Starting phenix.real_space_refine on Fri Jul 3 03:04:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8guk_34275/07_2026/8guk_34275.cif Found real_map, /net/cci-nas-00/data/ceres_data/8guk_34275/07_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_34275/07_2026/8guk_34275.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8guk_34275/07_2026/8guk_34275.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8guk_34275/07_2026/8guk_34275.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8guk_34275/07_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-dev-6108/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: 2.58, per 1000 atoms: 0.21 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: 1.00 Conformation dependent library (CDL) restraints added in 300.9 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: 1.72 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: 2.06 Time building geometry restraints manager: 1.38 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: 17782 1.80 - 3.60: 869 3.60 - 5.40: 33 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: 3.200 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: 0.330 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.240 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.400 ------------------------------------------------------------------------------- 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 : 0.762 9.002 18690 Z= 0.664 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 0.76209 / 0.66 (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 : 0.265 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: 0.7838 time to fit residues: 162.9933 Evaluate side-chains 191 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 177 time to evaluate : 0.315 ------------------------------------------------------------------------------- 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: 0.9980 chunk 65 optimal weight: 0.9990 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 = 0.104214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.083039 restraints weight = 19399.405| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.25 r_work: 0.3086 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.0655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12911 Z= 0.164 Angle : 0.658 8.482 18690 Z= 0.386 Chirality : 0.047 0.338 2125 Planarity : 0.005 0.039 1345 Dihedral : 32.303 176.438 4087 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.57 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: 2.32 (0.30), residues: 749 helix: 2.15 (0.22), residues: 554 sheet: None (None), residues: 0 loop : -0.23 (0.40), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 99 TYR 0.014 0.001 TYR H 83 PHE 0.010 0.001 PHE E 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.16 (12911) covalent geometry : angle 0.65800 / 0.39 (18690) hydrogen bonds : bond 0.04342 / 2.94 ( 799) hydrogen bonds : angle 3.30698 / 2.41 ( 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 235 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 199 time to evaluate : 0.324 Fit side-chains REVERT: A 120 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.8102 (mtt) REVERT: B 95 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.7745 (mmm160) REVERT: C 77 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.7592 (ttp-170) REVERT: D 34 LYS cc_start: 0.8765 (mmmm) cc_final: 0.8502 (mppt) REVERT: D 93 GLU cc_start: 0.8205 (mp0) cc_final: 0.7966 (mp0) REVERT: E 50 GLU cc_start: 0.8870 (pt0) cc_final: 0.8665 (pt0) REVERT: E 59 GLU cc_start: 0.8937 (pm20) cc_final: 0.8447 (pm20) REVERT: G 73 ASN cc_start: 0.8676 (OUTLIER) cc_final: 0.8373 (t0) REVERT: H 63 ASN cc_start: 0.8691 (t0) cc_final: 0.8428 (m-40) outliers start: 36 outliers final: 16 residues processed: 214 average time/residue: 0.7783 time to fit residues: 177.2970 Evaluate side-chains 209 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 189 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 23 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 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: 0.9980 chunk 100 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 chunk 71 optimal weight: 0.5980 chunk 97 optimal weight: 8.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN D 67 ASN D 95 GLN E 108 ASN F 25 ASN F 27 GLN G 73 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.100122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.078398 restraints weight = 19218.585| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.31 r_work: 0.2985 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 12911 Z= 0.295 Angle : 0.730 10.763 18690 Z= 0.412 Chirality : 0.052 0.376 2125 Planarity : 0.005 0.038 1345 Dihedral : 32.606 171.387 4075 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 5.99 % Allowed : 26.18 % 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: 1.97 (0.22), residues: 555 sheet: None (None), residues: 0 loop : -0.39 (0.39), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 99 TYR 0.019 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 0.00609 / 0.29 (12911) covalent geometry : angle 0.72960 / 0.41 (18690) hydrogen bonds : bond 0.06232 / 4.29 ( 799) hydrogen bonds : angle 3.36207 / 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 215 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 177 time to evaluate : 0.347 Fit side-chains REVERT: A 53 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.7921 (ttp-110) REVERT: A 59 GLU cc_start: 0.8915 (pm20) cc_final: 0.8685 (pm20) REVERT: A 94 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8374 (mm-30) REVERT: A 120 MET cc_start: 0.8862 (mtt) cc_final: 0.8194 (mtt) REVERT: C 77 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.7581 (ttp-170) REVERT: D 34 LYS cc_start: 0.8779 (mmmm) cc_final: 0.8456 (mppt) REVERT: E 59 GLU cc_start: 0.8980 (pm20) cc_final: 0.8693 (pm20) REVERT: F 95 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.8341 (mtp85) REVERT: G 73 ASN cc_start: 0.8861 (OUTLIER) cc_final: 0.8239 (t0) REVERT: G 104 GLN cc_start: 0.8593 (mm-40) cc_final: 0.8239 (mm110) outliers start: 38 outliers final: 24 residues processed: 199 average time/residue: 0.7874 time to fit residues: 166.2822 Evaluate side-chains 200 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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 A residue 79 LYS 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 33 ARG Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 88 THR 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 73 ASN Chi-restraints excluded: chain G residue 75 LYS 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: 0.8980 chunk 37 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 99 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 94 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 G 73 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.101648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.079983 restraints weight = 19089.025| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.23 r_work: 0.3016 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12911 Z= 0.193 Angle : 0.679 9.596 18690 Z= 0.388 Chirality : 0.048 0.365 2125 Planarity : 0.005 0.040 1345 Dihedral : 32.661 174.002 4071 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 4.57 % Allowed : 27.44 % 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: 2.14 (0.30), residues: 749 helix: 2.02 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -0.32 (0.39), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 99 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 0.00372 / 0.19 (12911) covalent geometry : angle 0.67862 / 0.39 (18690) hydrogen bonds : bond 0.04440 / 3.03 ( 799) hydrogen bonds : angle 3.25082 / 2.38 ( 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 218 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 189 time to evaluate : 0.358 Fit side-chains REVERT: A 53 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.7877 (ttp-110) REVERT: A 59 GLU cc_start: 0.8973 (pm20) cc_final: 0.8651 (pm20) REVERT: A 120 MET cc_start: 0.8823 (mtt) cc_final: 0.8168 (mtt) REVERT: B 77 LYS cc_start: 0.9209 (OUTLIER) cc_final: 0.8964 (mtmp) REVERT: C 77 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.7476 (ttp-170) REVERT: D 34 LYS cc_start: 0.8712 (mmmm) cc_final: 0.8510 (mppt) REVERT: E 59 GLU cc_start: 0.8992 (pm20) cc_final: 0.8780 (pm20) REVERT: H 63 ASN cc_start: 0.8818 (t0) cc_final: 0.8369 (m-40) outliers start: 29 outliers final: 18 residues processed: 202 average time/residue: 0.8040 time to fit residues: 172.1470 Evaluate side-chains 202 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 181 time to evaluate : 0.319 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain H residue 47 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 92 optimal weight: 8.9990 chunk 72 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 56 optimal weight: 0.5980 chunk 97 optimal weight: 8.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3542 r_free = 0.3542 target = 0.102501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.080868 restraints weight = 19004.919| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.25 r_work: 0.3033 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12911 Z= 0.162 Angle : 0.655 8.758 18690 Z= 0.379 Chirality : 0.047 0.362 2125 Planarity : 0.005 0.058 1345 Dihedral : 32.590 174.851 4071 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.42 % Allowed : 28.55 % 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: 2.22 (0.30), residues: 749 helix: 2.08 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -0.30 (0.40), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 99 TYR 0.015 0.001 TYR H 83 PHE 0.014 0.002 PHE H 65 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.16 (12911) covalent geometry : angle 0.65547 / 0.38 (18690) hydrogen bonds : bond 0.04131 / 2.80 ( 799) hydrogen bonds : angle 3.19500 / 2.33 ( 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: 28 poor density : 187 time to evaluate : 0.372 Fit side-chains REVERT: A 53 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.7891 (ttp-110) REVERT: A 59 GLU cc_start: 0.9008 (pm20) cc_final: 0.8722 (pm20) REVERT: A 120 MET cc_start: 0.8806 (mtt) cc_final: 0.8147 (mtt) REVERT: B 77 LYS cc_start: 0.9211 (OUTLIER) cc_final: 0.8971 (mtmp) REVERT: C 77 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.7457 (ttp-170) REVERT: E 49 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8120 (ptp90) REVERT: E 59 GLU cc_start: 0.8988 (pm20) cc_final: 0.8763 (pm20) REVERT: G 104 GLN cc_start: 0.8480 (mm-40) cc_final: 0.8173 (mm110) REVERT: H 63 ASN cc_start: 0.8865 (t0) cc_final: 0.8424 (m-40) REVERT: H 99 ARG cc_start: 0.8862 (ptp-110) cc_final: 0.8528 (ptp90) outliers start: 28 outliers final: 16 residues processed: 199 average time/residue: 0.8103 time to fit residues: 170.8866 Evaluate side-chains 200 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 0.326 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 17 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 94 optimal weight: 8.9990 chunk 50 optimal weight: 0.9980 chunk 98 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 24 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.101126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.079457 restraints weight = 19153.442| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.26 r_work: 0.3011 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12911 Z= 0.219 Angle : 0.685 10.068 18690 Z= 0.391 Chirality : 0.049 0.371 2125 Planarity : 0.005 0.042 1345 Dihedral : 32.624 172.980 4071 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.10 % Allowed : 28.55 % Favored : 67.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.30), residues: 749 helix: 2.04 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -0.32 (0.39), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 35 TYR 0.020 0.002 TYR H 83 PHE 0.010 0.002 PHE E 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.22 (12911) covalent geometry : angle 0.68491 / 0.39 (18690) hydrogen bonds : bond 0.04989 / 3.41 ( 799) hydrogen bonds : angle 3.22603 / 2.36 ( 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 208 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 0.348 Fit side-chains REVERT: A 53 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.7888 (ttp-110) REVERT: A 59 GLU cc_start: 0.8997 (pm20) cc_final: 0.8730 (pm20) REVERT: A 120 MET cc_start: 0.8824 (mtt) cc_final: 0.8173 (mtt) REVERT: B 23 ARG cc_start: 0.6967 (pmm-80) cc_final: 0.6554 (pmm-80) REVERT: B 77 LYS cc_start: 0.9203 (OUTLIER) cc_final: 0.8954 (mtmp) REVERT: C 77 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.7538 (ttp-170) REVERT: D 40 TYR cc_start: 0.9035 (m-80) cc_final: 0.8830 (m-80) REVERT: E 49 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8165 (ptp90) REVERT: E 59 GLU cc_start: 0.8998 (pm20) cc_final: 0.8773 (pm20) REVERT: H 63 ASN cc_start: 0.8894 (t0) cc_final: 0.8385 (m-40) outliers start: 26 outliers final: 18 residues processed: 196 average time/residue: 0.7851 time to fit residues: 163.1160 Evaluate side-chains 203 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 181 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 20 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 64 optimal weight: 0.0970 chunk 14 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 104 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.101978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.080342 restraints weight = 19068.942| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.23 r_work: 0.3032 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12911 Z= 0.167 Angle : 0.670 9.788 18690 Z= 0.385 Chirality : 0.048 0.367 2125 Planarity : 0.005 0.061 1345 Dihedral : 32.632 173.600 4071 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.42 % Allowed : 28.55 % 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: 2.21 (0.30), residues: 749 helix: 2.07 (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 0.013 0.000 ARG H 99 TYR 0.017 0.001 TYR H 83 PHE 0.011 0.002 PHE E 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.17 (12911) covalent geometry : angle 0.66958 / 0.38 (18690) hydrogen bonds : bond 0.04484 / 3.06 ( 799) hydrogen bonds : angle 3.20991 / 2.34 ( 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 211 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 183 time to evaluate : 0.317 Fit side-chains REVERT: A 53 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.7865 (ttp-110) REVERT: A 59 GLU cc_start: 0.9001 (pm20) cc_final: 0.8718 (pm20) REVERT: A 120 MET cc_start: 0.8785 (mtt) cc_final: 0.8122 (mtt) REVERT: B 77 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8943 (mtmp) REVERT: C 75 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8514 (mttm) REVERT: C 77 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7429 (ttp-170) REVERT: E 49 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.8101 (ptp90) REVERT: E 59 GLU cc_start: 0.8985 (pm20) cc_final: 0.8746 (pm20) REVERT: F 95 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8364 (mtp85) REVERT: H 63 ASN cc_start: 0.8897 (t0) cc_final: 0.8406 (m-40) REVERT: H 99 ARG cc_start: 0.8837 (ptp-110) cc_final: 0.8473 (ptp90) outliers start: 28 outliers final: 20 residues processed: 198 average time/residue: 0.7572 time to fit residues: 158.8658 Evaluate side-chains 207 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 181 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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 75 LYS 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 59 LYS 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 75 LYS 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: 0.0770 chunk 67 optimal weight: 0.0980 chunk 56 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 94 optimal weight: 7.9990 chunk 79 optimal weight: 8.9990 chunk 36 optimal weight: 0.6980 chunk 76 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 overall best weight: 0.4338 ------------------------------------------------------------------------------- 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 = 0.102610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.080976 restraints weight = 19050.584| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.23 r_work: 0.3043 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12911 Z= 0.152 Angle : 0.671 9.558 18690 Z= 0.385 Chirality : 0.047 0.365 2125 Planarity : 0.005 0.047 1345 Dihedral : 32.616 174.135 4071 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 4.57 % Allowed : 28.71 % 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: 2.29 (0.30), residues: 749 helix: 2.13 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -0.29 (0.40), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG H 99 TYR 0.021 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 0.00267 / 0.15 (12911) covalent geometry : angle 0.67093 / 0.38 (18690) hydrogen bonds : bond 0.04200 / 2.85 ( 799) hydrogen bonds : angle 3.18380 / 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: 29 poor density : 184 time to evaluate : 0.340 Fit side-chains REVERT: A 53 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.7858 (ttp-110) REVERT: A 59 GLU cc_start: 0.8998 (pm20) cc_final: 0.8690 (pm20) REVERT: A 120 MET cc_start: 0.8783 (mtt) cc_final: 0.8121 (mtt) REVERT: B 77 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8948 (mtmp) REVERT: C 75 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8506 (mttm) REVERT: C 77 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7428 (ttp-170) REVERT: E 49 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.8097 (ptp90) REVERT: E 59 GLU cc_start: 0.8979 (pm20) cc_final: 0.8725 (pm20) REVERT: G 73 ASN cc_start: 0.8553 (t160) cc_final: 0.8028 (t0) REVERT: H 63 ASN cc_start: 0.8884 (t0) cc_final: 0.8391 (m-40) REVERT: H 99 ARG cc_start: 0.8792 (ptp-110) cc_final: 0.8469 (ptp90) outliers start: 29 outliers final: 18 residues processed: 200 average time/residue: 0.7996 time to fit residues: 169.8227 Evaluate side-chains 205 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 182 time to evaluate : 0.283 ------------------------------------------------------------------------------- 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 75 LYS 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 75 LYS 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: 0.9990 chunk 86 optimal weight: 9.9990 chunk 91 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 31 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 = 0.3542 r_free = 0.3542 target = 0.102330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.080761 restraints weight = 18894.975| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.24 r_work: 0.3036 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1259 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= 0.180 Angle : 0.664 9.607 18690 Z= 0.382 Chirality : 0.047 0.366 2125 Planarity : 0.005 0.049 1345 Dihedral : 32.551 174.275 4071 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.11 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: 2.29 (0.30), residues: 749 helix: 2.11 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -0.21 (0.40), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 35 TYR 0.023 0.002 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 0.00343 / 0.18 (12911) covalent geometry : angle 0.66428 / 0.38 (18690) hydrogen bonds : bond 0.04298 / 2.93 ( 799) hydrogen bonds : angle 3.16071 / 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 210 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 183 time to evaluate : 0.323 Fit side-chains REVERT: A 53 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.7869 (ttp-110) REVERT: A 59 GLU cc_start: 0.8992 (pm20) cc_final: 0.8675 (pm20) REVERT: B 77 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8934 (mtmp) REVERT: C 77 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.7594 (ttp-170) REVERT: D 33 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.6997 (mmt-90) REVERT: D 40 TYR cc_start: 0.8981 (m-80) cc_final: 0.8778 (m-80) REVERT: E 49 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8101 (ptp90) REVERT: E 59 GLU cc_start: 0.8981 (pm20) cc_final: 0.8729 (pm20) REVERT: G 73 ASN cc_start: 0.8579 (t160) cc_final: 0.8021 (t0) REVERT: H 63 ASN cc_start: 0.8887 (t0) cc_final: 0.8422 (m-40) outliers start: 27 outliers final: 18 residues processed: 198 average time/residue: 0.7872 time to fit residues: 165.2447 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 : 0.312 ------------------------------------------------------------------------------- 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 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 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 75 LYS 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: 8.9990 chunk 15 optimal weight: 0.6980 chunk 91 optimal weight: 8.9990 chunk 97 optimal weight: 9.9990 chunk 82 optimal weight: 6.9990 chunk 27 optimal weight: 0.0770 chunk 3 optimal weight: 0.8980 chunk 76 optimal weight: 9.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.9340 ------------------------------------------------------------------------------- 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 = 0.3545 r_free = 0.3545 target = 0.102502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.080845 restraints weight = 19193.105| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.24 r_work: 0.3039 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12911 Z= 0.180 Angle : 0.667 10.014 18690 Z= 0.383 Chirality : 0.047 0.366 2125 Planarity : 0.005 0.059 1345 Dihedral : 32.538 174.371 4071 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.10 % Allowed : 29.81 % 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: 2.33 (0.30), residues: 749 helix: 2.14 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -0.19 (0.40), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG H 99 TYR 0.025 0.002 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 0.00343 / 0.18 (12911) covalent geometry : angle 0.66664 / 0.38 (18690) hydrogen bonds : bond 0.04235 / 2.88 ( 799) hydrogen bonds : angle 3.15737 / 2.31 ( 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: 26 poor density : 179 time to evaluate : 0.367 Fit side-chains REVERT: A 53 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.7861 (ttp-110) REVERT: A 59 GLU cc_start: 0.8995 (pm20) cc_final: 0.8703 (pm20) REVERT: A 120 MET cc_start: 0.8762 (mtt) cc_final: 0.8092 (mtt) REVERT: B 77 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8922 (mtmp) REVERT: C 77 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7435 (ttp-170) REVERT: E 49 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8105 (ptp90) REVERT: E 59 GLU cc_start: 0.8981 (pm20) cc_final: 0.8729 (pm20) REVERT: G 73 ASN cc_start: 0.8598 (t160) cc_final: 0.8109 (t0) REVERT: H 63 ASN cc_start: 0.8848 (t0) cc_final: 0.8398 (m-40) outliers start: 26 outliers final: 17 residues processed: 191 average time/residue: 0.7584 time to fit residues: 153.9008 Evaluate side-chains 200 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 179 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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 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 75 LYS 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: 9.9990 chunk 3 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 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: 1.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.102730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.081217 restraints weight = 18953.333| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.23 r_work: 0.3041 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1316 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= 0.163 Angle : 0.669 9.932 18690 Z= 0.384 Chirality : 0.047 0.365 2125 Planarity : 0.005 0.057 1345 Dihedral : 32.525 174.427 4069 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.47 % Allowed : 30.76 % Favored : 65.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.36 (0.30), residues: 749 helix: 2.16 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -0.18 (0.40), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG H 99 TYR 0.024 0.001 TYR H 83 PHE 0.014 0.002 PHE E 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.16 (12911) covalent geometry : angle 0.66902 / 0.38 (18690) hydrogen bonds : bond 0.04186 / 2.85 ( 799) hydrogen bonds : angle 3.17057 / 2.32 ( 1992) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4640.47 seconds wall clock time: 79 minutes 39.17 seconds (4779.17 seconds total)