Starting phenix.real_space_refine on Wed Feb 4 23:26:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qv6_53387/02_2026/9qv6_53387.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qv6_53387/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9qv6_53387/02_2026/9qv6_53387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qv6_53387/02_2026/9qv6_53387.map" model { file = "/net/cci-nas-00/data/ceres_data/9qv6_53387/02_2026/9qv6_53387.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qv6_53387/02_2026/9qv6_53387.cif" } 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-2.0-5952/lib/python3.9/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: 2.58, per 1000 atoms: 0.19 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: 1.09 Conformation dependent library (CDL) restraints added in 392.2 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: 2.00 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: 2.38 Time building geometry restraints manager: 1.47 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: 15155 1.65 - 3.29: 4357 3.29 - 4.94: 1388 4.94 - 6.58: 650 6.58 - 8.23: 54 Bond angle restraints: 21604 Sorted by residual: 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=" 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 angle pdb=" O3' DA Y 172 " pdb=" P DT Y 173 " pdb=" O5' DT Y 173 " ideal model delta sigma weight residual 104.00 97.75 6.25 1.50e+00 4.44e-01 1.73e+01 angle pdb=" O3' DG X 163 " pdb=" P DC X 164 " pdb=" O5' DC X 164 " ideal model delta sigma weight residual 104.00 97.89 6.11 1.50e+00 4.44e-01 1.66e+01 angle pdb=" O3' DG X 85 " pdb=" P DT X 86 " pdb=" O5' DT X 86 " ideal model delta sigma weight residual 104.00 110.09 -6.09 1.50e+00 4.44e-01 1.65e+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 - 0.125: 1989 0.125 - 0.251: 75 0.251 - 0.376: 15 0.376 - 0.502: 233 0.502 - 0.627: 112 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 2.35 -2.97 -0.63 2.00e-01 2.50e+01 9.83e+00 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 2.35 -2.96 -0.61 2.00e-01 2.50e+01 9.43e+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 2.35 -2.96 -0.61 2.00e-01 2.50e+01 9.35e+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: 2.390 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: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.620 Find NCS groups from input model: 0.080 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: 0.010 Load rotamer database and sin/cos tables:7.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 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= 0.658 Angle : 1.911 8.228 21604 Z= 1.083 Chirality : 0.194 0.627 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 covalent geometry : bond 0.01190 (14878) covalent geometry : angle 1.91086 (21604) hydrogen bonds : bond 0.28067 ( 731) hydrogen bonds : angle 9.69340 ( 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 : 0.358 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: 0.8475 time to fit residues: 276.6537 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 : 0.237 ------------------------------------------------------------------------------- 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: 10.0000 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 10.0000 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: 9.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4301 r_free = 0.4301 target = 0.200431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.128260 restraints weight = 14297.955| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.38 r_work: 0.3259 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3127 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= 0.167 Angle : 0.572 4.078 21604 Z= 0.354 Chirality : 0.031 0.119 2424 Planarity : 0.004 0.044 1524 Dihedral : 32.179 179.617 4822 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.23 % Allowed : 10.96 % 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: 2.73 (0.28), residues: 828 helix: 2.30 (0.19), residues: 648 sheet: None (None), residues: 0 loop : 0.03 (0.47), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 15 TYR 0.006 0.002 TYR K 44 PHE 0.011 0.003 PHE E 5 TRP 0.025 0.005 TRP L 37 HIS 0.001 0.000 HIS K 51 Details of bonding type rmsd covalent geometry : bond 0.00357 (14878) covalent geometry : angle 0.57236 (21604) hydrogen bonds : bond 0.05625 ( 731) hydrogen bonds : angle 2.85630 ( 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 282 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 274 time to evaluate : 0.260 Fit side-chains REVERT: A 12 LYS cc_start: 0.8578 (ttpt) cc_final: 0.8301 (tttp) REVERT: A 21 ARG cc_start: 0.8732 (mtp85) cc_final: 0.8504 (mtp85) REVERT: A 28 ASP cc_start: 0.8632 (m-30) cc_final: 0.8328 (m-30) REVERT: A 43 LYS cc_start: 0.8548 (mttt) cc_final: 0.8309 (mttp) REVERT: A 52 SER cc_start: 0.8516 (t) cc_final: 0.8225 (m) REVERT: A 60 ASN cc_start: 0.8419 (m-40) cc_final: 0.7707 (OUTLIER) REVERT: B 60 ASN cc_start: 0.8269 (m-40) cc_final: 0.7709 (p0) REVERT: C 32 GLU cc_start: 0.8326 (tt0) cc_final: 0.8035 (tt0) REVERT: C 60 ASN cc_start: 0.8286 (m-40) cc_final: 0.7761 (OUTLIER) REVERT: D 60 ASN cc_start: 0.8060 (m-40) cc_final: 0.7657 (OUTLIER) REVERT: E 12 LYS cc_start: 0.8779 (ttpp) cc_final: 0.8510 (tttp) REVERT: E 39 LYS cc_start: 0.8817 (mttt) cc_final: 0.8504 (mtpt) REVERT: E 60 ASN cc_start: 0.8369 (m-40) cc_final: 0.7638 (p0) REVERT: F 60 ASN cc_start: 0.8167 (m-40) cc_final: 0.7682 (OUTLIER) REVERT: G 60 ASN cc_start: 0.8223 (m-40) cc_final: 0.7683 (OUTLIER) REVERT: H 39 LYS cc_start: 0.8755 (mttt) cc_final: 0.8486 (mtpt) REVERT: H 60 ASN cc_start: 0.8106 (m-40) cc_final: 0.7690 (OUTLIER) REVERT: I 55 LYS cc_start: 0.8962 (mttt) cc_final: 0.8737 (mttp) REVERT: I 60 ASN cc_start: 0.8230 (m-40) cc_final: 0.7478 (p0) REVERT: J 25 ASP cc_start: 0.8460 (m-30) cc_final: 0.8201 (m-30) REVERT: J 32 GLU cc_start: 0.8333 (tt0) cc_final: 0.8075 (tt0) REVERT: J 60 ASN cc_start: 0.8237 (m-40) cc_final: 0.7703 (OUTLIER) REVERT: K 12 LYS cc_start: 0.8719 (ttpt) cc_final: 0.8474 (ttpt) REVERT: K 60 ASN cc_start: 0.8247 (m-40) cc_final: 0.7477 (p0) REVERT: L 39 LYS cc_start: 0.8782 (mttt) cc_final: 0.8452 (mtpt) REVERT: L 60 ASN cc_start: 0.8224 (m-40) cc_final: 0.7770 (OUTLIER) outliers start: 8 outliers final: 10 residues processed: 274 average time/residue: 0.7826 time to fit residues: 227.6128 Evaluate side-chains 255 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 253 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain C residue 41 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 36 optimal weight: 0.4980 chunk 89 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 109 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 GLN C 51 HIS D 4 ASN E 51 HIS F 67 GLN H 51 HIS J 4 ASN J 20 GLN J 51 HIS K 67 GLN L 20 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.194220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.119469 restraints weight = 14217.242| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.41 r_work: 0.3108 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 14878 Z= 0.243 Angle : 0.565 4.669 21604 Z= 0.345 Chirality : 0.031 0.105 2424 Planarity : 0.004 0.041 1524 Dihedral : 32.107 174.641 4822 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 3.09 % Allowed : 15.59 % 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: 2.70 (0.27), residues: 828 helix: 2.33 (0.18), residues: 648 sheet: None (None), residues: 0 loop : -0.21 (0.51), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 15 TYR 0.009 0.002 TYR K 44 PHE 0.015 0.004 PHE I 5 TRP 0.013 0.003 TRP I 37 HIS 0.005 0.002 HIS K 51 Details of bonding type rmsd covalent geometry : bond 0.00560 (14878) covalent geometry : angle 0.56476 (21604) hydrogen bonds : bond 0.06748 ( 731) hydrogen bonds : angle 2.95006 ( 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 270 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 250 time to evaluate : 0.262 Fit side-chains REVERT: A 12 LYS cc_start: 0.8609 (ttpt) cc_final: 0.8242 (tttp) REVERT: A 21 ARG cc_start: 0.8914 (mtp85) cc_final: 0.8650 (mtp85) REVERT: A 28 ASP cc_start: 0.8718 (m-30) cc_final: 0.8455 (m-30) REVERT: A 60 ASN cc_start: 0.8475 (m-40) cc_final: 0.7839 (OUTLIER) REVERT: B 60 ASN cc_start: 0.8332 (m-40) cc_final: 0.7725 (OUTLIER) REVERT: C 60 ASN cc_start: 0.8326 (m-40) cc_final: 0.7804 (OUTLIER) REVERT: D 60 ASN cc_start: 0.8099 (m-40) cc_final: 0.7624 (OUTLIER) REVERT: E 12 LYS cc_start: 0.8787 (ttpp) cc_final: 0.8502 (tttp) REVERT: E 60 ASN cc_start: 0.8477 (m-40) cc_final: 0.7730 (OUTLIER) REVERT: F 60 ASN cc_start: 0.8272 (m-40) cc_final: 0.7746 (OUTLIER) REVERT: G 60 ASN cc_start: 0.8328 (m-40) cc_final: 0.7760 (OUTLIER) REVERT: H 39 LYS cc_start: 0.8822 (mttt) cc_final: 0.8531 (mtpt) REVERT: H 60 ASN cc_start: 0.8146 (m-40) cc_final: 0.7764 (OUTLIER) REVERT: I 55 LYS cc_start: 0.9033 (mttt) cc_final: 0.8795 (mttp) REVERT: I 60 ASN cc_start: 0.8305 (m-40) cc_final: 0.7508 (p0) REVERT: J 25 ASP cc_start: 0.8550 (m-30) cc_final: 0.8260 (m-30) REVERT: J 32 GLU cc_start: 0.8370 (tt0) cc_final: 0.8081 (tt0) REVERT: J 60 ASN cc_start: 0.8288 (m-40) cc_final: 0.7706 (p0) REVERT: K 52 SER cc_start: 0.8681 (t) cc_final: 0.8463 (m) REVERT: K 60 ASN cc_start: 0.8328 (m-40) cc_final: 0.7548 (p0) REVERT: L 39 LYS cc_start: 0.8860 (mttt) cc_final: 0.8578 (mtpt) REVERT: L 60 ASN cc_start: 0.8236 (m-40) cc_final: 0.7828 (OUTLIER) outliers start: 20 outliers final: 12 residues processed: 253 average time/residue: 0.7653 time to fit residues: 205.6060 Evaluate side-chains 243 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 240 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain F residue 1 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 47 optimal weight: 0.7980 chunk 77 optimal weight: 0.0980 chunk 90 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 4 ASN C 20 GLN F 20 GLN F 67 GLN G 67 GLN J 67 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.196995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.122432 restraints weight = 14142.982| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.42 r_work: 0.3159 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14878 Z= 0.154 Angle : 0.511 3.266 21604 Z= 0.320 Chirality : 0.029 0.100 2424 Planarity : 0.002 0.020 1524 Dihedral : 31.901 176.490 4822 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 2.31 % Allowed : 17.28 % Favored : 80.40 % 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: 3.38 (0.27), residues: 828 helix: 2.85 (0.18), residues: 648 sheet: None (None), residues: 0 loop : -0.15 (0.50), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 15 TYR 0.010 0.002 TYR F 44 PHE 0.011 0.002 PHE J 5 TRP 0.015 0.003 TRP I 37 HIS 0.002 0.000 HIS K 51 Details of bonding type rmsd covalent geometry : bond 0.00320 (14878) covalent geometry : angle 0.51103 (21604) hydrogen bonds : bond 0.05469 ( 731) hydrogen bonds : angle 2.80816 ( 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 265 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 250 time to evaluate : 0.333 Fit side-chains REVERT: A 12 LYS cc_start: 0.8641 (ttpt) cc_final: 0.8266 (tttp) REVERT: A 28 ASP cc_start: 0.8707 (m-30) cc_final: 0.8446 (m-30) REVERT: A 60 ASN cc_start: 0.8464 (m-40) cc_final: 0.7873 (OUTLIER) REVERT: B 60 ASN cc_start: 0.8312 (m-40) cc_final: 0.7768 (p0) REVERT: C 60 ASN cc_start: 0.8343 (m-40) cc_final: 0.7855 (OUTLIER) REVERT: D 60 ASN cc_start: 0.8095 (m-40) cc_final: 0.7697 (OUTLIER) REVERT: E 12 LYS cc_start: 0.8810 (ttpp) cc_final: 0.8528 (tttp) REVERT: E 60 ASN cc_start: 0.8440 (m-40) cc_final: 0.7791 (OUTLIER) REVERT: F 60 ASN cc_start: 0.8255 (m-40) cc_final: 0.7794 (OUTLIER) REVERT: G 60 ASN cc_start: 0.8286 (m-40) cc_final: 0.7791 (OUTLIER) REVERT: H 39 LYS cc_start: 0.8816 (mttt) cc_final: 0.8509 (mtpt) REVERT: H 60 ASN cc_start: 0.8133 (m-40) cc_final: 0.7793 (OUTLIER) REVERT: I 55 LYS cc_start: 0.8987 (mttt) cc_final: 0.8768 (mttp) REVERT: I 60 ASN cc_start: 0.8276 (m-40) cc_final: 0.7574 (p0) REVERT: J 25 ASP cc_start: 0.8531 (m-30) cc_final: 0.8246 (m-30) REVERT: J 60 ASN cc_start: 0.8272 (m-40) cc_final: 0.7768 (p0) REVERT: K 52 SER cc_start: 0.8620 (t) cc_final: 0.8374 (m) REVERT: K 60 ASN cc_start: 0.8311 (m-40) cc_final: 0.7587 (p0) REVERT: L 39 LYS cc_start: 0.8878 (mttt) cc_final: 0.8598 (mtpt) REVERT: L 60 ASN cc_start: 0.8255 (m-40) cc_final: 0.7886 (OUTLIER) outliers start: 15 outliers final: 14 residues processed: 251 average time/residue: 0.7232 time to fit residues: 193.1476 Evaluate side-chains 248 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 242 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain F residue 32 GLU Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain K residue 20 GLN Chi-restraints excluded: chain K residue 41 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 57 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 20 GLN J 67 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.192031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.116928 restraints weight = 14123.017| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.45 r_work: 0.3064 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 14878 Z= 0.343 Angle : 0.608 5.547 21604 Z= 0.364 Chirality : 0.035 0.145 2424 Planarity : 0.005 0.049 1524 Dihedral : 32.408 174.354 4822 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.09 % Allowed : 17.44 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.57 (0.26), residues: 828 helix: 2.32 (0.17), residues: 648 sheet: None (None), residues: 0 loop : -0.64 (0.46), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 54 TYR 0.009 0.002 TYR K 44 PHE 0.016 0.004 PHE L 5 TRP 0.005 0.002 TRP E 37 HIS 0.007 0.004 HIS J 51 Details of bonding type rmsd covalent geometry : bond 0.00804 (14878) covalent geometry : angle 0.60800 (21604) hydrogen bonds : bond 0.07607 ( 731) hydrogen bonds : angle 3.09382 ( 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 255 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 235 time to evaluate : 0.307 Fit side-chains REVERT: A 12 LYS cc_start: 0.8582 (ttpt) cc_final: 0.8252 (tttp) REVERT: A 28 ASP cc_start: 0.8764 (m-30) cc_final: 0.8536 (m-30) REVERT: A 60 ASN cc_start: 0.8490 (m-40) cc_final: 0.7881 (p0) REVERT: B 60 ASN cc_start: 0.8431 (m-40) cc_final: 0.7803 (p0) REVERT: C 60 ASN cc_start: 0.8357 (m-40) cc_final: 0.7844 (OUTLIER) REVERT: D 60 ASN cc_start: 0.8114 (m-40) cc_final: 0.7677 (OUTLIER) REVERT: E 12 LYS cc_start: 0.8799 (ttpp) cc_final: 0.8482 (tttp) REVERT: E 43 LYS cc_start: 0.8508 (mttp) cc_final: 0.8250 (mttm) REVERT: E 60 ASN cc_start: 0.8566 (m-40) cc_final: 0.7820 (OUTLIER) REVERT: F 60 ASN cc_start: 0.8378 (m-40) cc_final: 0.7830 (OUTLIER) REVERT: G 60 ASN cc_start: 0.8450 (m-40) cc_final: 0.7858 (p0) REVERT: H 60 ASN cc_start: 0.8192 (m-40) cc_final: 0.7826 (p0) REVERT: I 55 LYS cc_start: 0.9072 (mttt) cc_final: 0.8839 (mttp) REVERT: I 60 ASN cc_start: 0.8380 (m-40) cc_final: 0.7587 (p0) REVERT: J 25 ASP cc_start: 0.8566 (m-30) cc_final: 0.8275 (m-30) REVERT: J 60 ASN cc_start: 0.8344 (m-40) cc_final: 0.7696 (p0) REVERT: K 60 ASN cc_start: 0.8367 (m-40) cc_final: 0.7640 (p0) REVERT: L 39 LYS cc_start: 0.8927 (mttt) cc_final: 0.8623 (mtpt) REVERT: L 60 ASN cc_start: 0.8238 (m-40) cc_final: 0.7840 (OUTLIER) outliers start: 20 outliers final: 12 residues processed: 240 average time/residue: 0.7585 time to fit residues: 193.6873 Evaluate side-chains 236 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 229 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 32 GLU Chi-restraints excluded: chain J residue 41 ILE 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: 2.9990 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 20 GLN F 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 = 0.195491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.122090 restraints weight = 14075.343| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.37 r_work: 0.3143 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14878 Z= 0.170 Angle : 0.510 3.177 21604 Z= 0.318 Chirality : 0.028 0.100 2424 Planarity : 0.003 0.023 1524 Dihedral : 31.794 176.406 4822 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 2.47 % Allowed : 19.29 % Favored : 78.24 % 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: 3.15 (0.27), residues: 828 helix: 2.78 (0.17), residues: 648 sheet: None (None), residues: 0 loop : -0.66 (0.46), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 9 TYR 0.010 0.002 TYR K 44 PHE 0.008 0.002 PHE L 5 TRP 0.010 0.002 TRP D 37 HIS 0.002 0.001 HIS K 51 Details of bonding type rmsd covalent geometry : bond 0.00374 (14878) covalent geometry : angle 0.50976 (21604) hydrogen bonds : bond 0.05537 ( 731) hydrogen bonds : angle 2.84982 ( 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 255 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 239 time to evaluate : 0.352 Fit side-chains REVERT: A 12 LYS cc_start: 0.8559 (ttpt) cc_final: 0.8182 (tttp) REVERT: A 28 ASP cc_start: 0.8692 (m-30) cc_final: 0.8414 (m-30) REVERT: A 60 ASN cc_start: 0.8454 (m-40) cc_final: 0.7867 (OUTLIER) REVERT: B 60 ASN cc_start: 0.8294 (m-40) cc_final: 0.7736 (p0) REVERT: C 60 ASN cc_start: 0.8323 (m-40) cc_final: 0.7800 (OUTLIER) REVERT: D 60 ASN cc_start: 0.8044 (m-40) cc_final: 0.7614 (OUTLIER) REVERT: E 12 LYS cc_start: 0.8763 (ttpp) cc_final: 0.8474 (tttp) REVERT: E 60 ASN cc_start: 0.8447 (m-40) cc_final: 0.7721 (OUTLIER) REVERT: F 60 ASN cc_start: 0.8238 (m-40) cc_final: 0.7731 (OUTLIER) REVERT: G 60 ASN cc_start: 0.8306 (m-40) cc_final: 0.7752 (OUTLIER) REVERT: H 39 LYS cc_start: 0.8790 (mtmm) cc_final: 0.8442 (mtpt) REVERT: H 60 ASN cc_start: 0.8100 (m-40) cc_final: 0.7711 (OUTLIER) REVERT: I 55 LYS cc_start: 0.8970 (mttt) cc_final: 0.8705 (mttp) REVERT: I 60 ASN cc_start: 0.8303 (m-40) cc_final: 0.7494 (p0) REVERT: J 25 ASP cc_start: 0.8498 (m-30) cc_final: 0.8206 (m-30) REVERT: J 60 ASN cc_start: 0.8246 (m-40) cc_final: 0.7694 (p0) REVERT: K 28 ASP cc_start: 0.8395 (m-30) cc_final: 0.8177 (m-30) REVERT: K 60 ASN cc_start: 0.8274 (m-40) cc_final: 0.7545 (p0) REVERT: L 39 LYS cc_start: 0.8843 (mttt) cc_final: 0.8538 (mtpt) REVERT: L 55 LYS cc_start: 0.8766 (mttp) cc_final: 0.8402 (mttt) REVERT: L 60 ASN cc_start: 0.8169 (m-40) cc_final: 0.7786 (OUTLIER) outliers start: 16 outliers final: 13 residues processed: 243 average time/residue: 0.7385 time to fit residues: 191.2324 Evaluate side-chains 240 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 235 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain F residue 67 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 4 ASN K 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.193391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.118875 restraints weight = 13998.740| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.39 r_work: 0.3095 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 14878 Z= 0.246 Angle : 0.538 4.146 21604 Z= 0.329 Chirality : 0.030 0.099 2424 Planarity : 0.003 0.028 1524 Dihedral : 31.857 175.845 4822 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.85 % Allowed : 19.60 % Favored : 78.55 % 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: 2.93 (0.26), residues: 828 helix: 2.61 (0.17), residues: 648 sheet: None (None), residues: 0 loop : -0.66 (0.45), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 54 TYR 0.010 0.002 TYR K 44 PHE 0.010 0.003 PHE L 5 TRP 0.006 0.001 TRP E 37 HIS 0.004 0.002 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00570 (14878) covalent geometry : angle 0.53815 (21604) hydrogen bonds : bond 0.06574 ( 731) hydrogen bonds : angle 2.97098 ( 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 244 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 232 time to evaluate : 0.266 Fit side-chains REVERT: A 12 LYS cc_start: 0.8599 (ttpt) cc_final: 0.8259 (tttp) REVERT: A 28 ASP cc_start: 0.8716 (m-30) cc_final: 0.8475 (m-30) REVERT: A 60 ASN cc_start: 0.8507 (m-40) cc_final: 0.7924 (OUTLIER) REVERT: B 60 ASN cc_start: 0.8360 (m-40) cc_final: 0.7814 (p0) REVERT: C 60 ASN cc_start: 0.8352 (m-40) cc_final: 0.7846 (OUTLIER) REVERT: D 60 ASN cc_start: 0.8081 (m-40) cc_final: 0.7666 (OUTLIER) REVERT: E 12 LYS cc_start: 0.8803 (ttpp) cc_final: 0.8524 (tttp) REVERT: E 43 LYS cc_start: 0.8511 (mttt) cc_final: 0.8233 (mttm) REVERT: E 60 ASN cc_start: 0.8514 (m-40) cc_final: 0.7801 (OUTLIER) REVERT: F 60 ASN cc_start: 0.8292 (m-40) cc_final: 0.7786 (OUTLIER) REVERT: G 60 ASN cc_start: 0.8393 (m-40) cc_final: 0.7842 (OUTLIER) REVERT: H 39 LYS cc_start: 0.8856 (mtmm) cc_final: 0.8533 (mtpt) REVERT: H 60 ASN cc_start: 0.8154 (m-40) cc_final: 0.7759 (OUTLIER) REVERT: I 55 LYS cc_start: 0.9037 (mttt) cc_final: 0.8829 (mttp) REVERT: I 60 ASN cc_start: 0.8335 (m-40) cc_final: 0.7552 (p0) REVERT: J 25 ASP cc_start: 0.8564 (m-30) cc_final: 0.8276 (m-30) REVERT: J 60 ASN cc_start: 0.8312 (m-40) cc_final: 0.7771 (p0) REVERT: K 60 ASN cc_start: 0.8370 (m-40) cc_final: 0.7646 (p0) REVERT: L 39 LYS cc_start: 0.8913 (mttt) cc_final: 0.8633 (mtpt) REVERT: L 55 LYS cc_start: 0.8841 (mttp) cc_final: 0.8478 (mttt) REVERT: L 60 ASN cc_start: 0.8196 (m-40) cc_final: 0.7812 (OUTLIER) outliers start: 12 outliers final: 13 residues processed: 236 average time/residue: 0.7049 time to fit residues: 176.9669 Evaluate side-chains 235 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 230 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 67 GLN Chi-restraints excluded: chain J 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: 4.9990 chunk 26 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 89 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 4 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.193936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.119729 restraints weight = 13980.339| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.37 r_work: 0.3103 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14878 Z= 0.203 Angle : 0.524 3.847 21604 Z= 0.323 Chirality : 0.029 0.100 2424 Planarity : 0.003 0.027 1524 Dihedral : 31.853 176.163 4822 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.01 % Allowed : 19.14 % 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: 2.98 (0.26), residues: 828 helix: 2.65 (0.17), residues: 648 sheet: None (None), residues: 0 loop : -0.67 (0.45), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 54 TYR 0.010 0.002 TYR K 44 PHE 0.009 0.002 PHE L 5 TRP 0.005 0.001 TRP E 37 HIS 0.004 0.002 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00459 (14878) covalent geometry : angle 0.52388 (21604) hydrogen bonds : bond 0.06277 ( 731) hydrogen bonds : angle 2.97338 ( 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 247 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 234 time to evaluate : 0.312 Fit side-chains REVERT: A 12 LYS cc_start: 0.8592 (ttpt) cc_final: 0.8249 (tttp) REVERT: A 28 ASP cc_start: 0.8702 (m-30) cc_final: 0.8468 (m-30) REVERT: A 60 ASN cc_start: 0.8500 (m-40) cc_final: 0.7924 (OUTLIER) REVERT: B 60 ASN cc_start: 0.8343 (m-40) cc_final: 0.7810 (p0) REVERT: C 60 ASN cc_start: 0.8340 (m-40) cc_final: 0.7842 (OUTLIER) REVERT: D 60 ASN cc_start: 0.8081 (m-40) cc_final: 0.7677 (OUTLIER) REVERT: E 12 LYS cc_start: 0.8798 (ttpp) cc_final: 0.8518 (tttp) REVERT: E 43 LYS cc_start: 0.8499 (mttt) cc_final: 0.8220 (mttm) REVERT: E 60 ASN cc_start: 0.8497 (m-40) cc_final: 0.7795 (OUTLIER) REVERT: F 60 ASN cc_start: 0.8276 (m-40) cc_final: 0.7784 (OUTLIER) REVERT: G 60 ASN cc_start: 0.8378 (m-40) cc_final: 0.7840 (OUTLIER) REVERT: H 39 LYS cc_start: 0.8848 (mtmm) cc_final: 0.8524 (mtpt) REVERT: H 60 ASN cc_start: 0.8143 (m-40) cc_final: 0.7767 (OUTLIER) REVERT: I 55 LYS cc_start: 0.9031 (mttt) cc_final: 0.8762 (mttp) REVERT: I 60 ASN cc_start: 0.8321 (m-40) cc_final: 0.7547 (p0) REVERT: J 25 ASP cc_start: 0.8561 (m-30) cc_final: 0.8272 (m-30) REVERT: J 60 ASN cc_start: 0.8301 (m-40) cc_final: 0.7777 (p0) REVERT: K 60 ASN cc_start: 0.8345 (m-40) cc_final: 0.7643 (p0) REVERT: L 39 LYS cc_start: 0.8909 (mttt) cc_final: 0.8628 (mtpt) REVERT: L 55 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8471 (mttt) REVERT: L 60 ASN cc_start: 0.8181 (m-40) cc_final: 0.7815 (OUTLIER) outliers start: 13 outliers final: 15 residues processed: 237 average time/residue: 0.6975 time to fit residues: 176.2718 Evaluate side-chains 240 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 232 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 67 GLN Chi-restraints excluded: chain J residue 20 GLN Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 55 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 75 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 108 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.193596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.118912 restraints weight = 14094.236| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.39 r_work: 0.3095 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14878 Z= 0.237 Angle : 0.533 3.971 21604 Z= 0.327 Chirality : 0.030 0.100 2424 Planarity : 0.003 0.027 1524 Dihedral : 31.826 176.231 4822 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 2.01 % Allowed : 19.60 % Favored : 78.40 % 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: 2.91 (0.26), residues: 828 helix: 2.60 (0.17), residues: 648 sheet: None (None), residues: 0 loop : -0.69 (0.45), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 9 TYR 0.009 0.002 TYR K 44 PHE 0.010 0.003 PHE L 5 TRP 0.005 0.001 TRP E 37 HIS 0.004 0.002 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00547 (14878) covalent geometry : angle 0.53284 (21604) hydrogen bonds : bond 0.06464 ( 731) hydrogen bonds : angle 2.98070 ( 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 244 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 231 time to evaluate : 0.381 Fit side-chains REVERT: A 12 LYS cc_start: 0.8604 (ttpt) cc_final: 0.8271 (tttp) REVERT: A 28 ASP cc_start: 0.8717 (m-30) cc_final: 0.8462 (m-30) REVERT: A 60 ASN cc_start: 0.8511 (m-40) cc_final: 0.7922 (OUTLIER) REVERT: B 60 ASN cc_start: 0.8355 (m-40) cc_final: 0.7813 (p0) REVERT: C 60 ASN cc_start: 0.8352 (m-40) cc_final: 0.7840 (OUTLIER) REVERT: D 60 ASN cc_start: 0.8068 (m-40) cc_final: 0.7669 (OUTLIER) REVERT: E 12 LYS cc_start: 0.8805 (ttpp) cc_final: 0.8526 (tttp) REVERT: E 43 LYS cc_start: 0.8512 (mttt) cc_final: 0.8237 (mttm) REVERT: E 60 ASN cc_start: 0.8511 (m-40) cc_final: 0.7794 (OUTLIER) REVERT: F 60 ASN cc_start: 0.8283 (m-40) cc_final: 0.7782 (OUTLIER) REVERT: G 60 ASN cc_start: 0.8390 (m-40) cc_final: 0.7839 (OUTLIER) REVERT: H 39 LYS cc_start: 0.8856 (mtmm) cc_final: 0.8529 (mtpt) REVERT: H 60 ASN cc_start: 0.8150 (m-40) cc_final: 0.7753 (OUTLIER) REVERT: I 60 ASN cc_start: 0.8334 (m-40) cc_final: 0.7555 (p0) REVERT: J 25 ASP cc_start: 0.8565 (m-30) cc_final: 0.8278 (m-30) REVERT: J 60 ASN cc_start: 0.8312 (m-40) cc_final: 0.7768 (p0) REVERT: K 60 ASN cc_start: 0.8369 (m-40) cc_final: 0.7640 (p0) REVERT: L 39 LYS cc_start: 0.8915 (mttt) cc_final: 0.8634 (mtpt) REVERT: L 55 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8471 (mttt) REVERT: L 60 ASN cc_start: 0.8195 (m-40) cc_final: 0.7814 (OUTLIER) outliers start: 13 outliers final: 18 residues processed: 235 average time/residue: 0.8309 time to fit residues: 207.6849 Evaluate side-chains 240 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 229 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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 41 ILE Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain F residue 32 GLU Chi-restraints excluded: chain F residue 67 GLN Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain J residue 20 GLN Chi-restraints excluded: chain J residue 41 ILE Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 55 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 78 optimal weight: 0.8980 chunk 84 optimal weight: 10.0000 chunk 67 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 25 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 7 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 4 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.195665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.122400 restraints weight = 14107.644| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.37 r_work: 0.3142 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14878 Z= 0.149 Angle : 0.504 5.079 21604 Z= 0.316 Chirality : 0.028 0.103 2424 Planarity : 0.002 0.018 1524 Dihedral : 31.713 176.458 4822 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.54 % Allowed : 20.06 % Favored : 78.40 % 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: 3.32 (0.27), residues: 828 helix: 2.91 (0.18), residues: 648 sheet: None (None), residues: 0 loop : -0.63 (0.44), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 15 TYR 0.013 0.003 TYR J 44 PHE 0.003 0.001 PHE I 5 TRP 0.014 0.002 TRP E 37 HIS 0.002 0.001 HIS K 51 Details of bonding type rmsd covalent geometry : bond 0.00314 (14878) covalent geometry : angle 0.50440 (21604) hydrogen bonds : bond 0.05428 ( 731) hydrogen bonds : angle 2.91207 ( 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 246 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 236 time to evaluate : 0.294 Fit side-chains REVERT: A 12 LYS cc_start: 0.8589 (ttpt) cc_final: 0.8253 (tttp) REVERT: A 28 ASP cc_start: 0.8688 (m-30) cc_final: 0.8424 (m-30) REVERT: A 60 ASN cc_start: 0.8469 (m-40) cc_final: 0.7925 (OUTLIER) REVERT: B 60 ASN cc_start: 0.8310 (m-40) cc_final: 0.7808 (p0) REVERT: C 60 ASN cc_start: 0.8355 (m-40) cc_final: 0.7870 (OUTLIER) REVERT: D 60 ASN cc_start: 0.8041 (m-40) cc_final: 0.7693 (OUTLIER) REVERT: E 12 LYS cc_start: 0.8789 (ttpp) cc_final: 0.8514 (tttp) REVERT: E 60 ASN cc_start: 0.8464 (m-40) cc_final: 0.7805 (OUTLIER) REVERT: F 60 ASN cc_start: 0.8262 (m-40) cc_final: 0.7815 (OUTLIER) REVERT: G 60 ASN cc_start: 0.8351 (m-40) cc_final: 0.7842 (OUTLIER) REVERT: H 39 LYS cc_start: 0.8836 (mtmm) cc_final: 0.8487 (mtpt) REVERT: H 60 ASN cc_start: 0.8082 (m-40) cc_final: 0.7747 (OUTLIER) REVERT: I 60 ASN cc_start: 0.8323 (m-40) cc_final: 0.7578 (p0) REVERT: J 25 ASP cc_start: 0.8519 (m-30) cc_final: 0.8241 (m-30) REVERT: J 60 ASN cc_start: 0.8278 (m-40) cc_final: 0.7787 (p0) REVERT: K 60 ASN cc_start: 0.8316 (m-40) cc_final: 0.7635 (p0) REVERT: L 39 LYS cc_start: 0.8895 (mttt) cc_final: 0.8625 (mtpt) REVERT: L 55 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8423 (mttt) REVERT: L 60 ASN cc_start: 0.8170 (m-40) cc_final: 0.7836 (OUTLIER) outliers start: 10 outliers final: 14 residues processed: 238 average time/residue: 0.8537 time to fit residues: 216.1273 Evaluate side-chains 240 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 233 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain F residue 32 GLU Chi-restraints excluded: chain F residue 67 GLN Chi-restraints excluded: chain J residue 41 ILE Chi-restraints excluded: chain L residue 55 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 51 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 29 optimal weight: 0.6980 chunk 102 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 8 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 79 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 4 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.196249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.122839 restraints weight = 14124.397| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.38 r_work: 0.3152 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14878 Z= 0.166 Angle : 0.496 4.052 21604 Z= 0.311 Chirality : 0.028 0.102 2424 Planarity : 0.002 0.018 1524 Dihedral : 31.577 176.616 4822 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 0.77 % Allowed : 21.14 % Favored : 78.09 % 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: 3.51 (0.27), residues: 828 helix: 3.08 (0.18), residues: 648 sheet: None (None), residues: 0 loop : -0.69 (0.43), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 9 TYR 0.011 0.002 TYR G 44 PHE 0.006 0.002 PHE I 5 TRP 0.013 0.002 TRP D 37 HIS 0.002 0.001 HIS K 51 Details of bonding type rmsd covalent geometry : bond 0.00366 (14878) covalent geometry : angle 0.49624 (21604) hydrogen bonds : bond 0.05245 ( 731) hydrogen bonds : angle 2.81495 ( 1960) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4739.43 seconds wall clock time: 81 minutes 4.63 seconds (4864.63 seconds total)