Starting phenix.real_space_refine on Fri Jul 3 11:17:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qv6_53387/07_2026/9qv6_53387.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qv6_53387/07_2026/9qv6_53387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qv6_53387/07_2026/9qv6_53387.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qv6_53387/07_2026/9qv6_53387.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qv6_53387/07_2026/9qv6_53387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qv6_53387/07_2026/9qv6_53387.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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 360 5.49 5 S 24 5.16 5 C 7516 2.51 5 N 2636 2.21 5 O 3396 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 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: 13932 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 546 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'TRANS': 70} Chain: "B" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 546 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'TRANS': 70} Chain: "C" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 546 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'TRANS': 70} Chain: "D" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 546 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'TRANS': 70} Chain: "E" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 546 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'TRANS': 70} Chain: "F" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 546 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'TRANS': 70} Chain: "G" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 546 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'TRANS': 70} Chain: "H" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 546 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'TRANS': 70} Chain: "I" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 546 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'TRANS': 70} Chain: "J" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 546 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'TRANS': 70} Chain: "K" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 546 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'TRANS': 70} Chain: "L" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 546 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'TRANS': 70} Chain: "X" Number of atoms: 3674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 3674 Classifications: {'DNA': 180} Link IDs: {'rna3p': 179} Chain: "Y" Number of atoms: 3706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 3706 Classifications: {'DNA': 180} Link IDs: {'rna3p': 179} Time building chain proxies: 2.83, per 1000 atoms: 0.20 Number of scatterers: 13932 At special positions: 0 Unit cell: (114.165, 114.165, 93.525, 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 24 16.00 P 360 15.00 O 3396 8.00 N 2636 7.00 C 7516 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: 0.85 Conformation dependent library (CDL) restraints added in 340.9 milliseconds 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1608 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 12 sheets defined 74.6% alpha, 2.8% beta 100 base pairs and 300 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 6 through 17 Processing helix chain 'A' and resid 23 through 53 Processing helix chain 'A' and resid 58 through 67 Processing helix chain 'B' and resid 6 through 17 Processing helix chain 'B' and resid 23 through 53 Processing helix chain 'B' and resid 58 through 67 Processing helix chain 'C' and resid 6 through 17 Processing helix chain 'C' and resid 23 through 53 Processing helix chain 'C' and resid 58 through 67 Processing helix chain 'D' and resid 6 through 17 Processing helix chain 'D' and resid 23 through 53 Processing helix chain 'D' and resid 58 through 67 Processing helix chain 'E' and resid 6 through 17 Processing helix chain 'E' and resid 23 through 53 Processing helix chain 'E' and resid 58 through 67 Processing helix chain 'F' and resid 6 through 17 Processing helix chain 'F' and resid 23 through 53 Processing helix chain 'F' and resid 58 through 67 Processing helix chain 'G' and resid 6 through 17 Processing helix chain 'G' and resid 23 through 53 Processing helix chain 'G' and resid 58 through 67 Processing helix chain 'H' and resid 6 through 17 Processing helix chain 'H' and resid 23 through 53 Processing helix chain 'H' and resid 58 through 67 Processing helix chain 'I' and resid 6 through 17 Processing helix chain 'I' and resid 23 through 53 Processing helix chain 'I' and resid 58 through 67 Processing helix chain 'J' and resid 6 through 17 Processing helix chain 'J' and resid 23 through 53 Processing helix chain 'J' and resid 58 through 67 Processing helix chain 'K' and resid 6 through 17 Processing helix chain 'K' and resid 23 through 53 Processing helix chain 'K' and resid 58 through 67 Processing helix chain 'L' and resid 6 through 17 Processing helix chain 'L' and resid 23 through 53 Processing helix chain 'L' and resid 58 through 67 Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 22 removed outlier: 7.080A pdb=" N ARG A 21 " --> pdb=" O VAL B 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 57 Processing sheet with id=AA3, first strand: chain 'C' and resid 21 through 22 removed outlier: 7.034A pdb=" N ARG C 21 " --> pdb=" O VAL D 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 56 through 57 Processing sheet with id=AA5, first strand: chain 'E' and resid 21 through 22 removed outlier: 7.101A pdb=" N ARG E 21 " --> pdb=" O VAL F 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 56 through 57 Processing sheet with id=AA7, first strand: chain 'G' and resid 21 through 22 removed outlier: 7.144A pdb=" N ARG G 21 " --> pdb=" O VAL H 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 56 through 57 Processing sheet with id=AA9, first strand: chain 'I' and resid 21 through 22 removed outlier: 7.132A pdb=" N ARG I 21 " --> pdb=" O VAL J 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'I' and resid 56 through 57 Processing sheet with id=AB2, first strand: chain 'K' and resid 21 through 22 removed outlier: 7.110A pdb=" N ARG K 21 " --> pdb=" O VAL L 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'K' and resid 56 through 57 498 hydrogen bonds defined for protein. 1494 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 233 hydrogen bonds 466 hydrogen bond angles 0 basepair planarities 100 basepair parallelities 300 stacking parallelities Total time for adding SS restraints: 2.27 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1850 1.32 - 1.44: 5034 1.44 - 1.56: 7228 1.56 - 1.69: 718 1.69 - 1.81: 48 Bond restraints: 14878 Sorted by residual: bond pdb=" C ARG J 9 " pdb=" O ARG J 9 " ideal model delta sigma weight residual 1.236 1.192 0.044 1.28e-02 6.10e+03 1.17e+01 bond pdb=" C ARG B 9 " pdb=" O ARG B 9 " ideal model delta sigma weight residual 1.236 1.192 0.044 1.28e-02 6.10e+03 1.17e+01 bond pdb=" C ARG L 9 " pdb=" O ARG L 9 " ideal model delta sigma weight residual 1.236 1.192 0.044 1.28e-02 6.10e+03 1.16e+01 bond pdb=" C ARG A 9 " pdb=" O ARG A 9 " ideal model delta sigma weight residual 1.236 1.192 0.044 1.28e-02 6.10e+03 1.16e+01 bond pdb=" C ARG F 9 " pdb=" O ARG F 9 " ideal model delta sigma weight residual 1.236 1.192 0.043 1.28e-02 6.10e+03 1.15e+01 ... (remaining 14873 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 15299 1.65 - 3.29: 4146 3.29 - 4.94: 1451 4.94 - 6.58: 654 6.58 - 8.23: 54 Bond angle restraints: 21604 Sorted by residual: angle pdb=" O4' DT Y 91 " pdb=" C4' DT Y 91 " pdb=" C3' DT Y 91 " ideal model delta sigma weight residual 106.00 103.02 2.98 6.00e-01 2.78e+00 2.47e+01 angle pdb=" O3' DA Y 25 " pdb=" P DT Y 26 " pdb=" O5' DT Y 26 " ideal model delta sigma weight residual 104.00 97.36 6.64 1.50e+00 4.44e-01 1.96e+01 angle pdb=" C4' DG X 99 " pdb=" O4' DG X 99 " pdb=" C1' DG X 99 " ideal model delta sigma weight residual 110.10 105.85 4.25 1.00e+00 1.00e+00 1.81e+01 angle pdb=" O4' DT X 38 " pdb=" C4' DT X 38 " pdb=" C3' DT X 38 " ideal model delta sigma weight residual 106.00 103.46 2.54 6.00e-01 2.78e+00 1.80e+01 angle pdb=" O3' DT X 149 " pdb=" P DG X 150 " pdb=" O5' DG X 150 " ideal model delta sigma weight residual 104.00 97.64 6.36 1.50e+00 4.44e-01 1.80e+01 ... (remaining 21599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.07: 6300 35.07 - 70.13: 1686 70.13 - 105.20: 36 105.20 - 140.27: 0 140.27 - 175.34: 4 Dihedral angle restraints: 8026 sinusoidal: 5566 harmonic: 2460 Sorted by residual: dihedral pdb=" CD ARG L 9 " pdb=" NE ARG L 9 " pdb=" CZ ARG L 9 " pdb=" NH1 ARG L 9 " ideal model delta sinusoidal sigma weight residual 0.00 52.69 -52.69 1 1.00e+01 1.00e-02 3.78e+01 dihedral pdb=" CD ARG I 9 " pdb=" NE ARG I 9 " pdb=" CZ ARG I 9 " pdb=" NH1 ARG I 9 " ideal model delta sinusoidal sigma weight residual 0.00 52.67 -52.67 1 1.00e+01 1.00e-02 3.78e+01 dihedral pdb=" CD ARG D 9 " pdb=" NE ARG D 9 " pdb=" CZ ARG D 9 " pdb=" NH1 ARG D 9 " ideal model delta sinusoidal sigma weight residual 0.00 52.67 -52.67 1 1.00e+01 1.00e-02 3.78e+01 ... (remaining 8023 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 1988 0.127 - 0.255: 76 0.255 - 0.382: 15 0.382 - 0.510: 220 0.510 - 0.637: 125 Chirality restraints: 2424 Sorted by residual: chirality pdb=" P DC Y 1 " pdb=" OP1 DC Y 1 " pdb=" OP2 DC Y 1 " pdb=" O5' DC Y 1 " both_signs ideal model delta sigma weight residual True 2.34 -2.97 -0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" P DA Y 92 " pdb=" OP1 DA Y 92 " pdb=" OP2 DA Y 92 " pdb=" O5' DA Y 92 " both_signs ideal model delta sigma weight residual True 2.34 -2.96 -0.62 2.00e-01 2.50e+01 9.74e+00 chirality pdb=" P DC X 1 " pdb=" OP1 DC X 1 " pdb=" OP2 DC X 1 " pdb=" O5' DC X 1 " both_signs ideal model delta sigma weight residual True 2.34 -2.96 -0.62 2.00e-01 2.50e+01 9.67e+00 ... (remaining 2421 not shown) Planarity restraints: 1524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 9 " -0.879 9.50e-02 1.11e+02 3.94e-01 9.43e+01 pdb=" NE ARG B 9 " 0.051 2.00e-02 2.50e+03 pdb=" CZ ARG B 9 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 9 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG B 9 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 9 " -0.879 9.50e-02 1.11e+02 3.94e-01 9.43e+01 pdb=" NE ARG D 9 " 0.052 2.00e-02 2.50e+03 pdb=" CZ ARG D 9 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG D 9 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG D 9 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 9 " 0.879 9.50e-02 1.11e+02 3.94e-01 9.42e+01 pdb=" NE ARG E 9 " -0.051 2.00e-02 2.50e+03 pdb=" CZ ARG E 9 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG E 9 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG E 9 " 0.025 2.00e-02 2.50e+03 ... (remaining 1521 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 5549 3.00 - 3.47: 14403 3.47 - 3.95: 27242 3.95 - 4.42: 31292 4.42 - 4.90: 41244 Nonbonded interactions: 119730 Sorted by model distance: nonbonded pdb=" O4' DC X 157 " pdb=" O2 DC X 157 " model vdw 2.525 3.040 nonbonded pdb=" O5' DG X 150 " pdb=" O4' DG X 150 " model vdw 2.558 2.432 nonbonded pdb=" O5' DG X 161 " pdb=" O4' DG X 161 " model vdw 2.589 2.432 nonbonded pdb=" N1 DG X 67 " pdb=" C4 DG X 67 " model vdw 2.591 2.672 nonbonded pdb=" N1 DG Y 6 " pdb=" C4 DG Y 6 " model vdw 2.591 2.672 ... (remaining 119725 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 2.590 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: 0.340 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.600 Find NCS groups from input model: 0.090 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:9.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 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 : 0.012 0.044 14878 Z= 0.789 Angle : 1.904 8.228 21604 Z= 1.143 Chirality : 0.200 0.637 2424 Planarity : 0.054 0.394 1524 Dihedral : 30.013 175.337 6418 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.27), residues: 828 helix: 0.63 (0.19), residues: 636 sheet: None (None), residues: 0 loop : -1.28 (0.37), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.003 ARG A 15 TYR 0.047 0.023 TYR B 44 PHE 0.064 0.034 PHE H 5 TRP 0.065 0.029 TRP B 37 HIS 0.005 0.003 HIS H 51 Details of bonding type rmsd/Z covalent geometry : bond 0.01242 / 0.79 (14878) covalent geometry : angle 1.90396 / 1.14 (21604) hydrogen bonds : bond 0.28067 / 18.90 ( 731) hydrogen bonds : angle 9.69340 / 7.01 ( 1960) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 0.369 Fit side-chains REVERT: A 11 GLU cc_start: 0.8596 (tt0) cc_final: 0.8322 (tt0) REVERT: A 12 LYS cc_start: 0.8598 (ttpt) cc_final: 0.8324 (ttmm) REVERT: A 28 ASP cc_start: 0.8852 (m-30) cc_final: 0.8625 (m-30) REVERT: A 32 GLU cc_start: 0.8416 (tt0) cc_final: 0.8205 (tt0) REVERT: A 43 LYS cc_start: 0.8759 (mttt) cc_final: 0.8557 (mtpt) REVERT: A 52 SER cc_start: 0.8776 (t) cc_final: 0.8559 (m) REVERT: A 55 LYS cc_start: 0.8875 (mttt) cc_final: 0.8651 (mttp) REVERT: A 58 LYS cc_start: 0.8264 (mttt) cc_final: 0.8029 (mtmt) REVERT: A 60 ASN cc_start: 0.8454 (m-40) cc_final: 0.7662 (OUTLIER) REVERT: B 43 LYS cc_start: 0.8689 (mttt) cc_final: 0.8436 (mtpt) REVERT: B 47 GLU cc_start: 0.8236 (mm-30) cc_final: 0.8002 (mm-30) REVERT: B 58 LYS cc_start: 0.8379 (mttt) cc_final: 0.8146 (mtmt) REVERT: B 60 ASN cc_start: 0.8451 (m-40) cc_final: 0.7755 (p0) REVERT: C 12 LYS cc_start: 0.8600 (ttpt) cc_final: 0.8354 (ttpt) REVERT: C 28 ASP cc_start: 0.8769 (m-30) cc_final: 0.8452 (m-30) REVERT: C 58 LYS cc_start: 0.8305 (mttt) cc_final: 0.8080 (mtmt) REVERT: C 60 ASN cc_start: 0.8250 (m-40) cc_final: 0.7706 (p0) REVERT: D 47 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7934 (mm-30) REVERT: D 58 LYS cc_start: 0.8485 (mttt) cc_final: 0.8202 (mtpt) REVERT: D 60 ASN cc_start: 0.8131 (m-40) cc_final: 0.7522 (p0) REVERT: E 39 LYS cc_start: 0.8751 (mttt) cc_final: 0.8529 (mtpt) REVERT: E 43 LYS cc_start: 0.8654 (mttt) cc_final: 0.8390 (mtpt) REVERT: E 58 LYS cc_start: 0.8226 (mttt) cc_final: 0.7988 (mtmt) REVERT: E 60 ASN cc_start: 0.8360 (m-40) cc_final: 0.7553 (OUTLIER) REVERT: F 43 LYS cc_start: 0.8689 (mttt) cc_final: 0.8418 (mtpt) REVERT: F 60 ASN cc_start: 0.8314 (m-40) cc_final: 0.7757 (OUTLIER) REVERT: G 43 LYS cc_start: 0.8634 (mttt) cc_final: 0.8418 (mtpt) REVERT: G 52 SER cc_start: 0.8830 (t) cc_final: 0.8599 (m) REVERT: G 58 LYS cc_start: 0.8293 (mttt) cc_final: 0.8069 (mtmt) REVERT: G 60 ASN cc_start: 0.8223 (m-40) cc_final: 0.7593 (p0) REVERT: H 29 LYS cc_start: 0.9033 (tppt) cc_final: 0.8832 (tptt) REVERT: H 39 LYS cc_start: 0.8774 (mttt) cc_final: 0.8459 (mtpt) REVERT: H 55 LYS cc_start: 0.8866 (mttt) cc_final: 0.8665 (mttp) REVERT: H 58 LYS cc_start: 0.8159 (mttt) cc_final: 0.7776 (mtpt) REVERT: H 60 ASN cc_start: 0.8105 (m-40) cc_final: 0.7577 (p0) REVERT: I 12 LYS cc_start: 0.8585 (ttpt) cc_final: 0.8379 (ttpm) REVERT: I 55 LYS cc_start: 0.8850 (mttt) cc_final: 0.8618 (mttp) REVERT: I 60 ASN cc_start: 0.8154 (m-40) cc_final: 0.7329 (p0) REVERT: J 12 LYS cc_start: 0.8605 (ttpt) cc_final: 0.8373 (ttpt) REVERT: J 25 ASP cc_start: 0.8581 (m-30) cc_final: 0.8271 (m-30) REVERT: J 29 LYS cc_start: 0.8819 (tppt) cc_final: 0.8464 (tptt) REVERT: J 32 GLU cc_start: 0.8264 (tt0) cc_final: 0.7764 (mt-10) REVERT: J 43 LYS cc_start: 0.8746 (mttt) cc_final: 0.8523 (mtmp) REVERT: J 60 ASN cc_start: 0.8298 (m-40) cc_final: 0.7726 (OUTLIER) REVERT: K 12 LYS cc_start: 0.8705 (ttpt) cc_final: 0.8490 (ttpt) REVERT: K 43 LYS cc_start: 0.8662 (mttt) cc_final: 0.8437 (mtpt) REVERT: K 60 ASN cc_start: 0.8206 (m-40) cc_final: 0.7479 (p0) REVERT: L 12 LYS cc_start: 0.8631 (ttpt) cc_final: 0.8417 (ttpt) REVERT: L 39 LYS cc_start: 0.8827 (mttt) cc_final: 0.8604 (mtmp) REVERT: L 47 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7956 (mm-30) REVERT: L 58 LYS cc_start: 0.8232 (mttt) cc_final: 0.8028 (mtmm) REVERT: L 60 ASN cc_start: 0.8298 (m-40) cc_final: 0.7706 (OUTLIER) outliers start: 0 outliers final: 5 residues processed: 308 average time/residue: 0.8368 time to fit residues: 273.6318 Evaluate side-chains 262 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 30.0000 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 30.0000 chunk 113 optimal weight: 20.0000 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 117 optimal weight: 30.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 20 GLN B 51 HIS B 67 GLN C 20 GLN D 51 HIS D 67 GLN E 20 GLN F 51 HIS F 67 GLN G 51 HIS G 67 GLN H 20 GLN H 67 GLN I 16 GLN I 51 HIS I 67 GLN K 16 GLN K 51 HIS K 67 GLN L 67 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.198642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.125385 restraints weight = 14035.540| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.38 r_work: 0.3197 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14878 Z= 0.195 Angle : 0.816 9.174 21604 Z= 0.464 Chirality : 0.051 0.298 2424 Planarity : 0.007 0.074 1524 Dihedral : 32.787 167.477 4822 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.39 % Allowed : 10.80 % Favored : 87.81 % 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: 2.17 (0.28), residues: 828 helix: 1.92 (0.19), residues: 648 sheet: None (None), residues: 0 loop : -0.27 (0.47), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 15 TYR 0.005 0.002 TYR L 44 PHE 0.010 0.003 PHE I 5 TRP 0.029 0.007 TRP A 37 HIS 0.002 0.001 HIS B 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.20 (14878) covalent geometry : angle 0.81607 / 0.46 (21604) hydrogen bonds : bond 0.07990 / 5.42 ( 731) hydrogen bonds : angle 3.25501 / 2.34 ( 1960) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 266 time to evaluate : 0.340 Fit side-chains REVERT: A 28 ASP cc_start: 0.8666 (m-30) cc_final: 0.8383 (m-30) REVERT: A 43 LYS cc_start: 0.8599 (mttt) cc_final: 0.8354 (mttp) REVERT: A 52 SER cc_start: 0.8640 (t) cc_final: 0.8406 (m) REVERT: A 60 ASN cc_start: 0.8425 (m-40) cc_final: 0.7741 (OUTLIER) REVERT: B 60 ASN cc_start: 0.8307 (m-40) cc_final: 0.7776 (p0) REVERT: C 12 LYS cc_start: 0.8618 (ttpt) cc_final: 0.8343 (ttpt) REVERT: C 28 ASP cc_start: 0.8634 (m-30) cc_final: 0.8325 (m-30) REVERT: C 60 ASN cc_start: 0.8294 (m-40) cc_final: 0.7798 (OUTLIER) REVERT: D 60 ASN cc_start: 0.8164 (m-40) cc_final: 0.7688 (p0) REVERT: E 12 LYS cc_start: 0.8794 (ttpp) cc_final: 0.8484 (tttp) REVERT: E 39 LYS cc_start: 0.8809 (mttt) cc_final: 0.8505 (mtpt) REVERT: E 60 ASN cc_start: 0.8395 (m-40) cc_final: 0.7673 (p0) REVERT: F 1 MET cc_start: 0.6242 (OUTLIER) cc_final: 0.6009 (ttm) REVERT: F 60 ASN cc_start: 0.8209 (m-40) cc_final: 0.7754 (OUTLIER) REVERT: G 60 ASN cc_start: 0.8249 (m-40) cc_final: 0.7699 (OUTLIER) REVERT: H 39 LYS cc_start: 0.8758 (mttt) cc_final: 0.8493 (mtpt) REVERT: H 60 ASN cc_start: 0.8159 (m-40) cc_final: 0.7757 (OUTLIER) REVERT: I 12 LYS cc_start: 0.8635 (ttpt) cc_final: 0.8395 (ttpm) REVERT: I 60 ASN cc_start: 0.8254 (m-40) cc_final: 0.7510 (p0) REVERT: J 12 LYS cc_start: 0.8601 (ttpt) cc_final: 0.8383 (ttpt) REVERT: J 25 ASP cc_start: 0.8526 (m-30) cc_final: 0.8234 (m-30) REVERT: J 29 LYS cc_start: 0.8823 (tppt) cc_final: 0.8620 (tptt) REVERT: J 32 GLU cc_start: 0.8291 (tt0) cc_final: 0.7949 (tt0) REVERT: J 60 ASN cc_start: 0.8266 (m-40) cc_final: 0.7772 (OUTLIER) REVERT: K 60 ASN cc_start: 0.8206 (m-40) cc_final: 0.7497 (p0) REVERT: L 39 LYS cc_start: 0.8765 (mttt) cc_final: 0.8474 (mtpt) REVERT: L 60 ASN cc_start: 0.8219 (m-40) cc_final: 0.7766 (OUTLIER) outliers start: 9 outliers final: 10 residues processed: 267 average time/residue: 0.8648 time to fit residues: 245.4290 Evaluate side-chains 252 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 248 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain F residue 1 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 36 optimal weight: 2.9990 chunk 89 optimal weight: 30.0000 chunk 77 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 109 optimal weight: 40.0000 chunk 103 optimal weight: 40.0000 chunk 119 optimal weight: 40.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 20 GLN I 16 GLN L 20 GLN L 67 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.196927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.122318 restraints weight = 14063.813| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.38 r_work: 0.3155 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14878 Z= 0.174 Angle : 0.650 6.592 21604 Z= 0.387 Chirality : 0.044 0.221 2424 Planarity : 0.004 0.045 1524 Dihedral : 32.700 174.069 4822 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.16 % Allowed : 14.20 % Favored : 83.64 % 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: 2.99 (0.27), residues: 828 helix: 2.59 (0.18), residues: 648 sheet: None (None), residues: 0 loop : -0.37 (0.49), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 15 TYR 0.006 0.002 TYR K 44 PHE 0.013 0.003 PHE G 5 TRP 0.016 0.003 TRP I 37 HIS 0.004 0.001 HIS G 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.17 (14878) covalent geometry : angle 0.64975 / 0.39 (21604) hydrogen bonds : bond 0.06532 / 4.44 ( 731) hydrogen bonds : angle 2.92474 / 2.08 ( 1960) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 253 time to evaluate : 0.358 Fit side-chains REVERT: A 28 ASP cc_start: 0.8676 (m-30) cc_final: 0.8382 (m-30) REVERT: A 43 LYS cc_start: 0.8634 (mttt) cc_final: 0.8387 (mttp) REVERT: A 52 SER cc_start: 0.8607 (t) cc_final: 0.8361 (m) REVERT: A 60 ASN cc_start: 0.8436 (m-40) cc_final: 0.7718 (OUTLIER) REVERT: B 12 LYS cc_start: 0.8848 (ttpp) cc_final: 0.8634 (ttpp) REVERT: B 60 ASN cc_start: 0.8248 (m-40) cc_final: 0.7677 (OUTLIER) REVERT: C 60 ASN cc_start: 0.8339 (m-40) cc_final: 0.7804 (OUTLIER) REVERT: D 60 ASN cc_start: 0.8099 (m-40) cc_final: 0.7652 (OUTLIER) REVERT: E 12 LYS cc_start: 0.8805 (ttpp) cc_final: 0.8509 (tttp) REVERT: E 39 LYS cc_start: 0.8799 (mttt) cc_final: 0.8491 (mtpt) REVERT: E 60 ASN cc_start: 0.8413 (m-40) cc_final: 0.7661 (OUTLIER) REVERT: F 60 ASN cc_start: 0.8260 (m-40) cc_final: 0.7765 (OUTLIER) REVERT: G 60 ASN cc_start: 0.8263 (m-40) cc_final: 0.7703 (p0) REVERT: H 39 LYS cc_start: 0.8809 (mttt) cc_final: 0.8509 (mtpt) REVERT: H 60 ASN cc_start: 0.8161 (m-40) cc_final: 0.7744 (p0) REVERT: I 55 LYS cc_start: 0.9042 (mttp) cc_final: 0.8800 (mttp) REVERT: I 60 ASN cc_start: 0.8276 (m-40) cc_final: 0.7488 (OUTLIER) REVERT: J 25 ASP cc_start: 0.8507 (m-30) cc_final: 0.8226 (m-30) REVERT: J 60 ASN cc_start: 0.8277 (m-40) cc_final: 0.7736 (OUTLIER) REVERT: K 60 ASN cc_start: 0.8234 (m-40) cc_final: 0.7511 (p0) REVERT: L 20 GLN cc_start: 0.8789 (tt0) cc_final: 0.8587 (tt0) REVERT: L 39 LYS cc_start: 0.8791 (mttt) cc_final: 0.8523 (mtpt) REVERT: L 60 ASN cc_start: 0.8217 (m-40) cc_final: 0.7762 (OUTLIER) outliers start: 14 outliers final: 18 residues processed: 256 average time/residue: 0.7354 time to fit residues: 200.9078 Evaluate side-chains 258 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 249 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain G residue 20 GLN Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain K residue 20 GLN Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 41 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 47 optimal weight: 8.9990 chunk 77 optimal weight: 6.9990 chunk 90 optimal weight: 30.0000 chunk 107 optimal weight: 30.0000 chunk 116 optimal weight: 40.0000 chunk 86 optimal weight: 40.0000 chunk 50 optimal weight: 3.9990 chunk 106 optimal weight: 40.0000 chunk 43 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 20 GLN F 20 GLN H 20 GLN H 51 HIS I 20 GLN J 51 HIS K 67 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.194206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.118749 restraints weight = 13969.266| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.36 r_work: 0.3096 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14878 Z= 0.229 Angle : 0.658 7.005 21604 Z= 0.380 Chirality : 0.043 0.200 2424 Planarity : 0.005 0.042 1524 Dihedral : 32.637 171.291 4822 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.24 % Allowed : 15.43 % Favored : 81.33 % 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: 2.94 (0.27), residues: 828 helix: 2.59 (0.17), residues: 648 sheet: None (None), residues: 0 loop : -0.52 (0.48), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 54 TYR 0.007 0.002 TYR K 44 PHE 0.012 0.003 PHE K 5 TRP 0.008 0.002 TRP L 37 HIS 0.005 0.002 HIS K 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.23 (14878) covalent geometry : angle 0.65774 / 0.38 (21604) hydrogen bonds : bond 0.07052 / 4.79 ( 731) hydrogen bonds : angle 2.96876 / 2.11 ( 1960) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 246 time to evaluate : 0.346 Fit side-chains REVERT: A 28 ASP cc_start: 0.8698 (m-30) cc_final: 0.8423 (m-30) REVERT: A 43 LYS cc_start: 0.8627 (mttt) cc_final: 0.8381 (mttp) REVERT: A 52 SER cc_start: 0.8645 (t) cc_final: 0.8431 (m) REVERT: A 60 ASN cc_start: 0.8435 (m-40) cc_final: 0.7725 (OUTLIER) REVERT: B 12 LYS cc_start: 0.8826 (ttpp) cc_final: 0.8604 (ttpp) REVERT: B 60 ASN cc_start: 0.8295 (m-40) cc_final: 0.7699 (OUTLIER) REVERT: C 60 ASN cc_start: 0.8328 (m-40) cc_final: 0.7775 (OUTLIER) REVERT: D 60 ASN cc_start: 0.8093 (m-40) cc_final: 0.7626 (OUTLIER) REVERT: E 12 LYS cc_start: 0.8778 (ttpp) cc_final: 0.8485 (tttp) REVERT: E 60 ASN cc_start: 0.8444 (m-40) cc_final: 0.7676 (OUTLIER) REVERT: F 60 ASN cc_start: 0.8276 (m-40) cc_final: 0.7765 (OUTLIER) REVERT: G 60 ASN cc_start: 0.8286 (m-40) cc_final: 0.7718 (p0) REVERT: H 12 LYS cc_start: 0.8652 (ttpt) cc_final: 0.8413 (tttm) REVERT: H 39 LYS cc_start: 0.8820 (mttt) cc_final: 0.8492 (mtpt) REVERT: H 60 ASN cc_start: 0.8184 (m-40) cc_final: 0.7748 (p0) REVERT: I 60 ASN cc_start: 0.8272 (m-40) cc_final: 0.7451 (OUTLIER) REVERT: J 25 ASP cc_start: 0.8532 (m-30) cc_final: 0.8232 (m-30) REVERT: J 60 ASN cc_start: 0.8276 (m-40) cc_final: 0.7675 (p0) REVERT: K 60 ASN cc_start: 0.8216 (m-40) cc_final: 0.7472 (p0) REVERT: L 39 LYS cc_start: 0.8844 (mttt) cc_final: 0.8546 (mtpt) REVERT: L 60 ASN cc_start: 0.8235 (m-40) cc_final: 0.7778 (OUTLIER) outliers start: 21 outliers final: 17 residues processed: 250 average time/residue: 0.7616 time to fit residues: 202.9168 Evaluate side-chains 249 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 240 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain K residue 20 GLN Chi-restraints excluded: chain K residue 41 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 57 optimal weight: 2.9990 chunk 105 optimal weight: 30.0000 chunk 47 optimal weight: 3.9990 chunk 84 optimal weight: 40.0000 chunk 18 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 103 optimal weight: 40.0000 chunk 98 optimal weight: 30.0000 chunk 28 optimal weight: 5.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 20 GLN F 20 GLN L 20 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.195159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.120889 restraints weight = 14229.483| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.37 r_work: 0.3123 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14878 Z= 0.190 Angle : 0.626 6.589 21604 Z= 0.367 Chirality : 0.041 0.207 2424 Planarity : 0.003 0.031 1524 Dihedral : 32.578 170.377 4822 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.47 % Allowed : 16.36 % Favored : 81.17 % 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: 3.10 (0.27), residues: 828 helix: 2.72 (0.17), residues: 648 sheet: None (None), residues: 0 loop : -0.53 (0.48), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG K 9 TYR 0.008 0.002 TYR F 44 PHE 0.010 0.002 PHE K 5 TRP 0.010 0.002 TRP I 37 HIS 0.004 0.002 HIS J 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.19 (14878) covalent geometry : angle 0.62639 / 0.37 (21604) hydrogen bonds : bond 0.06360 / 4.33 ( 731) hydrogen bonds : angle 2.90786 / 2.07 ( 1960) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 246 time to evaluate : 0.362 Fit side-chains REVERT: A 28 ASP cc_start: 0.8732 (m-30) cc_final: 0.8470 (m-30) REVERT: A 43 LYS cc_start: 0.8678 (mttt) cc_final: 0.8458 (mttp) REVERT: A 60 ASN cc_start: 0.8476 (m-40) cc_final: 0.7821 (OUTLIER) REVERT: B 12 LYS cc_start: 0.8880 (ttpp) cc_final: 0.8664 (ttpp) REVERT: B 60 ASN cc_start: 0.8327 (m-40) cc_final: 0.7783 (OUTLIER) REVERT: C 60 ASN cc_start: 0.8363 (m-40) cc_final: 0.7864 (OUTLIER) REVERT: D 60 ASN cc_start: 0.8114 (m-40) cc_final: 0.7695 (OUTLIER) REVERT: E 12 LYS cc_start: 0.8806 (ttpp) cc_final: 0.8515 (tttp) REVERT: E 60 ASN cc_start: 0.8485 (m-40) cc_final: 0.7783 (OUTLIER) REVERT: F 60 ASN cc_start: 0.8320 (m-40) cc_final: 0.7858 (OUTLIER) REVERT: G 60 ASN cc_start: 0.8328 (m-40) cc_final: 0.7806 (OUTLIER) REVERT: H 39 LYS cc_start: 0.8832 (mttt) cc_final: 0.8531 (mtpt) REVERT: H 60 ASN cc_start: 0.8205 (m-40) cc_final: 0.7830 (p0) REVERT: I 60 ASN cc_start: 0.8315 (m-40) cc_final: 0.7570 (p0) REVERT: J 25 ASP cc_start: 0.8560 (m-30) cc_final: 0.8276 (m-30) REVERT: J 60 ASN cc_start: 0.8320 (m-40) cc_final: 0.7780 (p0) REVERT: K 60 ASN cc_start: 0.8278 (m-40) cc_final: 0.7592 (p0) REVERT: L 39 LYS cc_start: 0.8891 (mttt) cc_final: 0.8616 (mtpt) REVERT: L 60 ASN cc_start: 0.8280 (m-40) cc_final: 0.7872 (OUTLIER) outliers start: 16 outliers final: 18 residues processed: 250 average time/residue: 0.7375 time to fit residues: 196.6457 Evaluate side-chains 251 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 241 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain F residue 32 GLU Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain J residue 41 ILE Chi-restraints excluded: chain K residue 20 GLN Chi-restraints excluded: chain K residue 41 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 88 optimal weight: 40.0000 chunk 113 optimal weight: 20.0000 chunk 118 optimal weight: 50.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 51 HIS E 51 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.193876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.119263 restraints weight = 14091.881| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.38 r_work: 0.3094 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14878 Z= 0.221 Angle : 0.628 6.426 21604 Z= 0.366 Chirality : 0.041 0.222 2424 Planarity : 0.004 0.040 1524 Dihedral : 32.518 168.578 4822 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Rotamer: Outliers : 2.93 % Allowed : 17.13 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.90 (0.27), residues: 828 helix: 2.58 (0.17), residues: 648 sheet: None (None), residues: 0 loop : -0.63 (0.47), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 54 TYR 0.010 0.002 TYR K 44 PHE 0.010 0.003 PHE L 5 TRP 0.006 0.002 TRP I 37 HIS 0.006 0.002 HIS K 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.22 (14878) covalent geometry : angle 0.62774 / 0.37 (21604) hydrogen bonds : bond 0.06986 / 4.76 ( 731) hydrogen bonds : angle 2.97326 / 2.11 ( 1960) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 243 time to evaluate : 0.350 Fit side-chains REVERT: A 28 ASP cc_start: 0.8750 (m-30) cc_final: 0.8487 (m-30) REVERT: A 60 ASN cc_start: 0.8461 (m-40) cc_final: 0.7802 (OUTLIER) REVERT: B 60 ASN cc_start: 0.8340 (m-40) cc_final: 0.7768 (p0) REVERT: C 60 ASN cc_start: 0.8343 (m-40) cc_final: 0.7834 (OUTLIER) REVERT: D 60 ASN cc_start: 0.8087 (m-40) cc_final: 0.7654 (OUTLIER) REVERT: E 12 LYS cc_start: 0.8827 (ttpp) cc_final: 0.8525 (tttp) REVERT: E 60 ASN cc_start: 0.8514 (m-40) cc_final: 0.7782 (OUTLIER) REVERT: F 60 ASN cc_start: 0.8310 (m-40) cc_final: 0.7829 (OUTLIER) REVERT: G 60 ASN cc_start: 0.8377 (m-40) cc_final: 0.7824 (OUTLIER) REVERT: H 12 LYS cc_start: 0.8698 (ttpt) cc_final: 0.8480 (tttm) REVERT: H 39 LYS cc_start: 0.8846 (mttt) cc_final: 0.8568 (mtpt) REVERT: H 60 ASN cc_start: 0.8193 (m-40) cc_final: 0.7831 (p0) REVERT: I 60 ASN cc_start: 0.8323 (m-40) cc_final: 0.7551 (p0) REVERT: J 25 ASP cc_start: 0.8544 (m-30) cc_final: 0.8253 (m-30) REVERT: J 29 LYS cc_start: 0.9031 (tptt) cc_final: 0.8818 (tptt) REVERT: J 60 ASN cc_start: 0.8320 (m-40) cc_final: 0.7754 (p0) REVERT: K 60 ASN cc_start: 0.8310 (m-40) cc_final: 0.7615 (p0) REVERT: L 39 LYS cc_start: 0.8906 (mttt) cc_final: 0.8631 (mtpt) REVERT: L 60 ASN cc_start: 0.8252 (m-40) cc_final: 0.7862 (OUTLIER) outliers start: 19 outliers final: 16 residues processed: 247 average time/residue: 0.7596 time to fit residues: 200.1810 Evaluate side-chains 246 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 237 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain F residue 32 GLU Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain J residue 41 ILE Chi-restraints excluded: chain K residue 41 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 30.0000 chunk 107 optimal weight: 30.0000 chunk 106 optimal weight: 40.0000 chunk 5 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 117 optimal weight: 40.0000 chunk 14 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 20 GLN F 67 GLN J 4 ASN K 20 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.195190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.120824 restraints weight = 14108.643| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.35 r_work: 0.3124 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14878 Z= 0.163 Angle : 0.605 7.423 21604 Z= 0.356 Chirality : 0.040 0.206 2424 Planarity : 0.003 0.030 1524 Dihedral : 32.481 168.778 4822 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 1.70 % Allowed : 18.52 % Favored : 79.78 % 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: 3.06 (0.27), residues: 828 helix: 2.69 (0.17), residues: 648 sheet: None (None), residues: 0 loop : -0.55 (0.48), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 15 TYR 0.012 0.003 TYR E 44 PHE 0.008 0.002 PHE L 5 TRP 0.006 0.001 TRP E 37 HIS 0.003 0.002 HIS K 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.16 (14878) covalent geometry : angle 0.60504 / 0.36 (21604) hydrogen bonds : bond 0.06242 / 4.25 ( 731) hydrogen bonds : angle 2.99567 / 2.12 ( 1960) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 243 time to evaluate : 0.280 Fit side-chains REVERT: A 28 ASP cc_start: 0.8695 (m-30) cc_final: 0.8417 (m-30) REVERT: A 60 ASN cc_start: 0.8402 (m-40) cc_final: 0.7732 (OUTLIER) REVERT: B 60 ASN cc_start: 0.8266 (m-40) cc_final: 0.7697 (p0) REVERT: C 60 ASN cc_start: 0.8300 (m-40) cc_final: 0.7776 (OUTLIER) REVERT: D 60 ASN cc_start: 0.8035 (m-40) cc_final: 0.7574 (OUTLIER) REVERT: E 12 LYS cc_start: 0.8765 (ttpp) cc_final: 0.8457 (tttp) REVERT: E 60 ASN cc_start: 0.8434 (m-40) cc_final: 0.7699 (OUTLIER) REVERT: F 1 MET cc_start: 0.6115 (OUTLIER) cc_final: 0.5874 (ttp) REVERT: F 60 ASN cc_start: 0.8248 (m-40) cc_final: 0.7757 (OUTLIER) REVERT: G 60 ASN cc_start: 0.8317 (m-40) cc_final: 0.7753 (OUTLIER) REVERT: H 39 LYS cc_start: 0.8794 (mttt) cc_final: 0.8461 (mtpt) REVERT: H 60 ASN cc_start: 0.8122 (m-40) cc_final: 0.7744 (p0) REVERT: I 60 ASN cc_start: 0.8273 (m-40) cc_final: 0.7483 (p0) REVERT: J 25 ASP cc_start: 0.8497 (m-30) cc_final: 0.8192 (m-30) REVERT: J 60 ASN cc_start: 0.8263 (m-40) cc_final: 0.7695 (p0) REVERT: K 60 ASN cc_start: 0.8270 (m-40) cc_final: 0.7545 (p0) REVERT: L 39 LYS cc_start: 0.8851 (mttt) cc_final: 0.8546 (mtpt) REVERT: L 60 ASN cc_start: 0.8195 (m-40) cc_final: 0.7789 (OUTLIER) outliers start: 11 outliers final: 13 residues processed: 247 average time/residue: 0.8125 time to fit residues: 213.8716 Evaluate side-chains 247 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 240 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain K residue 41 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 33 optimal weight: 0.4980 chunk 26 optimal weight: 8.9990 chunk 29 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 108 optimal weight: 30.0000 chunk 28 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 89 optimal weight: 30.0000 chunk 2 optimal weight: 10.0000 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 67 GLN K 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.195039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.120288 restraints weight = 14096.120| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.36 r_work: 0.3118 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14878 Z= 0.182 Angle : 0.597 6.426 21604 Z= 0.352 Chirality : 0.040 0.205 2424 Planarity : 0.003 0.026 1524 Dihedral : 32.440 168.829 4822 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 1.23 % Allowed : 19.14 % Favored : 79.63 % 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: 3.09 (0.27), residues: 828 helix: 2.71 (0.17), residues: 648 sheet: None (None), residues: 0 loop : -0.53 (0.48), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 9 TYR 0.011 0.003 TYR K 44 PHE 0.008 0.002 PHE L 5 TRP 0.010 0.002 TRP E 37 HIS 0.003 0.001 HIS B 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.18 (14878) covalent geometry : angle 0.59666 / 0.35 (21604) hydrogen bonds : bond 0.06346 / 4.32 ( 731) hydrogen bonds : angle 2.93610 / 2.08 ( 1960) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 238 time to evaluate : 0.293 Fit side-chains REVERT: A 28 ASP cc_start: 0.8707 (m-30) cc_final: 0.8431 (m-30) REVERT: A 60 ASN cc_start: 0.8408 (m-40) cc_final: 0.7735 (OUTLIER) REVERT: B 12 LYS cc_start: 0.8857 (ttpp) cc_final: 0.8636 (ttpp) REVERT: B 60 ASN cc_start: 0.8288 (m-40) cc_final: 0.7714 (p0) REVERT: C 60 ASN cc_start: 0.8312 (m-40) cc_final: 0.7780 (OUTLIER) REVERT: D 60 ASN cc_start: 0.8045 (m-40) cc_final: 0.7588 (OUTLIER) REVERT: E 12 LYS cc_start: 0.8782 (ttpp) cc_final: 0.8476 (tttp) REVERT: E 60 ASN cc_start: 0.8455 (m-40) cc_final: 0.7707 (OUTLIER) REVERT: F 1 MET cc_start: 0.6348 (OUTLIER) cc_final: 0.6110 (ttp) REVERT: F 60 ASN cc_start: 0.8234 (m-40) cc_final: 0.7750 (OUTLIER) REVERT: G 60 ASN cc_start: 0.8325 (m-40) cc_final: 0.7758 (OUTLIER) REVERT: H 39 LYS cc_start: 0.8811 (mttt) cc_final: 0.8471 (mtpt) REVERT: H 60 ASN cc_start: 0.8136 (m-40) cc_final: 0.7749 (p0) REVERT: I 60 ASN cc_start: 0.8286 (m-40) cc_final: 0.7495 (p0) REVERT: J 25 ASP cc_start: 0.8509 (m-30) cc_final: 0.8210 (m-30) REVERT: J 60 ASN cc_start: 0.8258 (m-40) cc_final: 0.7697 (p0) REVERT: K 11 GLU cc_start: 0.8758 (tt0) cc_final: 0.8500 (tt0) REVERT: K 60 ASN cc_start: 0.8256 (m-40) cc_final: 0.7540 (p0) REVERT: L 39 LYS cc_start: 0.8860 (mttt) cc_final: 0.8530 (mtpt) REVERT: L 55 LYS cc_start: 0.8857 (mttp) cc_final: 0.8573 (mttt) REVERT: L 60 ASN cc_start: 0.8198 (m-40) cc_final: 0.7781 (OUTLIER) outliers start: 8 outliers final: 13 residues processed: 242 average time/residue: 0.7753 time to fit residues: 200.1204 Evaluate side-chains 243 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 236 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain K residue 41 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 75 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 108 optimal weight: 30.0000 chunk 34 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 114 optimal weight: 30.0000 chunk 91 optimal weight: 40.0000 chunk 72 optimal weight: 0.0770 chunk 94 optimal weight: 40.0000 chunk 4 optimal weight: 0.7980 overall best weight: 1.5542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 67 GLN G 20 GLN J 67 GLN K 20 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.195580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.121219 restraints weight = 14225.253| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.39 r_work: 0.3126 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14878 Z= 0.150 Angle : 0.585 6.408 21604 Z= 0.349 Chirality : 0.039 0.205 2424 Planarity : 0.003 0.020 1524 Dihedral : 32.404 169.145 4822 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 1.23 % Allowed : 19.60 % Favored : 79.17 % 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: 3.24 (0.27), residues: 828 helix: 2.82 (0.17), residues: 648 sheet: None (None), residues: 0 loop : -0.48 (0.48), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 9 TYR 0.012 0.003 TYR G 44 PHE 0.007 0.002 PHE L 5 TRP 0.012 0.002 TRP E 37 HIS 0.003 0.001 HIS K 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.15 (14878) covalent geometry : angle 0.58523 / 0.35 (21604) hydrogen bonds : bond 0.05976 / 4.07 ( 731) hydrogen bonds : angle 2.93380 / 2.08 ( 1960) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 240 time to evaluate : 0.380 Fit side-chains REVERT: A 28 ASP cc_start: 0.8719 (m-30) cc_final: 0.8454 (m-30) REVERT: A 60 ASN cc_start: 0.8440 (m-40) cc_final: 0.7795 (OUTLIER) REVERT: B 12 LYS cc_start: 0.8874 (ttpp) cc_final: 0.8634 (ttpp) REVERT: B 60 ASN cc_start: 0.8300 (m-40) cc_final: 0.7777 (p0) REVERT: C 60 ASN cc_start: 0.8345 (m-40) cc_final: 0.7855 (OUTLIER) REVERT: D 60 ASN cc_start: 0.8068 (m-40) cc_final: 0.7643 (OUTLIER) REVERT: E 12 LYS cc_start: 0.8804 (ttpp) cc_final: 0.8508 (tttp) REVERT: E 60 ASN cc_start: 0.8481 (m-40) cc_final: 0.7777 (OUTLIER) REVERT: F 1 MET cc_start: 0.6284 (OUTLIER) cc_final: 0.6058 (ttp) REVERT: F 60 ASN cc_start: 0.8284 (m-40) cc_final: 0.7827 (OUTLIER) REVERT: G 60 ASN cc_start: 0.8339 (m-40) cc_final: 0.7807 (OUTLIER) REVERT: H 39 LYS cc_start: 0.8828 (mttt) cc_final: 0.8513 (mtpt) REVERT: H 60 ASN cc_start: 0.8151 (m-40) cc_final: 0.7802 (p0) REVERT: I 60 ASN cc_start: 0.8306 (m-40) cc_final: 0.7560 (p0) REVERT: J 25 ASP cc_start: 0.8517 (m-30) cc_final: 0.8228 (m-30) REVERT: J 60 ASN cc_start: 0.8289 (m-40) cc_final: 0.7762 (p0) REVERT: K 11 GLU cc_start: 0.8776 (tt0) cc_final: 0.8563 (tt0) REVERT: K 60 ASN cc_start: 0.8282 (m-40) cc_final: 0.7604 (p0) REVERT: L 39 LYS cc_start: 0.8886 (mttt) cc_final: 0.8581 (mtpt) REVERT: L 55 LYS cc_start: 0.8889 (mttp) cc_final: 0.8617 (mttt) REVERT: L 60 ASN cc_start: 0.8218 (m-40) cc_final: 0.7835 (OUTLIER) outliers start: 8 outliers final: 12 residues processed: 242 average time/residue: 0.7685 time to fit residues: 198.5699 Evaluate side-chains 243 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 237 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain K residue 41 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 78 optimal weight: 6.9990 chunk 84 optimal weight: 40.0000 chunk 67 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 92 optimal weight: 30.0000 chunk 9 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 56 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 89 optimal weight: 40.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 4 ASN G 20 GLN K 20 GLN L 20 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.192827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.117659 restraints weight = 14104.211| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.41 r_work: 0.3076 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 14878 Z= 0.269 Angle : 0.650 6.276 21604 Z= 0.372 Chirality : 0.043 0.224 2424 Planarity : 0.005 0.045 1524 Dihedral : 32.540 168.269 4822 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Rotamer: Outliers : 1.23 % Allowed : 19.91 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.62 (0.26), residues: 828 helix: 2.38 (0.17), residues: 648 sheet: None (None), residues: 0 loop : -0.71 (0.46), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 54 TYR 0.011 0.002 TYR K 44 PHE 0.009 0.003 PHE L 5 TRP 0.005 0.001 TRP E 37 HIS 0.007 0.003 HIS F 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00600 / 0.27 (14878) covalent geometry : angle 0.64985 / 0.37 (21604) hydrogen bonds : bond 0.07605 / 5.16 ( 731) hydrogen bonds : angle 3.08198 / 2.18 ( 1960) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 234 time to evaluate : 0.266 Fit side-chains REVERT: A 28 ASP cc_start: 0.8726 (m-30) cc_final: 0.8476 (m-30) REVERT: A 60 ASN cc_start: 0.8434 (m-40) cc_final: 0.7738 (OUTLIER) REVERT: B 12 LYS cc_start: 0.8869 (ttpp) cc_final: 0.8635 (ttpp) REVERT: B 60 ASN cc_start: 0.8342 (m-40) cc_final: 0.7738 (p0) REVERT: C 60 ASN cc_start: 0.8316 (m-40) cc_final: 0.7778 (OUTLIER) REVERT: D 60 ASN cc_start: 0.8080 (m-40) cc_final: 0.7612 (OUTLIER) REVERT: E 12 LYS cc_start: 0.8775 (ttpp) cc_final: 0.8473 (tttp) REVERT: E 60 ASN cc_start: 0.8505 (m-40) cc_final: 0.7731 (OUTLIER) REVERT: F 60 ASN cc_start: 0.8295 (m-40) cc_final: 0.7770 (OUTLIER) REVERT: G 60 ASN cc_start: 0.8369 (m-40) cc_final: 0.7788 (p0) REVERT: H 39 LYS cc_start: 0.8844 (mttt) cc_final: 0.8523 (mtpt) REVERT: H 60 ASN cc_start: 0.8150 (m-40) cc_final: 0.7738 (p0) REVERT: I 60 ASN cc_start: 0.8267 (m-40) cc_final: 0.7470 (p0) REVERT: J 25 ASP cc_start: 0.8528 (m-30) cc_final: 0.8221 (m-30) REVERT: J 60 ASN cc_start: 0.8273 (m-40) cc_final: 0.7650 (p0) REVERT: K 11 GLU cc_start: 0.8793 (tt0) cc_final: 0.8571 (tt0) REVERT: K 60 ASN cc_start: 0.8313 (m-40) cc_final: 0.7563 (p0) REVERT: L 39 LYS cc_start: 0.8887 (mttt) cc_final: 0.8581 (mtpt) REVERT: L 55 LYS cc_start: 0.8899 (mttp) cc_final: 0.8621 (mttt) REVERT: L 60 ASN cc_start: 0.8199 (m-40) cc_final: 0.7775 (OUTLIER) outliers start: 8 outliers final: 8 residues processed: 237 average time/residue: 0.7515 time to fit residues: 189.9265 Evaluate side-chains 234 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 232 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain K residue 41 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 51 optimal weight: 1.9990 chunk 103 optimal weight: 40.0000 chunk 29 optimal weight: 0.8980 chunk 102 optimal weight: 30.0000 chunk 47 optimal weight: 3.9990 chunk 113 optimal weight: 40.0000 chunk 8 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 20 GLN F 67 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.195184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.120893 restraints weight = 14166.064| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.39 r_work: 0.3119 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14878 Z= 0.152 Angle : 0.593 6.313 21604 Z= 0.352 Chirality : 0.040 0.205 2424 Planarity : 0.003 0.023 1524 Dihedral : 32.410 168.691 4822 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 0.77 % Allowed : 19.91 % Favored : 79.32 % 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: 2.97 (0.27), residues: 828 helix: 2.60 (0.18), residues: 648 sheet: None (None), residues: 0 loop : -0.51 (0.47), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 9 TYR 0.013 0.003 TYR F 44 PHE 0.003 0.001 PHE L 5 TRP 0.013 0.003 TRP E 37 HIS 0.003 0.001 HIS B 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.15 (14878) covalent geometry : angle 0.59296 / 0.35 (21604) hydrogen bonds : bond 0.05952 / 4.06 ( 731) hydrogen bonds : angle 3.04889 / 2.16 ( 1960) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4925.85 seconds wall clock time: 84 minutes 18.83 seconds (5058.83 seconds total)