 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8129 (ptp90) REVERT: E 59 GLU cc_start: 0.8998 (pm20) cc_final: 0.8365 (pm20) REVERT: G 73 ASN cc_start: 0.8658 (OUTLIER) cc_final: 0.8171 (t0) REVERT: H 63 ASN cc_start: 0.8831 (t0) cc_final: 0.8333 (m-40) outliers start: 27 outliers final: 18 residues processed: 201 average time/residue: 0.8020 time to fit residues: 171.0676 Evaluate side-chains 204 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 181 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 20 optimal weight: 0.9980 chunk 82 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN F 27 GLN G 104 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.102339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.080794 restraints weight = 18915.397| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.24 r_work: 0.3035 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12911 Z= 0.173 Angle : 0.683 8.015 18690 Z= 0.388 Chirality : 0.048 0.387 2125 Planarity : 0.005 0.056 1345 Dihedral : 32.483 173.997 4071 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.79 % Allowed : 29.65 % Favored : 66.56 % 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: 2.24 (0.30), residues: 749 helix: 2.12 (0.22), residues: 555 sheet: None (None), residues: 0 loop : -0.37 (0.39), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 99 TYR 0.017 0.001 TYR H 83 PHE 0.012 0.002 PHE E 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.17 (12911) covalent geometry : angle 0.68274 / 0.39 (18690) hydrogen bonds : bond 0.04300 / 2.93 ( 799) hydrogen bonds : angle 3.18657 / 2.33 ( 1992) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 184 time to evaluate : 0.251 Fit side-chains REVERT: A 53 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.7836 (ttp-110) REVERT: A 120 MET cc_start: 0.8793 (mtt) cc_final: 0.8108 (mtt) REVERT: B 77 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8947 (mtmp) REVERT: C 77 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7486 (ttp-170) REVERT: E 49 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8131 (ptp90) REVERT: E 59 GLU cc_start: 0.8998 (pm20) cc_final: 0.8679 (pm20) REVERT: G 73 ASN cc_start: 0.8652 (t160) cc_final: 0.8128 (t0) REVERT: H 63 ASN cc_start: 0.8866 (t0) cc_final: 0.8395 (m-40) outliers start: 24 outliers final: 17 residues processed: 195 average time/residue: 0.7771 time to fit residues: 160.6615 Evaluate side-chains 204 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 87 optimal weight: 9.9990 chunk 35 optimal weight: 0.0270 chunk 67 optimal weight: 0.0470 chunk 56 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 94 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 chunk 76 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN F 27 GLN G 104 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.102656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.081073 restraints weight = 18877.031| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.24 r_work: 0.3043 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12911 Z= 0.153 Angle : 0.680 8.131 18690 Z= 0.387 Chirality : 0.048 0.387 2125 Planarity : 0.005 0.055 1345 Dihedral : 32.476 174.142 4071 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.26 % Allowed : 29.02 % Favored : 66.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.30), residues: 749 helix: 2.15 (0.22), residues: 555 sheet: None (None), residues: 0 loop : -0.35 (0.39), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 99 TYR 0.015 0.001 TYR H 83 PHE 0.013 0.002 PHE E 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.15 (12911) covalent geometry : angle 0.67995 / 0.39 (18690) hydrogen bonds : bond 0.04163 / 2.83 ( 799) hydrogen bonds : angle 3.17687 / 2.32 ( 1992) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 186 time to evaluate : 0.263 Fit side-chains REVERT: A 53 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.7832 (ttp-110) REVERT: A 120 MET cc_start: 0.8793 (mtt) cc_final: 0.8109 (mtt) REVERT: B 77 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8949 (mtmp) REVERT: C 77 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7427 (ttp-170) REVERT: D 76 GLU cc_start: 0.8847 (tp30) cc_final: 0.8594 (tp30) REVERT: E 49 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.8082 (ptp90) REVERT: E 59 GLU cc_start: 0.8995 (pm20) cc_final: 0.8662 (pm20) REVERT: G 73 ASN cc_start: 0.8543 (OUTLIER) cc_final: 0.8090 (t0) REVERT: H 63 ASN cc_start: 0.8857 (t0) cc_final: 0.8383 (m-40) outliers start: 27 outliers final: 17 residues processed: 198 average time/residue: 0.7885 time to fit residues: 165.4913 Evaluate side-chains 206 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 184 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 0.0870 chunk 86 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 55 optimal weight: 0.0970 chunk 72 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 61 optimal weight: 0.0980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN F 27 GLN G 104 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.103328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.081978 restraints weight = 18849.995| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.23 r_work: 0.3057 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12911 Z= 0.152 Angle : 0.678 8.284 18690 Z= 0.385 Chirality : 0.048 0.383 2125 Planarity : 0.005 0.069 1345 Dihedral : 32.455 174.531 4071 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.94 % Allowed : 29.18 % Favored : 66.88 % 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: 2.32 (0.30), residues: 749 helix: 2.17 (0.22), residues: 555 sheet: None (None), residues: 0 loop : -0.32 (0.39), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 99 TYR 0.019 0.001 TYR H 83 PHE 0.013 0.002 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.15 (12911) covalent geometry : angle 0.67762 / 0.39 (18690) hydrogen bonds : bond 0.04031 / 2.74 ( 799) hydrogen bonds : angle 3.16348 / 2.31 ( 1992) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 186 time to evaluate : 0.337 Fit side-chains REVERT: A 53 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.7824 (ttp-110) REVERT: A 120 MET cc_start: 0.8780 (mtt) cc_final: 0.8143 (mtt) REVERT: C 77 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.7476 (ttp-170) REVERT: D 34 LYS cc_start: 0.8740 (mmmm) cc_final: 0.8394 (mppt) REVERT: E 49 ARG cc_start: 0.8961 (OUTLIER) cc_final: 0.8070 (ptp90) REVERT: E 59 GLU cc_start: 0.8984 (pm20) cc_final: 0.8645 (pm20) REVERT: G 73 ASN cc_start: 0.8553 (OUTLIER) cc_final: 0.8082 (t0) REVERT: H 63 ASN cc_start: 0.8856 (t0) cc_final: 0.8386 (m-40) outliers start: 25 outliers final: 17 residues processed: 197 average time/residue: 0.8226 time to fit residues: 171.9004 Evaluate side-chains 205 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 184 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 30 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 27 optimal weight: 0.3980 chunk 3 optimal weight: 0.8980 chunk 76 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN F 27 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.100739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.079233 restraints weight = 18972.068| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.22 r_work: 0.3007 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12911 Z= 0.245 Angle : 0.733 9.539 18690 Z= 0.407 Chirality : 0.051 0.396 2125 Planarity : 0.005 0.055 1345 Dihedral : 32.561 171.498 4071 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.79 % Allowed : 30.28 % Favored : 65.93 % 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: 2.12 (0.30), residues: 749 helix: 2.00 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -0.31 (0.39), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG H 99 TYR 0.025 0.002 TYR H 83 PHE 0.011 0.002 PHE A 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.24 (12911) covalent geometry : angle 0.73282 / 0.41 (18690) hydrogen bonds : bond 0.05452 / 3.75 ( 799) hydrogen bonds : angle 3.26111 / 2.39 ( 1992) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 181 time to evaluate : 0.338 Fit side-chains REVERT: A 53 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.7926 (ttp-110) REVERT: B 23 ARG cc_start: 0.6661 (pmm-80) cc_final: 0.6262 (pmm-80) REVERT: C 77 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.7564 (ttp-170) REVERT: D 34 LYS cc_start: 0.8735 (mmmm) cc_final: 0.8412 (mppt) REVERT: D 76 GLU cc_start: 0.9041 (tp30) cc_final: 0.8827 (tp30) REVERT: E 49 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.8147 (ptp90) REVERT: E 59 GLU cc_start: 0.9001 (pm20) cc_final: 0.8670 (pm20) REVERT: G 73 ASN cc_start: 0.8587 (OUTLIER) cc_final: 0.8055 (t0) REVERT: H 63 ASN cc_start: 0.8902 (t0) cc_final: 0.8385 (m-40) outliers start: 24 outliers final: 17 residues processed: 193 average time/residue: 0.8440 time to fit residues: 172.2140 Evaluate side-chains 199 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 178 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 3 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 95 optimal weight: 8.9990 chunk 56 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN D 95 GLN F 27 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.101724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.080272 restraints weight = 18849.668| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.23 r_work: 0.3021 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12911 Z= 0.169 Angle : 0.721 9.245 18690 Z= 0.403 Chirality : 0.050 0.396 2125 Planarity : 0.005 0.056 1345 Dihedral : 32.587 172.144 4071 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.79 % Allowed : 30.13 % Favored : 66.09 % 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: 2.18 (0.30), residues: 749 helix: 2.05 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -0.29 (0.39), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 99 TYR 0.024 0.002 TYR H 83 PHE 0.013 0.002 PHE E 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.17 (12911) covalent geometry : angle 0.72112 / 0.40 (18690) hydrogen bonds : bond 0.04996 / 3.43 ( 799) hydrogen bonds : angle 3.26164 / 2.39 ( 1992) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4434.88 seconds wall clock time: 76 minutes 3.59 seconds (4563.59 seconds total)